R/the_mode_jumping_package4.r
In aliaksah/EMJMCMC2016: EMJMCMC
Defines functions
runemjmcmc
parall.gmj
do.call.emjmcmc
simplifyposteriors
simplify.formula
estimate.glm
parallelize
estimate.gamma.cpen
estimate.inla.poisson
estimate.inla
estimate.bas.lm
erf
sigmoid
estimate.bigm
estimate.speedglm
estimate.elnet
estimate.logic.lm
pinferunemjmcmc
mcgmjpse
mcgmjpar
LogicRegr
estimate.logic.lm.jef
estimate.logic.lm.tCCH
estimate.logic.bern.tCCH
estimate.logic.bern
runpar.infer
simplifyposteriors.infer
estimate.logic.lm
estimate.logic.lm.tCCH
estimate.logic.bern.tCCH
estimate.logic.bern
estimate.logic.glm
factorial
estimate.bas.glm
m
Documented in
do.call.emjmcmc
erf
estimate.bas.glm
estimate.bas.lm
estimate.bigm
estimate.elnet
estimate.glm
estimate.inla
estimate.logic.glm
estimate.logic.lm
estimate.speedglm
factorial
LogicRegr
m
parallelize
parall.gmj
pinferunemjmcmc
runemjmcmc
sigmoid
simplify.formula
simplifyposteriors
#rm(list = ls(all = TRUE))
#install the following packages if required!
if(!("sp" %in% rownames(installed.packages())))
install.packages("sp")
if(!("INLA" %in% rownames(installed.packages())))
install.packages("INLA", repos=c(getOption("repos"), INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE)
if(!("bigmemory" %in% rownames(installed.packages())))
install.packages("bigmemory")
if(!("ade4" %in% rownames(installed.packages())))
install.packages("ade4")
if(!("hash" %in% rownames(installed.packages())))
install.packages("hash")
if(!("speedglm" %in% rownames(installed.packages())))
install.packages("speedglm")
if(!("stringi" %in% rownames(installed.packages())))
install.packages("stringi")
if(!("biglm" %in% rownames(installed.packages())))
install.packages("biglm")
if(!("glmnet" %in% rownames(installed.packages())))
install.packages("glmnet")
if(!("BAS" %in% rownames(installed.packages())))
install.packages("https://github.com/aliaksah/EMJMCMC2016/blob/master/examples/BAS%20archive/BAS_0.91.tar.gz?raw=true", repos = NULL)
if(!("BAS" %in% rownames(installed.packages())))
install.packages("BAS")
if(!("MASS" %in% rownames(installed.packages())))
install.packages("MASS")
if(!("parallel" %in% rownames(installed.packages())))
install.packages("parallel")
if(!("stats" %in% rownames(installed.packages())))
install.packages("stats")
#if(!("inline" %in% rownames(installed.packages())))
# install.packages("inline")
if(!("RCurl" %in% rownames(installed.packages())))
install.packages("RCurl")
if(!("gnlm" %in% rownames(installed.packages())))
install.packages("gnlm")
#library(inline)
library(gnlm)
library(glmnet)
library(biglm)
library(hash)
library(sp)
library(INLA)
library(parallel)
library(bigmemory)
library(MASS)
library(ade4)
library(BAS)# should be version 0.9 !!!! otherwise some dependencies might not work!
library(stringi)
require(stats)
#includes <- '#include <sys/wait.h>'
#code <- 'int wstat; while (waitpid(-1, &wstat, WNOHANG) > 0) {};'
#wait <- cfunction(body=code, includes=includes, convention='.C')
m<-function(a,b)a*b
estimate.bas.glm <- function(formula, data, family, prior, logn)
{
#only poisson and binomial families are currently adopted
X <- model.matrix(object = formula,data = data)
out <- bayesglm.fit(x = X, y = data[,1], family=family,coefprior=prior)
# use dic and aic as bic and aic correspondinly
return(list(mlik = out$logmarglik,waic = -(out$deviance + 2*out$rank) , dic = -(out$deviance + logn*out$rank),summary.fixed =list(mean = coefficients(out))))
}
factorial<-function(x) ifelse(x<=170,gamma(abs(x) + 1),gamma(171))
estimate.logic.glm <- function(formula, data, family, n, m, r = 1)
{
X <- model.matrix(object = formula,data = data)
out <- bayesglm.fit(x = X, y = data[,51], family=family,coefprior=aic.prior())
p <- out$rank
fmla.proc<-as.character(formula)[2:3]
fobserved <- fmla.proc[1]
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam <-stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj<-(stri_count_fixed(str = fparam, pattern = "&"))
sj<-sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj<-sj+1
Jprior <- sum(log(factorial(sj)/((m^sj)*2^(2*sj-2))))
mlik = (-(out$deviance + log(n)*(out$rank)) + 2*(Jprior))/2+n
if(mlik==-Inf)
mlik = -10000
return(list(mlik = mlik,waic = -(out$deviance + 2*out$rank) , dic = -(out$deviance + log(n)*out$rank),summary.fixed =list(mean = coefficients(out))))
}
#define the function estimating parameters of a given Bernoulli logic regression with Jeffrey's prior
estimate.logic.bern = function(formula = NULL, data, family = binomial(), n=1000, m=50, r = 1,k.max=21)
{
if(length(formula)==0)
return(list(mlik = -10000 + rnorm(1,0,1),waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
if(is.na(formula))
return(list(mlik = -10000 + rnorm(1,0,1),waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
out = glm(formula = formula,data = data, family=family)
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc=as.character(formula)[2:3]
fobserved = fmla.proc[1]
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
Jprior = sum(log(factorial(sj)/((m^sj)*2^(2*sj-2))))
mlik = (-(out$deviance + log(n)*(out$rank)) + 2*(Jprior))/2+n
if(mlik==-Inf)
mlik = -10000
return(list(mlik = mlik,waic = -(out$deviance + 2*out$rank) , dic = -(out$deviance + log(n)*out$rank),summary.fixed =list(mean = coefficients(out))))
}
#define the function estimating parameters of a given Bernoulli logic regression with robust g prior
estimate.logic.bern.tCCH = function(formula = NULL,y.id = 51, data, n=1000, m=50, r = 1, p.a = 1, p.b = 2, p.r = 1.5, p.s = 0, p.v=-1, p.k = 1,k.max=21)
{
if(length(formula)==0)
return(list(mlik = -10000 + rnorm(1,0,1),waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
if(is.na(formula))
return(list(mlik = -10000 + rnorm(1,0,1),waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
X = scale(model.matrix(object = formula,data = data),center = T,scale = F)
X[,1] = 1
fmla.proc=as.character(formula)[2:3]
out = glm(formula = as.formula(paste0(fmla.proc[1],"~X+0")),data=data,family = binomial())
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
beta=coef(out)[-1]
if(length(which(is.na(beta)))>0)
{
return(list(mlik = -10000 + rnorm(1,0,1),waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
p.v = (n+1)/(p+1)
sout = summary(out)
J.a.hat = 1/sout$cov.unscaled[1,1]
if(length(beta)>0&&length(beta)==(dim(sout$cov.unscaled)[1]-1)&&length(which(is.na(beta)))==0)
{
Q = t(beta)%*%solve(sout$cov.unscaled[-1,-1])%*%beta
}else{
return(list(mlik = -10000 + rnorm(1,0,1),waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
Jprior = sum(log(factorial(sj)/((m^sj)*2^(2*sj-2))))
mlik = (logLik(out)- 0.5*log(J.a.hat) - 0.5*p*log(p.v) -0.5*Q/p.v + log(beta((p.a+p)/2,p.b/2)) + log(phi1(p.b/2,p.r,(p.a+p.b+p)/2,(p.s+Q)/2/p.v,1-p.k))+Jprior + p*log(r)+n)
if(is.na(mlik)||mlik==-Inf)
mlik = -10000+ rnorm(1,0,1)
return(list(mlik = mlik,waic = AIC(out) , dic = BIC(out),summary.fixed =list(mean = coefficients(out))))
}
#define the function estimating parameters of a given Gaussian logic regression with robust g prior
estimate.logic.lm.tCCH = function(formula = NULL, data, n=1000, m=50, r = 1, p.a = 1, p.b = 2, p.r = 1.5, p.s = 0, p.v=-1, p.k = 1,k.max=21)
{
if(is.null(formula))
return(list(mlik = -10000,waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
fmla.proc=as.character(formula)[2:3]
fobserved = fmla.proc[1]
if(fmla.proc[2]=="-1")
return(list(mlik = -10000,waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
out = lm(formula = formula,data = data)
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
Jprior = prod(factorial(sj)/((m^sj)*2^(2*sj-2)))
p.v = (n+1)/(p+1)
R.2 = summary(out)$r.squared
mlik = (-0.5*p*log(p.v) -0.5*(n-1)*log(1-(1-1/p.v)*R.2) + log(beta((p.a+p)/2,p.b/2)) - log(beta(p.a/2,p.b/2)) + log(phi1(p.b/2,(n-1)/2,(p.a+p.b+p)/2,p.s/2/p.v,R.2/(p.v-(p.v-1)*R.2))) - hypergeometric1F1(p.b/2,(p.a+p.b)/2,p.s/2/p.v,log = T)+log(Jprior) + p*log(r)+n)
if(mlik==-Inf||is.na(mlik)||is.nan(mlik))
mlik = -10000
return(list(mlik = mlik,waic = AIC(out)-n , dic = BIC(out)-n,summary.fixed =list(mean = coef(out))))
}
#define the function estimating parameters of a given Gaussian logic regression with Jeffrey's prior
estimate.logic.lm = function(formula= NULL, data, n, m, r = 1,k.max=21)
{
if(is.null(formula))
return(list(mlik = -10000,waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
out = lm(formula = formula,data = data)
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc=as.character(formula)[2:3]
fobserved = fmla.proc[1]
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
Jprior = prod(factorial(sj)/((m^sj)*2^(2*sj-2)))
mlik = (-BIC(out)+2*log(Jprior) + 2*p*log(r)+n)/2
if(mlik==-Inf)
mlik = -10000
return(list(mlik = mlik,waic = AIC(out)-n , dic = BIC(out)-n,summary.fixed =list(mean = coef(out))))
}
#define the function simplifying logical expressions at the end of the search
simplifyposteriors.infer=function(X,posteriors,th=0.0000001,thf=0.5, resp)
{
todel = which(posteriors[,2]<th)
if(length(todel)>0)
posteriors=posteriors[-todel,]
rhash=hash()
for(i in 1:length(posteriors[,1]))
{
expr=posteriors[i,1]
#print(expr)
res=model.matrix(data=X,object = as.formula(paste0(resp,"~",expr)))
res[,1]=res[,1]-res[,2]
ress=c(stri_flatten(res[,1],collapse = ""),stri_flatten(res[,2],collapse = ""),posteriors[i,2],expr)
ress[1] = stri_sub(ress[1],from = 1,to = 9999)
if(!(ress[1] %in% values(rhash)||(ress[2] %in% values(rhash))))
rhash[[ress[1]]]=ress
else
{
if(ress[1] %in% keys(rhash))
{
rhash[[ress[1]]][3]= (as.numeric(rhash[[ress[1]]][3]) + as.numeric(ress[3]))
if(stri_length(rhash[[ress[1]]][4])>stri_length(expr))
rhash[[ress[1]]][4]=expr
}
else
{
rhash[[ress[2]]][3]= (as.numeric(rhash[[ress[2]]][3]) + as.numeric(ress[3]))
if(stri_length(rhash[[ress[2]]][4])>stri_length(expr))
rhash[[ress[2]]][4]=expr
}
}
}
res=as.data.frame(t(values(rhash)[c(3,4),]))
res$V1=as.numeric(as.character(res$V1))
tokeep = which(res$V1>thf)
if(length(tokeep)>0)
{
res=res[tokeep,]
}else
warning(paste0("No features with posteriors above ",thf,". Returning everything"))
res=res[order(res$V1, decreasing = T),]
clear(rhash)
rm(rhash)
tokeep = which(res[,1]>1)
if(length(tokeep)>0)
res[tokeep,1]=1
colnames(res)=c("posterior","feature")
rownames(res) = NULL
return(res)
}
#define a function performing the map step for a given thread
runpar.infer=function(vect)
{
ret = NULL
tryCatch({
set.seed(as.integer(vect$cpu))
do.call(runemjmcmc, vect[1:(length(vect)-5)])
vals=values(hashStat)
fparam=mySearch$fparam
cterm=max(vals[1,],na.rm = T)
ppp=mySearch$post_proceed_results_hash(hashStat = hashStat)
post.populi=sum(exp(values(hashStat)[1,][1:vect$NM]-cterm),na.rm = T)
betas = NULL
mliks = NULL
if(vect$save.beta){
#get the modes of beta coefficients for the explored models
Nvars=mySearch$Nvars
linx =mySearch$Nvars+4
lHash=length(hashStat)
mliks = values(hashStat)[which((1:(lHash * linx)) %% linx == 1)]
betas = values(hashStat)[which((1:(lHash * linx)) %% linx == 4)]
for(i in 1:(Nvars-1))
{
betas=cbind(betas,values(hashStat)[which((1:(lHash * linx)) %% linx == (4+i))])
}
betas=cbind(betas,values(hashStat)[which((1:(lHash * linx)) %% linx == (0))])
}
preds = NULL
if(vect$predict)
{
preds=mySearch$forecast.matrix.na(link.g = vect$link, covariates = (vect$test),betas = betas,mliks.in = mliks)$forecast
}
ret = list(post.populi = post.populi, p.post = ppp$p.post, cterm = cterm, preds = preds, fparam = fparam, betas = betas, mliks = mliks )
if(length(cterm)==0){
vect$cpu=as.integer(vect$cpu)+as.integer(runif(1,1,10000))
if(vect$cpu<50000)
ret = runpar.infer(vect)
else
ret = NULL
}
},error = function(err){
print(paste0("error in thread", vect[length(vect)]))
print(err)
vect$cpu=as.integer(vect$cpu)+as.integer(runif(1,1,10000))
if(vect$cpu<50000)
ret = runpar.infer(vect)
else
ret =err
},finally = {
#clear(hashStat)
#rm(hashStat)
#rm(vals)
gc()
return(ret)
})
}
#define the function estimating parameters of a given Bernoulli logic regression with Jeffrey's prior
estimate.logic.bern = function(formula, data, family = binomial(), n=1000, m=50, r = 1,k.max=21)
{
if(is.null(formula))
return(list(mlik = -10000 + rnorm(1,0,1),waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
out = glm(formula = formula,data = data, family=family)
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc=as.character(formula)[2:3]
fobserved = fmla.proc[1]
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
Jprior = sum(log(factorial(sj)/((m^sj)*2^(2*sj-2))))
mlik = (-(out$deviance + log(n)*(out$rank)) + 2*(Jprior))/2+n
if(mlik==-Inf)
mlik = -10000
return(list(mlik = mlik,waic = -(out$deviance + 2*out$rank) , dic = -(out$deviance + log(n)*out$rank),summary.fixed =list(mean = coefficients(out))))
}
#define the function estimating parameters of a given Bernoulli logic regression with robust g prior
estimate.logic.bern.tCCH = function(formula = NULL,y.id = 51, data, n=1000, m=50, r = 1, p.a = 1, p.b = 2, p.r = 1.5, p.s = 0, p.v=-1, p.k = 1,k.max=21)
{
if(is.null(formula))
return(list(mlik = -10000 + rnorm(1,0,1),waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
X = scale(model.matrix(object = formula,data = data),center = T,scale = F)
X[,1] = 1
fmla.proc=as.character(formula)[2:3]
out = glm(formula = as.formula(paste0(fmla.proc[1],"~X+0")),data=data,family = binomial())
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
beta=coef(out)[-1]
if(length(which(is.na(beta)))>0)
{
return(list(mlik = -10000 + rnorm(1,0,1),waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
p.v = (n+1)/(p+1)
sout = summary(out)
J.a.hat = 1/sout$cov.unscaled[1,1]
if(length(beta)>0&&length(beta)==(dim(sout$cov.unscaled)[1]-1)&&length(which(is.na(beta)))==0)
{
Q = t(beta)%*%solve(sout$cov.unscaled[-1,-1])%*%beta
}else{
return(list(mlik = -10000 + rnorm(1,0,1),waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
Jprior = sum(log(factorial(sj)/((m^sj)*2^(2*sj-2))))
mlik = (logLik(out)- 0.5*log(J.a.hat) - 0.5*p*log(p.v) -0.5*Q/p.v + log(beta((p.a+p)/2,p.b/2)) + log(phi1(p.b/2,p.r,(p.a+p.b+p)/2,(p.s+Q)/2/p.v,1-p.k))+Jprior + p*log(r)+n)
if(is.na(mlik)||mlik==-Inf)
mlik = -10000+ rnorm(1,0,1)
return(list(mlik = mlik,waic = AIC(out) , dic = BIC(out),summary.fixed =list(mean = coefficients(out))))
}
#define the function estimating parameters of a given Gaussian logic regression with robust g prior
estimate.logic.lm.tCCH = function(formula = NULL, data, n=1000, m=50, r = 1, p.a = 1, p.b = 2, p.r = 1.5, p.s = 0, p.v=-1, p.k = 1,k.max=21)
{
if(is.null(formula))
return(list(mlik = -10000,waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
fmla.proc=as.character(formula)[2:3]
fobserved = fmla.proc[1]
if(fmla.proc[2]=="-1")
return(list(mlik = -10000,waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
out = lm(formula = formula,data = data)
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
Jprior = prod(factorial(sj)/((m^sj)*2^(2*sj-2)))
p.v = (n+1)/(p+1)
R.2 = summary(out)$r.squared
mlik = (-0.5*p*log(p.v) -0.5*(n-1)*log(1-(1-1/p.v)*R.2) + log(beta((p.a+p)/2,p.b/2)) - log(beta(p.a/2,p.b/2)) + log(phi1(p.b/2,(n-1)/2,(p.a+p.b+p)/2,p.s/2/p.v,R.2/(p.v-(p.v-1)*R.2))) - hypergeometric1F1(p.b/2,(p.a+p.b)/2,p.s/2/p.v,log = T)+log(Jprior) + p*log(r)+n)
if(mlik==-Inf||is.na(mlik)||is.nan(mlik))
mlik = -10000
return(list(mlik = mlik,waic = AIC(out)-n , dic = BIC(out)-n,summary.fixed =list(mean = coef(out))))
}
#define the function estimating parameters of a given Gaussian logic regression with Jeffrey's prior
estimate.logic.lm.jef = function(formula= NULL, data, n, m, r = 1,k.max=21)
{
if(is.null(formula))
return(list(mlik = -10000,waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
out = lm(formula = formula,data = data)
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc=as.character(formula)[2:3]
fobserved = fmla.proc[1]
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
Jprior = prod(factorial(sj)/((m^sj)*2^(2*sj-2)))
mlik = (-BIC(out)+2*log(Jprior) + 2*p*log(r)+n)/2
if(mlik==-Inf)
mlik = -10000
return(list(mlik = mlik,waic = AIC(out)-n , dic = BIC(out)-n,summary.fixed =list(mean = coef(out))))
}
LogicRegr = function(formula, data, family = "Gaussian",prior = "J",report.level = 0.5, d = 20, cmax = 5, kmax = 20, p.and = 0.9, p.not = 0.05, p.surv = 0.1,ncores = -1, n.mods = 1000 ,advanced = list(presearch = T,locstop = F ,estimator = estimate.logic.bern.tCCH,estimator.args = list(data = data.example,n = 1000, m = 50,r=1),recalc_margin = 250, save.beta = F,interact = T,relations = c("","lgx2","cos","sigmoid","tanh","atan","erf"),relations.prob =c(0.4,0.0,0.0,0.0,0.0,0.0,0.0),interact.param=list(allow_offsprings=1,mutation_rate = 300,last.mutation = 5000, max.tree.size = 1, Nvars.max = 100,p.allow.replace=0.9,p.allow.tree=0.2,p.nor=0.2,p.and = 1),n.models = 10000,unique = T,max.cpu = 4,max.cpu.glob = 4,create.table = F,create.hash = T,pseudo.paral = T,burn.in = 50,outgraphs=F,print.freq = 1000,advanced.param = list(
max.N.glob=as.integer(10),
min.N.glob=as.integer(5),
max.N=as.integer(3),
min.N=as.integer(1),
printable = F)))
{
data.example = data
advanced$formula = formula
advanced$data = data
advanced$interact.param$Nvars.max = d
advanced$interact.param$ max.tree.size= cmax - 1
advanced$interact.param$p.and = p.and
advanced$interact.param$p.nor = p.not
advanced$interact.param$p.allow.tree = p.surv
if(!prior %in% c("J","G"))
{
warning("Wrong prior supplied. J (for Jeffrey's) and G (for robust g) priors are allowd only. Setting J as default.")
prior = "J"
}
if(!family %in% c("Gaussian","Bernoulli"))
{
warning("Wrong familty supplied. Gaussian and Bernoulli families are allowd only. Setting Gaussian as default.")
family = "Gaussian"
}
if(family == "Gaussian")
{
if(prior == "J")
{
advanced$estimator = estimate.logic.lm.jef
advanced$estimator.args = list(data = data, n = dim(data)[1], m =stri_count_fixed(as.character(formula)[3],"+"),k.max = kmax)
}else{
advanced$estimator = estimate.logic.lm.tCCH
advanced$estimator.args = list(data = data, n = dim(data)[1], m =stri_count_fixed(as.character(formula)[3],"+"),k.max = kmax)
}
}else{
if(prior == "J")
{
advanced$estimator = estimate.logic.bern
advanced$estimator.args = list(data = data, n = dim(data)[1], m =stri_count_fixed(as.character(formula)[3],"+"),k.max = kmax)
}else{
advanced$estimator = estimate.logic.bern.tCCH
advanced$estimator.args = list(data = data, n = dim(data)[1], m =stri_count_fixed(as.character(formula)[3],"+"),k.max = kmax)
}
}
if(ncores<1)
ncores = detectCores()
return(pinferunemjmcmc(n.cores = ncores,report.level = report.level, simplify = T, num.mod.best = n.mods, predict = F, runemjmcmc.params = advanced))
}
mcgmjpar = function(X,FUN,mc.cores) mclapply(X= X,FUN = FUN,mc.preschedule = T,mc.cores = mc.cores)
mcgmjpse = function(X,FUN,mc.cores) lapply(X,FUN)
pinferunemjmcmc = function(n.cores = 4, mcgmj = mcgmjpar, report.level = 0.5, simplify = F, num.mod.best = 1000, predict = F, test.data = 1, link.function = function(z)z, runemjmcmc.params)
{
if(predict)
{
runemjmcmc.params$save.beta = T
if(length(test.data)==0)
{
warning("Test data is not provided. No predictions will be made!")
}
}
params = list(runemjmcmc.params)[rep(1,n.cores)]
for(i in 1:n.cores)
{
params[[i]]$test = test.data
params[[i]]$link = link.function
params[[i]]$predict = predict
params[[i]]$NM = num.mod.best
params[[i]]$cpu=i
}
M = n.cores
#results = runpar.infer(params[[1]])
results=mcgmj(X = params,FUN = runpar.infer,mc.cores = n.cores)
#print(results)
#clean up
gc()
#prepare the data structures for final analysis of the runs
compmax = runemjmcmc.params$interact.param$Nvars.max + 1
resa=array(data = 0,dim = c(compmax,M*3))
post.popul = array(0,M)
max.popul = array(0,M)
nulls=NULL
not.null=1
#check which threads had non-zero exit status
for(k in 1:M)
{
if(length(results[[k]])<=1||length(results[[k]]$cterm)==0||length(results[[k]]$p.post)!=runemjmcmc.params$interact.param$Nvars.max)
{
nulls=c(nulls,k)
#warning(paste0("Thread ",k,"did not converge or was killed by OS!"))
next
}
else
{
not.null = k
}
}
if(length(nulls) == M)
{
warning("All threads did not converge or gave an error! Returning stats from the threads only!")
return(list(feat.stat = NULL,predictions = NULL,allposteriors = NULL, threads.stats = results))
}
#for all of the successful runs collect the results into the corresponding data structures
for(k in 1:M)
{
if(k %in% nulls)
{
results[[k]]=results[[not.null]]
}
max.popul[k]=results[[k]]$cterm
post.popul[k]=results[[k]]$post.populi
resa[,k*3-2]=c(results[[k]]$fparam,"Post.Gen.Max")
resa[,k*3-1]=c(results[[k]]$p.post,results[[k]]$cterm)
resa[,k*3]=rep(post.popul[k],length(results[[k]]$p.post)+1)
}
#renormalize estimates of the marginal inclusion probabilities
#based on all of the runs
ml.max=max(max.popul)
post.popul=post.popul*exp(-ml.max+max.popul)
p.gen.post=post.popul/sum(post.popul)
#perform BMA of the redictions across the runs
pred = NULL
if(predict){
pred = results[[1]]$preds*p.gen.post[1]
if(M > 1) {
for(i in 2:M)
{
pred=pred+results[[i]]$preds*p.gen.post[i]
}
}
}
hfinal=hash()
for(ii in 1:M)
{
resa[,ii*3]=p.gen.post[ii]*as.numeric(resa[,ii*3-1])
resa[length(resa[,ii*3]),ii*3]=p.gen.post[ii]
if(p.gen.post[ii]>0)
{
for(jj in 1:(length(resa[,ii*3])-1))
{
if(resa[jj,ii*3]>0)
{
if(as.integer(has.key(hash = hfinal,key =resa[jj,ii*3-2]))==0)
hfinal[[resa[jj,ii*3-2]]]=as.numeric(resa[jj,ii*3])
else
hfinal[[resa[jj,ii*3-2]]]=hfinal[[resa[jj,ii*3-2]]]+as.numeric(resa[jj,ii*3])
}
}
}
}
posteriors=values(hfinal)
clear(hfinal)
#delete the unused further variables
rm(hfinal)
rm(resa)
rm(post.popul)
rm(max.popul)
#simplify the found trees and their posteriors
posteriors=as.data.frame(posteriors)
posteriors=data.frame(X=row.names(posteriors),x=posteriors$posteriors)
posteriors$X=as.character(posteriors$X)
res1 = NULL
if(simplify){
res1=simplifyposteriors.infer(X = runemjmcmc.params$data,posteriors = posteriors, thf = report.level,resp = as.character(runemjmcmc.params$formula)[2])
rownames(res1) = NULL
res1$feature = as.character(res1$feature)
}
posteriors=posteriors[order(posteriors$x, decreasing = T),]
colnames(posteriors)=c("feature","posterior")
rm(params)
gc()
return(list(feat.stat = cbind(res1$feature,res1$posterior),predictions = pred,allposteriors = posteriors, threads.stats = results))
}
estimate.logic.lm <- function(formula, data, n, m, r = 1)
{
out <- lm(formula = formula,data = data)
p <- out$rank
fmla.proc<-as.character(formula)[2:3]
fobserved <- fmla.proc[1]
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam <-stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj<-(stri_count_fixed(str = fparam, pattern = "&"))
sj<-sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj<-sj+1
Jprior <- prod(factorial(sj)/((m^sj)*2^(2*sj-2)))
#tn<-sum(stri_count_fixed(str = fmla.proc[2], pattern = "I("))
mlik = (-BIC(out)+2*log(Jprior) + 2*p*log(r)+n)/2
if(mlik==-Inf)
mlik = -10000
return(list(mlik = mlik,waic = AIC(out)-n , dic = BIC(out)-n,summary.fixed =list(mean = coef(out))))
}
#estimate elastic nets
estimate.elnet <- function(formula,response, data, family,alpha)
{
X <- model.matrix(object = formula,data = data)
if(dim(X)[2]<=2)
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = array(0,dim=dim(X)[2]))))
out <- glmnet(x=X[,-1], y = data[[response]], family=family, a=alpha)
dout<- as.numeric(-deviance(out)[[out$dim[2]]])
return(list(mlik = dout,waic = -dout , dic = -dout,summary.fixed =list(mean = coef(out)[,out$dim[2]])))
}
# use dic and aic as bic and aic correspondinly
estimate.speedglm <- function(formula, data, family, prior, logn) # weird behaviour, bad control of singularity
{
X <- model.matrix(object = formula,data = data)
out <- speedglm.wfit(y = data[,1], X = X, intercept=FALSE, family=family,eigendec = T, method = "Cholesky")
if(prior == "AIC")
return(list(mlik = -out$aic ,waic = -(out$deviance + 2*out$rank) , dic = -(out$RSS),summary.fixed =list(mean = out$coefficients)))
if(prior=="BIC")
return(list(mlik = -out$RSS-logn*out$rank ,waic = -(out$deviance + 2*out$rank) , dic = -(out$RSS+logn*out$rank),summary.fixed =list(mean = out$coefficients)))
}
estimate.bigm <- function(formula, data, family, prior,n, maxit = 2,chunksize = 1000000) # nice behaviour
{
out <- bigglm(data = data, family=family,formula = formula, sandwich = F,maxit = maxit, chunksize = chunksize)
if(prior == "AIC")
return(list(mlik = -AIC(out,k = 2) ,waic = AIC(out,k = 2) , dic = AIC(out,k = n),summary.fixed =list(mean = coef(out))))
if(prior=="BIC")
return(list(mlik = -AIC(out,k = n) ,waic = AIC(out, k = 2) , dic = AIC(out,k = n),summary.fixed =list(mean = coef(out))))
}
sigmoid<- function(x)
{
return(1/(1+(exp(-x))))
}
erf <- function(x)
{
return(2 * pnorm(x * sqrt(2)) - 1)
}
estimate.bas.lm <- function(formula, data, prior, n, g = 0)
{
out <- lm(formula = formula,data = data)
# 1 for aic, 2 bic prior, else g.prior
p <- out$rank
if(prior == 1)
{
ss<-sum(out$residuals^2)
logmarglik <- -0.5*(log(ss)+2*p)
}
else if(prior ==2)
{
ss<-sum(out$residuals^2)
logmarglik <- -0.5*(log(ss)+log(n)*p)
}
else
{
Rsquare <- summary(out)$r.squared
#logmarglik = .5*(log(1.0 + g) * (n - p -1) - log(1.0 + g * (1.0 - Rsquare)) * (n - 1))*(p!=1)
logmarglik = .5*(log(1.0 + g) * (n - p) - log(1.0 + g * (1.0 - Rsquare)) * (n - 1))*(p!=1)
}
# use dic and aic as bic and aic correspondinly
return(list(mlik = logmarglik,waic = AIC(out) , dic = BIC(out),summary.fixed =list(mean = coef(out))))
}
estimate.inla <- function(formula, args)
{
out<-NULL
tryCatch(capture.output({
out <- do.call(inla, c(args,formula = formula))}))
if(is.null(out))
return(list(mlik = -10000,waic = 10000 , dic = 10000, summary.fixed =list(mean = NULL)))
# use dic and aic as bic and aic correspondinly
coef<-out$summary.fixed$mode
coef[1]<-coef[1]+out$summary.hyperpar$mode[1]
return(list(mlik = out$mlik[1],waic = out$waic[1] , dic = out$dic[1], summary.fixed =list(mean = coef)))
}
estimate.inla.poisson <- function(formula, data,r = 1.0/200.0,logn=log(200.0), relat=c("*","+","cos","sigmoid","tanh","atan","sin","erf"))
{
out<-NULL
capture.output({tryCatch(capture.output({
fmla.proc<-as.character(formula)[2:3]
sj<-sum(stri_count_fixed(str = fmla.proc[2],pattern = relat))
out <-inla(family = "poisson",silent = 2L,data = data,formula = formula,control.compute = list(dic = TRUE, waic = TRUE, mlik = TRUE))
}))})
if(is.null(out))
return(list(mlik = -10000+log(r)*(sj),waic = 10000 , dic = 10000, summary.fixed =list(mean = NULL)))
if(length(out$waic[1]$waic)==0)
return(list(mlik = -10000+log(r)*(sj),waic = 10000 , dic = 10000, summary.fixed =list(mean = NULL)))
# use dic and aic as bic and aic correspondinly
coef<-out$summary.fixed$mode
#coef[1]<-coef[1]+out$summary.hyperpar$mode[1]
return(list(mlik = out$mlik[1]+log(r)*(sj),waic = out$waic[1]$waic , dic = out$dic[1]$dic, summary.fixed =list(mean = coef)))
}
estimate.gamma.cpen <- function(formula, data,r = 1.0/1000.0,logn=log(1000.0),relat=c("cos","sigmoid","tanh","atan","sin","erf"))
{
fparam<-NULL
fmla.proc<-as.character(formula)[2:3]
fobserved <- fmla.proc[1]
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam <-stri_split_fixed(str = fmla.proc[2],pattern = "+I",omit_empty = F)[[1]]
sj<-(stri_count_fixed(str = fparam, pattern = "*"))
sj<-sj+(stri_count_fixed(str = fparam, pattern = "+"))
for(rel in relat)
sj<-sj+(stri_count_fixed(str = fparam, pattern = rel))
#sj<-sj+1
tryCatch(capture.output({
out <- glm(formula = formula,data = data, family = gaussian)
# 1 for aic, 2 bic prior, else g.prior
mlik = (-(BIC(out) -2*log(r)*sum(sj))+1000)/2
waic = (out$deviance + 2*out$rank)+10000
dic = (out$deviance + logn*out$rank)+10000
summary.fixed =list(mean = coefficients(out))
}, error = function(err) {
print(err)
mlik = -10000
waic = 10000
dic = 10000
summary.fixed =list(mean = array(0,dim=length(fparam)))
}))
return(list(mlik = mlik,waic = waic , dic = dic,summary.fixed =summary.fixed))
}
parallelize<-function(X,FUN)
{
max.cpu <- length(X)
cl <-makeCluster(max.cpu ,type = paral.type,outfile = "")#outfile = ""
clusterEvalQ(cl = cl,expr = c(library(INLA),library(bigmemory)))
if(exists("statistics"))
{
clusterExport(cl=cl, "statistics")
clusterEvalQ(cl,{statistics <- attach.resource(statistics);1})
}
res.par <- parLapply(cl = cl, X, FUN)
stopCluster(cl)
return(res.par)
}
estimate.glm <- function(formula, data, family, prior, n=1, g = 0)
{
out <- glm(formula = formula, family = family, data = data)
# 1 for aic, 2 bic prior, else g.prior
p <- out$rank
if(prior == 1)
{
logmarglik <- -AIC(out)
}
else if(prior ==2)
{
logmarglik <- -BIC(out)
}
else
{
Rsquare <- summary(out)$r.squared
#logmarglik = .5*(log(1.0 + g) * (n - p -1) - log(1.0 + g * (1.0 - Rsquare)) * (n - 1))*(p!=1)
logmarglik = .5*(log(1.0 + g) * (n - p) - log(1.0 + g * (1.0 - Rsquare)) * (n - 1))*(p!=1)
}
# use dic and aic as bic and aic correspondinly
return(list(mlik = logmarglik,waic = AIC(out) , dic = BIC(out),summary.fixed =list(mean = coef(out))))
}
simplify.formula<-function(fmla,names)
{
fmla.proc<-as.character(fmla)[2:3]
fobserved <- fmla.proc[1]
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam <- names[which(names %in% stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]] )]
return(list(fparam = fparam,fobserved = fobserved))
}
simplifyposteriors<-function(X,posteriors,th=0.0001,thf=0.2, resp)
{
posteriors<-posteriors[-which(posteriors[,2]<th),]
rhash<-hash()
for(i in 1:length(posteriors[,1]))
{
expr<-posteriors[i,1]
#print(expr)
res<-model.matrix(data=X,object = as.formula(paste0(resp,"~",expr)))
ress<-c(stri_flatten(round(res[,2],digits = 4),collapse = ""),stri_flatten(res[,2],collapse = ""),posteriors[i,2],expr)
if(!((ress[1] %in% values(rhash))))
rhash[[ress[1]]]<-ress
else
{
if(ress[1] %in% keys(rhash))
{
rhash[[ress[1]]][3]<- (as.numeric(rhash[[ress[1]]][3]) + as.numeric(ress[3]))
if(stri_length(rhash[[ress[1]]][4])>stri_length(expr))
rhash[[ress[1]]][4]<-expr
}
}
}
res<-as.data.frame(t(values(rhash)[c(3,4),]))
res$V1<-as.numeric(as.character(res$V1))
res<-res[which(res$V1>thf),]
res<-res[order(res$V1, decreasing = T),]
clear(rhash)
rm(rhash)
res[which(res[,1]>1),1]<-1
colnames(res)<-c("posterior","tree")
return(res)
}
do.call.emjmcmc<-function(vect)
{
set.seed(as.integer(vect$cpu))
do.call(runemjmcmc, vect[1:vect$simlen])
vals<-values(hashStat)
fparam<-mySearch$fparam
cterm<-max(vals[1,],na.rm = T)
ppp<-mySearch$post_proceed_results_hash(hashStat = hashStat)
post.populi<-sum(exp(values(hashStat)[1,][1:vect$NM]-cterm),na.rm = T)
clear(hashStat)
#rm(hashStat)
rm(vals)
gc()
return(list(post.populi = post.populi, p.post = ppp$p.post, cterm = cterm, fparam = fparam))
}
parall.gmj <- function(X,M=16,preschedule = F) mclapply(X = X, FUN = do.call.emjmcmc,mc.preschedule = preschedule, mc.cores = M,mc.cleanup = T)
# a function that creates an EMJMCMC2016 object with specified values of some parameters and default values of other parameters
runemjmcmc<-function(formula, data, secondary = vector(mode="character", length=0), latnames="",
estimator,estimator.args = "list",n.models,p.add.default = 1,p.add = 0.5, unique = F,save.beta=F, locstop.nd = F, latent="",max.cpu=4,max.cpu.glob=2,create.table=T, hash.length = 20, presearch=T, locstop =F ,pseudo.paral = F,interact = F,deep.method =1,relations = c("","sin","cos","sigmoid","tanh","atan","erf"),relations.prob =c(0.4,0.1,0.1,0.1,0.1,0.1,0.1),gen.prob = c(1,10,5,1,0),pool.cross = 0.9,p.epsilon = 0.0001, del.sigma = 0.5,pool.cor.prob = F, interact.param=list(allow_offsprings=2,mutation_rate = 100,last.mutation=2000, max.tree.size = 10000, Nvars.max = 100, p.allow.replace = 0.7,p.allow.tree=0.1,p.nor=0.3,p.and = 0.7), prand = 0.01,keep.origin = T, sup.large.n = 5000, recalc_margin = 2^10, create.hash=F,interact.order=1,burn.in=1, eps = 10^6, max.time = 120,max.it = 25000, print.freq = 100,outgraphs=F,advanced.param=NULL, distrib_of_neighbourhoods=t(array(data = c(7.6651604,16.773326,14.541629,12.839445,2.964227,13.048343,7.165434,
0.9936905,15.942490,11.040131,3.200394,15.349051,5.466632,14.676458,
1.5184551,9.285762,6.125034,3.627547,13.343413,2.923767,15.318774,
14.5295380,1.521960,11.804457,5.070282,6.934380,10.578945,12.455602,
6.0826035,2.453729,14.340435,14.863495,1.028312,12.685017,13.806295),dim = c(7,5))), distrib_of_proposals = c(76.91870,71.25264,87.68184,60.55921,15812.39852))
{
#first create the object
assign("data.example",data, envir=globalenv())
variables <- simplify.formula(formula,names(data.example))
assign("fparam.example",variables$fparam, envir=globalenv())
assign("fobserved.example",variables$fobserved, envir=globalenv())
#for(i in 1:length(fparam.example))
#{
# fparam.example[i]<<-paste("I(",variables$fparam[i],")",sep = "")
#}
fparam.tmp<- as.vector(sapply(FUN = paste,"I(",variables$fparam,")",sep="")[,1])
if(latnames[1]!="")
fparam.example<<-c(fparam.tmp,latnames)
else
fparam.example<<-fparam.tmp
#print(fparam.tmp)
#print(fparam.example)
assign("mySearch",EMJMCMC2016(), envir=globalenv())
if(length(secondary)>0)
mySearch$filtered <<- sapply(FUN = paste,"I(",secondary,")",sep="")
mySearch$estimator <<- estimator
mySearch$latnames <<- latnames
mySearch$estimator.args <<- estimator.args
mySearch$latent.formula <<- latent
mySearch$save.beta <<- save.beta
mySearch$prand<<-prand
mySearch$p.add<<-array(p.add,length(fparam.example))
mySearch$p.add.default<<-p.add.default
mySearch$recalc.margin <<- as.integer(recalc_margin)
mySearch$max.cpu <<- as.integer(max.cpu)
mySearch$locstop.nd <<- locstop.nd
mySearch$pool.cor.prob<<-pool.cor.prob
mySearch$sup.large.n<<-as.integer(sup.large.n)
mySearch$max.cpu.glob <<- as.integer(max.cpu.glob)
mySearch$deep.method <<- as.integer(deep.method)
if(interact)
{
mySearch$allow_offsprings <<- as.integer(interact.param$allow_offsprings)
mySearch$mutation_rate <<- as.integer(interact.param$mutation_rate)
mySearch$Nvars.max <<- as.integer(interact.param$Nvars.max)
mySearch$max.tree.size <<- as.integer(interact.param$max.tree.size)
mySearch$p.allow.replace <<- interact.param$p.allow.replace
mySearch$p.allow.tree <<- interact.param$p.allow.tree
mySearch$p.epsilon <<- p.epsilon
mySearch$keep.origin<<- keep.origin
mySearch$sigmas<<-relations
mySearch$sigmas.prob<<-relations.prob
mySearch$del.sigma<<-del.sigma
mySearch$pool.cross<<-pool.cross
mySearch$gen.prob<<-gen.prob
mySearch$p.nor <<- interact.param$p.nor
mySearch$p.and <<- interact.param$p.and
mySearch$last.mutation <<- as.integer(interact.param$last.mutation)
}
if(!is.null(advanced.param))
{
mySearch$max.N.glob<<-as.integer(advanced.param$max.N.glob)
mySearch$min.N.glob<<-as.integer(advanced.param$min.N.glob)
mySearch$max.N<<-as.integer(advanced.param$max.N)
mySearch$min.N<<-as.integer(advanced.param$min.N)
mySearch$printable.opt<<-advanced.param$printable
}
#distrib_of_proposals = с(0,0,0,0,10)
if(exists("hashStat"))
{
clear(hashStat)
remove(hashStat,envir=globalenv())
}
if(exists("statistics1"))
{
remove(statistics,envir=globalenv() )
remove(statistics1,envir=globalenv())
}
if(exists("hash.keys1"))
{
remove(hash.keys,envir=globalenv())
remove(hash.keys1,envir=globalenv())
}
if(create.table)
{
if(pseudo.paral)
mySearch$parallelize <<- lapply
#carry the search (training out)
assign("statistics1",big.matrix(nrow = 2 ^min((length(fparam.example)),hash.length)+1, ncol = 16+length(fparam.example)*save.beta,init = NA, type = "double"), envir=globalenv())
assign("statistics",describe(statistics1), envir=globalenv())
mySearch$g.results[4,1]<<-0
mySearch$g.results[4,2]<<-0
mySearch$p.add <<- array(data = 0.5,dim = length(fparam.example))
if((length(fparam.example))>20)
{
mySearch$hash.length<<-as.integer(hash.length)
mySearch$double.hashing<<-T
hash.keys1 <<- big.matrix(nrow = 2 ^(hash.length)+1, ncol = length(fparam.example),init = 0, type = "char")
hash.keys <<- describe(hash.keys1)
}
}else if(create.hash)
{
assign("hashStat",hash(), envir=globalenv())
mySearch$parallelize <<- lapply
mySearch$hash.length<<-as.integer(20)
mySearch$double.hashing<<-F
}
# now as the object is created run the algorithm
initsol=rbinom(n = length(fparam.example),size = 1,prob = 0.5)
if(unique)
resm<-mySearch$modejumping_mcmc(list(varcur=initsol,locstop=locstop,presearch=presearch,statid=5, distrib_of_proposals =distrib_of_proposals,distrib_of_neighbourhoods=distrib_of_neighbourhoods, eps = eps, trit = n.models*100, trest = n.models, burnin = burn.in, max.time = max.time, maxit = max.it, print.freq = print.freq))
else
resm<-mySearch$modejumping_mcmc(list(varcur=initsol,locstop=locstop,presearch=presearch,statid=5, distrib_of_proposals =distrib_of_proposals,distrib_of_neighbourhoods=distrib_of_neighbourhoods, eps = eps, trit = n.models, trest = n.models*100, burnin = burn.in, max.time = max.time, maxit = max.it, print.freq = print.freq))
ppp<-1
print("MJMCMC is completed")
if(create.table)
{
print("Post Proceed Results")
ppp<-mySearch$post_proceed_results(statistics1 = statistics1)
truth = ppp$p.post # make sure it is equal to Truth column from the article
truth.m = ppp$m.post
truth.prob = ppp$s.mass
ordering = sort(ppp$p.post,index.return=T)
print("pi truth")
sprintf("%.10f",truth[ordering$ix])
sprintf(fparam.example[ordering$ix])
}
else if(create.hash)
{
print("Post Proceed Results")
ppp<-mySearch$post_proceed_results_hash(hashStat = hashStat)
truth = ppp$p.post # make sure it is equal to Truth column from the article
truth.m = ppp$m.post
truth.prob = ppp$s.mass
ordering = sort(ppp$p.post,index.return=T)
print("pi truth")
sprintf("%.10f",truth[ordering$ix])
sprintf(fparam.example[ordering$ix])
}
if(outgraphs)
{
par(mar = c(10,4,4,2) + 4.1)
barplot(resm$bayes.results$p.post,density = 46,border="black",main = "Marginal Inclusion (RM)",ylab="Probability",names.arg = mySearch$fparam,las=2)
barplot(resm$p.post,density = 46,border="black",main = "Marginal Inclusion (MC)",ylab="Probability",names.arg = mySearch$fparam,las=2)
}
return(ppp)
}
# add plot(ppp), summary(ppp), print(ppp), ppp as a class itself, coef(ppp)
EMJMCMC2016 <- setRefClass(Class = "EMJMCMC2016",
fields = list(estimator.args = "list",
max.cpu = "integer",
objective = "integer",
p.prior = "numeric",
min.N = "integer",
estimator = "function",
parallelize = "function",
parallelize.global = "function",
parallelize.hyper = "function",
min.N.randomize = "integer",
max.N.randomize = "integer",
type.randomize = "integer",
thin_rate = "integer",
aa = "numeric",
cc = "numeric",
printable.opt = "logical",
fobserved = "vector",
switch.type = "integer",
n.size ="integer",
deep.method = "integer",
sup.large.n = "integer",
LocImprove = "array",
max.N = "integer",
save.beta = "logical",
keep.origin = "logical",
recalc.margin = "numeric",
max.N.glob = "integer",
min.N.glob = "integer",
max.cpu.glob = "integer",
max.cpu.hyper = "integer",
p.add.default="numeric",
switch.type.glob = "integer",
isobsbinary = "array",
filtered = "vector",
fparam = "vector",
latnames = "vector",
fparam.pool = "vector",
p.add = "array",
latent.formula = "character",
Nvars = "integer",
seed = "integer",
M.nd = "integer",
locstop.nd = "logical",
pool.cor.prob = "logical",
M.mcmc = "integer",
SA.param = "list",
p.epsilon = "numeric",
p.allow.tree = "numeric",
p.nor = "numeric",
p.and = "numeric",
sigmas.prob ="numeric",
del.sigma = "numeric",
pool.cross = "numeric",
gen.prob = "numeric",
sigmas = "vector",
p.allow.replace = "numeric",
max.tree.size = "integer",
double.hashing = "logical",
prand = "numeric",
hash.length = "integer",
update.marg.mc = "logical",
Nvars.max = "integer",
Nvars.init = "integer",
last.mutation = "integer",
allow_offsprings = "integer",
mutation_rate = "integer",
g.results = "big.matrix"
),
methods = list(
#class constructor
initialize = function(estimator.function = inla, estimator.args.list = list(family = "gaussian",data = data.example, control.fixed=list(prec=list(default= 0.00001),prec.intercept = 0.00001,mean=list(default= 0),mean.intercept = 0),
control.family = list(hyper = list(prec = list(prior = "loggamma",param = c(0.00001,0.00001),initial = 0))),
control.compute = list(dic = TRUE, waic = TRUE, mlik = TRUE)), search.args.list = NULL,latent.formula = "")
{
estimator <<- estimator.function
estimator.args <<- estimator.args.list
latent.formula <<- latent.formula
g.results <<- big.matrix(nrow = 4,ncol = 2)
g.results[1,1]<- -Inf
g.results[1,2]<- 1
g.results[2,1]<- Inf
g.results[2,2]<- 1
g.results[3,1]<- Inf
g.results[3,2]<- 1
g.results[4,1]<- 0
g.results[4,2]<- 0
if(is.null(search.args.list))
{
max.cpu <<- as.integer(Nvars*0.05 + 1)
objective <<- as.integer(1)
if(Sys.info()['sysname']=="Windows")
{
parallelize <<- lapply
parallelize.global <<- lapply
parallelize.hyper <<- lapply
}
else
{
parallelize <<- mclapply
parallelize.global <<- mclapply
parallelize.hyper <<- mclapply
}
Nvars <<- as.integer(length(fparam.example))
min.N <<- as.integer(Nvars/6)
min.N.glob <<- as.integer(Nvars/3)
max.N.glob <<- as.integer(Nvars/2)
max.N <<- as.integer(Nvars/5)
switch.type.glob <<- as.integer(2)
min.N.randomize <<- as.integer(1)
max.N.randomize <<- as.integer(1)
deep.method<<- as.integer(1)
type.randomize <<- as.integer(3)
pool.cor.prob<<-F
prand<<-0.01
max.cpu.glob <<- as.integer(Nvars*0.05 + 1)
max.cpu.hyper <<- as.integer(2)
sup.large.n<<-as.integer(1000)
save.beta <<- FALSE
filtered<<-vector(mode="character", length=0)
printable.opt <<- FALSE
keep.origin<<-FALSE
thin_rate<<- as.integer(-1)
p.allow.tree <<- 0.6
p.epsilon<<- 0.0001
latnames<<-""
p.add.default<<-1
p.allow.replace <<- 0.3
sigmas<<-c("","sin","cos","sigmoid","tanh","atan","erf")
sigmas.prob<<-c(0.4,0.1,0.1,0.1,0.1,0.1,0.1)
del.sigma<<-0.5
pool.cross<<-0.9
gen.prob<<-c(1,1,1,1,1)
p.nor <<- 0.3
p.and <<- 0.7
max.tree.size<<- as.integer(15)
Nvars.max <<- as.integer(Nvars)
Nvars.init <<- as.integer(Nvars)
allow_offsprings <<- as.integer(0)
mutation_rate <<- as.integer(100)
locstop.nd <<-FALSE
double.hashing <<- (Nvars > 20)
hash.length <<- as.integer(25)
filtered<<-vector(mode="character", length=0)
aa <<- 0.9
cc <<- 0.0
M.nd <<- as.integer(min(Nvars,100))
M.mcmc <<- as.integer(5)
SA.param <<- list(t.min = 0.0001,t.init = 10, dt = 3, M = as.integer(min(Nvars/5+1,20)))
fobserved <<- fobserved.example
switch.type <<- as.integer(2)
n.size <<- as.integer(10)
LocImprove <<- as.array(c(50,50,50,50,150))
isobsbinary <<- as.array(0:(length(fparam.example)-1))
fparam <<- fparam.example
fparam.pool <<- fparam.example
p.add <<- array(data = 0.5,dim = Nvars)
if(exists("statistics"))
{
recalc.margin <<- 2^Nvars
}else if(exists("statistics1"))
{
recalc.margin <<- 2^Nvars
}else
{
recalc.margin <<- 2^Nvars
}
last.mutation<<-as.integer(2^(Nvars/2)*0.01)
seed <<- as.integer(runif(n = 1,min = 1,max = 10000))
p.prior <<- runif(n = Nvars, min = 0.5,max = 0.5)
}
else
{
max.cpu <<- as.integer(search.args.list$max.cpu)
objective <<- as.integer(search.args.list$objective)
parallelize <<- search.args.list$parallelize
latnames <<- search.args.list$latnames
parallelize.global <<- search.args.list$parallelize.global
parallelize.hyper <<- search.args.list$parallelize.hyper
p.prior <<- search.args.list$p.prior
min.N <<- as.integer(search.args.list$min.N)
printable.opt <<- search.args.list$printable.opt
min.N.glob <<- as.integer(search.args.list$min.N.glob)
max.N.glob <<- as.integer(search.args.list$max.N.glob)
switch.type.glob <<- as.integer(search.args.list$switch.type.glob)
min.N.randomize <<- as.integer(search.args.list$min.N.randomize)
max.N.randomize <<- as.integer(search.args.list$max.N.randomize)
type.randomize <<- as.integer(search.args.list$type.randomize)
max.cpu.glob <<- as.integer(search.args.list$max.cpu.glob)
locstop.nd <<-search.args.list$locstop.nd
max.cpu.hyper <<- as.integer(search.args.list$max.cpu.hyper)
save.beta <<- search.args.list$save.beta
aa <<- search.args.list$lambda.a
prand<<-search.args.list$prand
p.add.default<<-search.args.list$ p.add.default
sup.large.n<<-search.args.list$sup.large.n
thin_rate <-search.args.list$thin_rate
keep.origin<<-search.args.list$keep.origin
cc <<- search.args.list$lambda.c
pool.cor.prob<<-search.args.list$pool.cor.prob
M.nd <<- as.integer(search.args.list$stepsGreedy)
M.mcmc <<- as.integer(search.args.list$stepsLocMCMC)
SA.param <<- search.args.list$SA.params
fobserved <<- search.args.list$fobserved
switch.type <<- as.integer(search.args.list$fswitch.type)
n.size <<- as.integer(search.args.list$n.size)
LocImprove <<-search.args.list$prior.optimizer.freq
max.N <<- as.integer(search.args.list$max.N)
fparam <<- search.args.list$fparam
fparam.pool <<- search.args.list$fparam
isobsbinary <<- as.array(0:(length(fparam)-1))
p.add <<- as.array(search.args.list$p.add)
recalc.margin <<- search.args.list$recalc.margin
Nvars <<- as.integer(length(fparam))
seed <<- search.args.list$seed
max.tree.size<<- as.integer(search.args.list$max.tree.size)
Nvars.max <<- as.integer(search.args.list$Nvars.max)
Nvars.init <<- as.integer(search.args.list$Nvars)
allow_offsprings <<- as.integer(search.args.list$allow_offsprings)
mutation_rate <<- as.integer(search.args.list$mutation_rate)
p.allow.tree <<- search.args.list$p.allow.tree
p.epsilon <<-search.args.list$p.epsilon
p.allow.replace <<- search.args.list$p.allow.replace
last.mutation<<-as.integer(search.args.list$last.mutation)
p.nor <<- search.args.list$p.nor
p.and <<- search.args.list$p.and
deep.method<<-as.integer(search.args.list$deep.method)
sigmas<<-search.args.list$sigmas
sigmas.prob<<-search.args.list$sigmas.prob
del.sigma<<-search.args.list$del.sigma
pool.cross<<-search.args.list$pool.cross
gen.prob<<-search.args.list$gen.prob
double.hashing <<- search.args.list$double.hashing
hash.length <<- as.integer(search.args.list$hash.length)
}
},
#transform binary numbers to decimal
bittodec.alt = function(bit) #transform a binary vector into a natural number to correspond between vector of solutions and storage array
{
n<-length(bit)
dec <- 0
for(i in 1:n)
{
j<-n-i
dec <- dec + ((2)^j)*bit[i]
}
return(dec)
},
bittodec = function(bit) #transform a binary vector into a natural number to correspond between vector of solutions and storage array
{
if(!double.hashing){
n<-length(bit)
dec <- 0
for(i in 1:n)
{
j<-n-i
dec <- dec + ((2)^j)*bit[i]
}
return(dec)
}
else
{
if(exists("statistics1"))
{
hash.level<-0
dec<- hashing(bit)+1
#print(dec)
sum.one<- sum(bit)*which.max(bit) + sum(bit[Nvars -7:Nvars+1])*Nvars
jjj<-1
while(!add.key(dec,bit,sum.one,T))
{
hash.level<-hash.level+1
bit1<- dectobit.alt(2654435761*(dec+97*sum.one+hash.level*36599)+hash.level*59+hash.level)
dec<- hashing(bit1)+1
#jjj<-jjj+1
#print(dec)
}
#print(jjj)
dec <- dec - 1
}
else if(exists("statistics"))
{
hash.level<-0
dec<- hashing(bit)+1
sum.one<- sum(bit)*which.max(bit) + sum(bit[Nvars -7:Nvars +1])*Nvars
while(!add.key(dec,bit,sum.one,F))
{
hash.level<-hash.level+1
bit1<- dectobit.alt(2654435761*(dec+97*sum.one+hash.level*36599)+hash.level*59+hash.level)
dec<- hashing(bit1)+1
#print(dec)
}
dec <- dec - 1
}
return(dec)
}
},
add.key = function(dec,bit,sum.one,levl)
{
lb<-length(bit)
if(dec>2^hash.length)
return(FALSE)
if(levl)
{
if(is.na(statistics1[dec,1]))
{
statistics1[dec,16]<-sum.one
hash.keys1[dec,]<-bit
return(TRUE)
}
if(is.na(statistics1[dec,16]))
{
statistics1[dec,16]<-sum.one
hash.keys1[dec,]<-bit#c(array(0,dim = Nvars-lb),bit)
return(TRUE)
}
if(statistics1[dec,16]!=sum.one)
return(FALSE)
i<-1
#print(lb)
lb <- length(bit)
while(i<=lb&&(hash.keys1[dec,Nvars-i+1])==bit[lb - i +1])
i<-i+1
return((i-1)==lb)
}
else
{
if(is.na(statistics[dec,1]))
{
statistics[dec,16]<-sum.one
hash.keys[dec,]<-bit
return(TRUE)
}
if(is.na(statistics[dec,16]))
{
statistics[dec,16]<-sum.one
hash.keys[dec,]<-bit#c(array(0,dim = Nvars-lb),bit)
return(TRUE)
}
if(statistics[dec,16]!=sum.one)
return(FALSE)
i<-1
lb <- length(bit)
while(i<=lb&&(hash.keys[dec,Nvars-i+1])==bit[lb - i +1])
i<-i+1
return((i-1)==lb)
}
},
hashing = function(bit)# a hash function to find where to place the key in the hash
{
n<-length(bit)
if(n<hash.length)
return(bittodec.alt(bit))
return(bittodec.alt(bit[(n-hash.length+1):n]))
},
binlog = function (x) # bitwise logorithm (base 2) computations based on Al Kashi's algorithm
{
lx <- length(x)
tol = -lx
y <- 0 # initialise output
b <- 0.5 # initialise mantissa
# arrange the input into a known range
if(lx == 1){
if(x[1] == 0)
return(-Inf)
if(x[1] == 1)
return(0)
}
# move one bit to the left end
# elsewhise
if(x[2]==0 && lx==2)
return(1)
powto<-2^(-c(1:(lx-1)))
float.x<-sum(x[2:lx]*powto)
x <- 1 + float.x
y <- lx -1
f<-0
fb<--1
# move one bit to the right end
# now x = 1.5
# loop until desired tolerance met
while(fb > tol)
{
x <- x*x
# update the index
if (x >= 2)
{
x <- x/2
y <- y + b
f <- log(exp(f)+exp(fb))
}
# scale for the next bit
b <- b/2
fb <- (fb-log(2))
}
return(list(y = y,z = lx -1, f = f))
},
#transform decimal numbers to binary
dectobit = function(dec) #transform a natural number into a binary vector to correspond between vector of solutions and storage array
{
if(!double.hashing){
if(dec == 0)
return(0)
q<-dec
bin<-NULL
while(q!=0)
{
r<-q/2
q=floor(r)
bin<-c(as.integer(2*(r-q)),bin)
}
return(bin)
}
return(dehash(dec+1))
},
dectobit.alt = function(dec) #transform a natural number into a binary vector to correspond between vector of solutions and storage array
{
if(dec == 0)
return(0)
q<-dec
bin<-NULL
while(q!=0)
{
r<-q/2
q=floor(r)
bin<-c(as.integer(2*(r-q)),bin)
}
return(bin)
},
dehash=function(dec)
{
if(exists("hash.keys1"))
return(hash.keys1[dec,])
if(exists("hash.keys"))
return(hash.keys[dec,])
return(NULL)
},
#calculate move probabilities
calculate.move.logprobabilities = function(varold, varnew, switch.type,min.N,max.N)
{
if(switch.type == 1) # random size random N(x)
{
#warning("This option should not be chosen for randomization unless p.add == 0.5 ", call. = FALSE)
min.N = max.N
log.mod.switch.prob <- log(1/(max.N - min.N +1)) # probability of having that many differences
KK<-sum(abs(varold-varnew))
log.mod.switch.prob <- 0 #always the same probabilities for moves within thenighbourhood for p=0.5
log.mod.switchback.prob <- 0
} else if(switch.type == 2) #fixed N(x) inverse operator
{
if(min.N!=max.N)
{
#warning("min.N should be equal to max.N in swap type neighbourhoods min.N:=max.N", call. = FALSE)
min.N = max.N
}
log.mod.switch.prob <- log(1/(max.N - min.N +1))
KK<-max.N
log.mod.switch.prob <- log.mod.switch.prob + KK*log(factorial(Nvars - KK + 1)/factorial(Nvars))
log.mod.switchback.prob <- log.mod.switch.prob
}else if(switch.type == 3) # random sized inverse N(x)
{
log.mod.switch.prob <- log(1/(max.N - min.N +1))
KK<-sum(abs(varold-varnew))
log.mod.switch.prob <- log.mod.switch.prob + KK*log(factorial(Nvars - KK + 1)/factorial(Nvars))
log.mod.switchback.prob <- log.mod.switch.prob
}else if(switch.type == 4) # fixed N(x) for reverse from type 2 swaps
{
if(min.N!=max.N)
{
#warning("min.N should be equal to max.N in swap type neighbourhoods min.N:=max.N", call. = FALSE)
min.N = max.N
}
log.mod.switch.prob <- log(1/(max.N - min.N +1))
KK<-max.N
log.mod.switch.prob <- log.mod.switch.prob + KK*log(factorial(Nvars - KK + 1)/factorial(Nvars))
log.mod.switchback.prob <- log.mod.switch.prob
}else if(switch.type > 4)
{
log.mod.switch.prob <- log(x = 1)
log.mod.switchback.prob <-log(x = 1)
}
return(list(log.switch.forw.prob = log.mod.switch.prob, log.switch.back.prob = log.mod.switchback.prob))
},
#build a new model to draw from the old one return selection probabilities
buildmodel= function(varcur.old,statid, shift.cpu,max.cpu,switch.type,min.N,max.N,changeble.coord = NULL)
{
vect<- vector(length = max.cpu,mode = "list")
shift<-0
for(cpu in 1:(max.cpu))
{
set.seed(runif(1,1,10000), kind = NULL, normal.kind = NULL)
if(!is.null(varcur.old)&&length(varcur.old==Nvars))
{
varcur.old[which(is.na(varcur.old))]<-1
varcur<-varcur.old
}else
{
varcur<-rbinom(n = (Nvars),size = 1,0.5)
varcur.old<-varcur
}
changeble <-FALSE
if(!is.null(changeble.coord))
{
changeble <- TRUE
}
if(switch.type == 1) # random size random N(x) # try avoiding when doing mcmc rather than optimization
{
log.mod.switch.prob <- log(1/(max.N - min.N +1))
KK<-floor(runif(n=1, min.N, max.N + 0.999999999))
log.mod.switch.prob <- log.mod.switch.prob + KK*log(factorial(Nvars - KK + 1)/factorial(Nvars))
log.mod.switchback.prob <- log.mod.switch.prob
change.buf <- array(data = 0,dim = Nvars)
if(changeble){
for(ttt in 1:KK)
{
iid<-floor(runif(n = 1,min = 1,max = Nvars+0.999999999))
if(changeble.coord[iid]==1)
next
change.buf[iid] = 1
varcur[iid] <-rbinom(n = 1,size = 1,prob =round(p.add[iid],digits = 8))
log.mod.switch.prob = 0#log.mod.switch.prob + log(dbinom(x = varcur[iid],size = 1,prob = p.add[iid])) # this is one of the pathes to get there in general
log.mod.switchback.prob = 0# log.mod.switchback.prob + log(dbinom(x = 1-varcur[iid],size = 1,prob = p.add[iid])) # but this is one of the ways to get back only
}
}else
{
iid<-floor(runif(n = KK,min = 1,max = Nvars+0.999999999))
change.buf[iid] = 1
varcur[iid] <-rbinom(n = KK,size = 1,prob = round(p.add,digits = 8))
}
}else if(switch.type == 2) # fixed sized inverse N(x)
{
if(min.N!=max.N)
{
#warning("min.N should be equal to max.N in swap type neighbourhoods min.N:=max.N", call. = FALSE)
min.N <- max.N
}
log.mod.switch.prob <- log(1/(max.N - min.N +1))
KK<-max.N
log.mod.switch.prob <- log.mod.switch.prob + KK*log(factorial(Nvars - KK + 1)/factorial(Nvars))
log.mod.switchback.prob <- log.mod.switch.prob
change.buf <- array(data = 0,dim = Nvars)
if(changeble){
for(ttt in 1:KK)
{
iid<-floor(runif(n = 1,min = 1,max = Nvars+0.999999999))
if(change.buf[iid]==1 || changeble.coord[iid]==1)
{
KK<-KK+1
next
}
change.buf[iid] = 1
varcur[iid] = 1-varcur[iid]
}
}else
{
iid<-floor(runif(n = KK,min = 1,max = Nvars+0.999999999))
change.buf[iid] = 1
varcur[iid] = 1-varcur[iid]
}
}else if(switch.type == 3) # random sized inverse N(x)
{
log.mod.switch.prob <- log(1/(max.N - min.N +1))
KK<-floor(runif(n=1, min.N, max.N + 0.999999999))
log.mod.switch.prob <- log.mod.switch.prob + KK*log(factorial(Nvars - KK + 1)/factorial(Nvars))
log.mod.switchback.prob <- log.mod.switch.prob
change.buf <- array(data = 0,dim = Nvars)
if(changeble){
for(ttt in 1:KK)
{
iid<-floor(runif(n = 1,min = 1,max = Nvars+0.999999999))
if(change.buf[iid]==1 || changeble.coord[iid]==1)
{
KK<-KK+1
next
}
change.buf[iid] = 1
varcur[iid] = 1-varcur[iid]
}
}else
{
iid<-floor(runif(n = KK,min = 1,max = Nvars+0.999999999))
change.buf[iid] = 1
varcur[iid] = 1-varcur[iid]
}
}else if(switch.type == 4) # fixed N(x) for reverse from type 2 swaps
{
if(min.N!=max.N)
{
#warning("min.N should be equal to max.N in swap type neighbourhoods min.N:=max.N", call. = FALSE)
min.N <- max.N
}
log.mod.switch.prob <- log(1/(max.N - min.N +1))
KK<-max.N
log.mod.switch.prob <- log.mod.switch.prob + KK*log(factorial(Nvars - KK + 1)/factorial(Nvars))
log.mod.switchback.prob <- log.mod.switch.prob
ids <- which(changeble.coord == 0)
change.buf <- array(data = 0,dim = Nvars)
if(changeble){
for(ttt in KK)
{
iid<-floor(runif(n = 1,min = 1,max = Nvars+0.999999999))
if(change.buf[iid]==1 || changeble.coord[iid]==1)
{
KK<-KK+1
next
}
change.buf[iid] = 1
varcur[iid] = 1-varcur[iid]
}}
else
{
iid<-floor(runif(n = KK,min = 1,max = Nvars+0.999999999))
change.buf[iid] = 1
varcur[iid] = 1-varcur[iid]
}
}else if(switch.type == 5)
{
change.buf <- array(data = 0,dim = (Nvars))
log.mod.switch.prob<-0
log.mod.switchback.prob <-0
add<-0
if(cpu+shift>Nvars)
{
shift<-1 - cpu
varcur.old<-rep(0,times = Nvars)
}
if(varcur.old[cpu+shift]!=1)
{
varcur<-varcur.old
varcur[cpu+shift]<-1
}else
{
if(cpu+shift<Nvars)
shift<-shift+1
while(varcur.old[cpu+shift]==1)
{
shift<-shift+1
if(cpu+shift>=Nvars)
{
shift <- (Nvars - cpu)
break
}
}
varcur<-varcur.old
varcur[cpu+shift]<-1
}
}else if(switch.type == 6)
{
change.buf <- array(data = 0,dim = (Nvars))
log.mod.switch.prob<-0
log.mod.switchback.prob <-0
add<-0
if(cpu+shift>Nvars)
{
shift<-1 - cpu
varcur.old<-rep(1,times = Nvars)
}
if(varcur.old[cpu+shift]!=0)
{
varcur<-varcur.old
varcur[cpu+shift]<-0
}else
{
if(cpu+shift<Nvars)
shift<-shift+1
while(varcur.old[cpu+shift]==0)
{
shift<-shift+1
if(cpu+shift>=Nvars)
{
shift <- (Nvars - cpu)
break
}
}
varcur<-varcur.old
varcur[cpu+shift]<-0
}
}else if(switch.type == 7)
{
change.buf <- array(data = 0,dim = (Nvars))
log.mod.switch.prob<-0
log.mod.switchback.prob <-0
vec<-dectobit(cpu + shift.cpu)
varcur<-c(array(0,dim = (Nvars -length(vec))),vec) #issues here
}else if(switch.type == 8)
{
log.mod.switch.prob <-0
log.mod.switchback.prob <-0
varcur<-varcur.old
change.buf <- array(data = 0,dim = Nvars)
#if(printable.opt)print("type 8 invoked")
#if(printable.opt)print(varcur)
}else if(switch.type==9)
{
log.mod.switch.prob <-0
log.mod.switchback.prob <-0
change.buf <- array(data = 1,dim = Nvars)
changevar<- rbinom(n = Nvars,size = 1,prob=prand)
varcur<-varcur.old
varcur[which(changevar==1)]<-(1-varcur[which(changevar==1)])
log.mod.switch.prob<-prand^length(which(changevar==1))
}else{
log.mod.switch.prob <- 0
log.mod.switchback.prob <-0
change.buf <- array(data = 1,dim = Nvars)
varcur <-rbinom(n = Nvars,size = 1,prob = round(p.add,digits = 8))
#if(printable.opt)print("type 8 invoked")
#if(printable.opt)print(varcur)
}
# for(g in 1:max(isobsbinary))
# {
# if(length(varcur[which(isobsbinary == g && varcur %in% c(1,3))])==length(which(isobsbinary == g)))
# varcur[which(isobsbinary == g && varcur %in% c(1,3))[1]]=0
# if(length(varcur[which(isobsbinary == g && varcur %in% c(2,3))])==length(which(isobsbinary == g)))
# varcur[which(isobsbinary == g && varcur %in% c(2,3))[1]]=0
# }
covobs <- if(fparam[1]=="Const")fparam[which(varcur[-1] == 1)+1]else fparam[which(varcur==1)]
#obsconst<-2*as.integer((varcur[1] %in% c(1,3)) || length(covobs) == 0 || (length(covobs)==length(which(isobsbinary != 0))) ) -1
obsconst<-ifelse(fparam[1]=="Const",2*as.integer((varcur[1])) -1,1)
id<-bittodec(varcur)
id<-id+1
if(ifelse(exists("statistics1"),is.na(statistics1[id,1]),ifelse(exists("statistics"),is.na(statistics[id,1,]),ifelse(exists("hashStat"),!has.key(hash = hashStat,key = paste(varcur,collapse = "")),TRUE))))#||TRUE)
{
# formula <- NULL
# formula <- as.formula(ifelse(length(covobs)>0,(stri_join(stri_flatten(fobserved[1]), " ~ ",obsconst,"+", stri_flatten(covobs, collapse=" + "), latent.formula)),(stri_join(stri_flatten(fobserved[1]), " ~ ",obsconst, latent.formula))))
#
# if(is.null(formula)){
# formula <- as.formula(ifelse(length(covobs)>0,(stri_join(stri_flatten(fobserved[1]), " ~ ",obsconst,"+", stri_flatten(covobs, collapse=" + "))),(stri_join(stri_flatten(fobserved[1]), " ~ ",obsconst))))
#
# }
formula <- NULL
capture.output({withRestarts(tryCatch(capture.output({formula <- as.formula(paste(paste(fobserved[1]), " ~ ",obsconst,ifelse(length(covobs)>0," + ",""), paste(covobs, collapse=" + "), latent.formula)) })), abort = function(){onerr<-TRUE;fm<-NULL})})
if(is.null(formula)){
formula <- as.formula(paste(paste(fobserved[1]), " ~ ",obsconst,ifelse(length(covobs)>0," + ",""), paste(covobs, collapse=" + ")))
}
}else
{
formula <- NULL
}
vect[[cpu]]<-list(formula = formula, varcur = varcur, statid = statid, changed = change.buf, log.mod.switch.prob = log.mod.switch.prob , log.mod.switchback.prob = log.mod.switchback.prob )
}
return(vect)
},
#fit the given model by means of the specified estimator
fitmodel = function(model)
{
if(!is.null(model))
{
fm<-NULL
id<-bittodec(model$varcur)
if(is.null(id))
id = 0
id<-id+1
if(exists("statistics1")){
if(is.na(statistics1[id,1]))
{
#if(printable.opt)print("Invoked from EMJMCMC environment")
onerr<-FALSE
#if(printable.opt)print("INLA internal error")
statistics1[id,c(2,3)]<-100000
statistics1[id,1]<--100000
statistics1[id,4:14]<-0
#prior = "normal",param = c(model$beta.mu.prior,model$beta.tau.prior))
# capture.output({withRestarts(tryCatch(capture.output({fm<-inla(formula = model$formula,family = "binomial",Ntrials = data$total_bases,data = data,control.fixed = list(mean = list(default = model$beta.mu.prior),mean.intercept = model$beta.mu.prior, prec = list(default = model$beta.tau.prior), prec.intercept = model$beta.tau.prior) ,control.compute = list(dic = model$dic.t, waic = model$waic.t, mlik = model$mlik.t))
# })), abort = function(){onerr<-TRUE;fm<-NULL})}) # fit the modal, get local improvements
#
capture.output({withRestarts(tryCatch(capture.output({fm<-do.call(estimator, c(estimator.args, model$formula))
})), abort = function(){onerr<-TRUE;fm<-NULL})}) # fit the model, get local improvements
if(!is.null(fm))
{
statistics1[id,2]<-fm$waic[[1]]
statistics1[id,1]<-fm$mlik[[1]]
statistics1[id,3]<-fm$dic[[1]]
if(save.beta)
{
if(fparam[1]=="Const")
{
inxx<-which(model$varcur==1)
if(length(inxx)==length(fm$summary.fixed$mean))
statistics1[id,15+inxx]<-fm$summary.fixed$mean
}else
{
inxx<-c(0,which(model$varcur==1))
if(length(inxx)==length(fm$summary.fixed$mean))
statistics1[id,16+inxx]<-fm$summary.fixed$mean
}
}
if(fm$waic[[1]]<g.results[2,1] && !is.na(fm$waic[[1]]))
{
g.results[2,1]<-fm$waic[[1]]
g.results[2,2]<-as.integer(id)
}
if(fm$mlik[[1]]>g.results[1,1] && !is.na(fm$mlik[[1]]))
{
g.results[1,1]<-fm$mlik[[1]]
g.results[1,2]<-as.integer(id)
}
if(fm$dic[[1]]<g.results[3,1]&& !is.na(fm$dic[[1]]))
{
g.results[3,1]<-fm$dic[[1]]
g.results[3,2]<-as.integer(id)
}
g.results[4,2] <- g.results[4,2]+1
if(g.results[4,2]%%recalc.margin == 0)
{
p.add <<- as.array(post_proceed_results(statistics1)$p.post)
}
}
}
if(model$statid!=-1)
statistics1[id,model$statid+1]<-statistics1[id,model$statid+1] + 1
g.results[4,1] <- g.results[4,1]+1
return(list(mlik=statistics1[id,1],waic=statistics1[id,2],dic=statistics1[id,3]))
}else if(exists("statistics")){
if(is.na(statistics[id,1]))
{
#if(printable.opt)print("Invoked from EMJMCMC SUB environment")
onerr<-FALSE
#if(printable.opt)print("INLA internal error")
statistics[id,c(2,3)]<-100000
statistics[id,1]<--100000
statistics[id,4:14]<-0
#prior = "normal",param = c(model$beta.mu.prior,model$beta.tau.prior))
# capture.output({withRestarts(tryCatch(capture.output({fm<-inla(formula = model$formula,family = "binomial",Ntrials = data$total_bases,data = data,control.fixed = list(mean = list(default = model$beta.mu.prior),mean.intercept = model$beta.mu.prior, prec = list(default = model$beta.tau.prior), prec.intercept = model$beta.tau.prior) ,control.compute = list(dic = model$dic.t, waic = model$waic.t, mlik = model$mlik.t))
# })), abort = function(){onerr<-TRUE;fm<-NULL})}) # fit the modal, get local improvements
#
capture.output({withRestarts(tryCatch(capture.output({fm<-do.call(estimator, c(estimator.args, model$formula))
})), abort = function(){onerr<-TRUE;fm<-NULL})}) # fit the modal, get local improvements
if(!is.null(fm))
{
statistics[id,2]<-fm$waic[[1]]
statistics[id,1]<-fm$mlik[[1]]
statistics[id,3]<-fm$dic[[1]]
if(save.beta)
{
if(fparam[1]=="Const")
{
inxx<-which(model$varcur==1)
if(length(inxx)==length(fm$summary.fixed$mean))
statistics[id,15+inxx]<-fm$summary.fixed$mean
}else
{
inxx<-c(0,which(model$varcur==1))
if(length(inxx)==length(fm$summary.fixed$mean))
statistics[id,16+inxx]<-fm$summary.fixed$mean
}
}
if(fm$waic[[1]]<g.results[2,1] && !is.na(fm$waic[[1]]))
{
g.results[2,1]<-fm$waic[[1]]
g.results[2,2]<-as.integer(id)
}
if(fm$mlik[[1]]>g.results[1,1] && !is.na(fm$mlik[[1]]))
{
g.results[1,1]<-fm$mlik[[1]]
g.results[1,2]<-as.integer(id)
}
if(fm$dic[[1]]<g.results[3,1]&& !is.na(fm$dic[[1]]))
{
g.results[3,1]<-fm$dic[[1]]
g.results[3,2]<-as.integer(id)
}
g.results[4,2] <- g.results[4,2]+1
if(g.results[4,2]%%recalc.margin == 0)
{
proceeeded <- post_proceed_results(statistics)
p.add <<- as.array(proceeeded$p.post)
#g.results[4,2] <-
}
}
}
if(model$statid!=-1)
statistics[id,model$statid+1]<-statistics[id,model$statid+1] + 1
g.results[4,1] <- g.results[4,1]+1
return(list(mlik=statistics[id,1],waic=statistics[id,2],dic=statistics[id,3]))
}else if(exists("hashStat")){
if(Nvars.max>Nvars)
idd<- as.character(paste(c(model$varcur,array(0,Nvars.max-Nvars)),collapse = ""))
else
idd<- as.character(paste(c(model$varcur),collapse = ""))
if(!has.key(key = idd,hash = hashStat))
{
#if(printable.opt)print("Invoked from EMJMCMC hash table environment")
onerr<-FALSE
#if(printable.opt)print("INLA internal error")
#prior = "normal",param = c(model$beta.mu.prior,model$beta.tau.prior))
# capture.output({withRestarts(tryCatch(capture.output({fm<-inla(formula = model$formula,family = "binomial",Ntrials = data$total_bases,data = data,control.fixed = list(mean = list(default = model$beta.mu.prior),mean.intercept = model$beta.mu.prior, prec = list(default = model$beta.tau.prior), prec.intercept = model$beta.tau.prior) ,control.compute = list(dic = model$dic.t, waic = model$waic.t, mlik = model$mlik.t))
# })), abort = function(){onerr<-TRUE;fm<-NULL})}) # fit the modal, get local improvements
#
capture.output({withRestarts(tryCatch(capture.output({fm<-do.call(estimator, c(estimator.args, model$formula))
})), abort = function(){onerr<-TRUE;fm<-NULL})}) # fit the modal, get local improvements
if(!save.beta)
{
hashBuf<-array(data = NA,dim = 3)
}else
{
if(allow_offsprings==0||Nvars.max<Nvars)
{
if(fparam[1]=="Const")
{
linx<-Nvars
inxx<-which(model$varcur==1)
}else
{
linx<-Nvars + 1
inxx<-c(0,which(model$varcur==1))
}
}else
{
if(fparam[1]=="Const")
{
linx<-Nvars.max
inxx<-which(model$varcur==1)
}else
{
linx<-Nvars.max + 1
inxx<-c(0,which(model$varcur==1))
}
}
hashBuf<-array(data = NA,dim = 3 + linx)
}
hashBuf[c(2,3)]<-100000
hashBuf[1]<- -100000
if(!is.null(fm))
{
hashBuf[2]<-fm$waic[[1]]
hashBuf[1]<-fm$mlik[[1]]
hashBuf[3]<-fm$dic[[1]]
if(save.beta)
{
if(fparam[1]=="Const")
{
if(length(inxx)==length(fm$summary.fixed$mean))
hashBuf[3+inxx]<-fm$summary.fixed$mean
}else
{
if(length(inxx)==length(fm$summary.fixed$mean))
hashBuf[4+inxx]<-fm$summary.fixed$mean
}
}
hashStat[idd] <- hashBuf
# if(id>1)
# {
# inxx<-which(model$varcur==1)
# if(length(inxx)==length(fm$summary.fixed$mean))
# statistics[id,14+inxx]<-fm$summary.fixed$mean
# }
if(fm$waic[[1]]<g.results[2,1] && !is.na(fm$waic[[1]]))
{
g.results[2,1]<-fm$waic[[1]]
g.results[2,2]<-(id)
}
if(fm$mlik[[1]]>g.results[1,1] && !is.na(fm$mlik[[1]]))
{
g.results[1,1]<-fm$mlik[[1]]
g.results[1,2]<-(id)
}
if(fm$dic[[1]]<g.results[3,1]&& !is.na(fm$dic[[1]]))
{
g.results[3,1]<-fm$dic[[1]]
g.results[3,2]<-(id)
}
g.results[4,2] <- g.results[4,2]+1
}
}
g.results[4,1] <- g.results[4,1]+1
if(has.key(hash = hashStat,key=idd))
hasRes<- values(hashStat[idd])
else
hasRes<-c(-10000,10000,10000)
if(g.results[4,2]%%recalc.margin == 0)
{
proceeeded <- post_proceed_results_hash(hashStat)
p.add <<- as.array(proceeeded$p.post)
#g.results[4,2] <-
}
return(list(mlik=hasRes[1],waic=hasRes[2],dic=hasRes[3]))
}else
{
capture.output({withRestarts(tryCatch(capture.output({fm<-do.call(estimator, c(estimator.args, model$formula))
})), abort = function(){onerr<-TRUE;fm<-NULL})}) # fit the modal, get local improvements
if(!is.null(fm)){
if(fm$waic[[1]]<g.results[2,1] && !is.na(fm$waic[[1]]))
{
g.results[2,1]<-fm$waic[[1]]
g.results[2,2]<-(id)
}
if(fm$mlik[[1]]>g.results[1,1] && !is.na(fm$mlik[[1]]))
{
g.results[1,1]<-fm$mlik[[1]]
g.results[1,2]<-(id)
}
if(fm$dic[[1]]<g.results[3,1]&& !is.na(fm$dic[[1]]))
{
g.results[3,1]<-fm$dic[[1]]
g.results[3,2]<-(id)
}
g.results[4,1] <- g.results[4,1]+1
g.results[4,2] <- g.results[4,2]+1
return(list(mlik=fm$mlik[[1]],waic=fm$waic[[1]],dic=fm$dic[[1]]))
}
else
{
g.results[4,1] <- g.results[4,1]+1
return(list(mlik=-Inf,waic=Inf,dic=Inf))
}
}
}
g.results[4,1] <- g.results[4,1]+1
g.results[4,2] <- g.results[4,2]+1
return(list(mlik=-Inf,waic=Inf,dic=Inf))
},
#lambda function for mtmcmc
lambda = function(c,alpha,g1,g2,g.domain.pos) # simmetric choice driving function
{
if((c!=0))
{
res<-((((1/c)*(1+(g1+g2)*(g.domain.pos))/(1-(g1+g2)*(1-g.domain.pos)))^alpha))
#!#if(printable.opt)print(res)
return(res)
}else
{
#!#if(printable.opt)print(1)
return(1)
}
},
#norm between probabilities vectors
normprob=function(p1,p2)
{
nn<-abs(1-sum((p1+0.1)/(p2+0.1))/length(p1))
if(is.na(nn))
nn<-Inf
return(nn)
},
#local mcmc procedure
learnlocalMCMC=function(model)
{
M<-M.mcmc
mlikcur<- model$mlikcur
waiccur<-model$waiccur
varcand<-model$varcur
varcur<-model$varcur
varcurb<-model$varcur
varglob<-model$varcur
modglob<-NULL
fm<-NULL
fmb<-NULL
# estimate large jump in a reverse move
if(model$reverse || is.infinite(mlikcur))
{
vectbg<-buildmodel(max.cpu = 1,varcur.old = varcur,statid = model$statid,switch.type=8, min.N = min.N,max.N = max.N)
if(!is.null(vectbg[[1]]$formula))
{
bgmod <- lapply(X = vectbg,FUN = .self$fitmodel)
waiccur<-bgmod[[1]]$waic
mlikcur<-bgmod[[1]]$mlik
}
else if(exists("statistics1"))
{
iidd<-bittodec(varcur)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcur,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
}
if(printable.opt)print(paste("Begin with ", mlikcur))
mlikglob<- mlikcur
mlikcand<- mlikcur
waiccand<- waiccur
waicglob<- waiccur
waiccur<- waiccur
for(m in 1:M)
{
withRestarts(tryCatch({
# statistics <- describe(statistics)
vect<-buildmodel(varcur.old = varcur,statid = model$statid,max.cpu = max.cpu,switch.type=switch.type, min.N = min.N, max.N = max.N)
cluster<-TRUE
flag1<-0
for(mod_id in 1:max.cpu)
{
if(is.null(vect[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
#flag1<-sum(is.null(vect[[]]$formula))
if(flag1==max.cpu)
{
cluster<-FALSE
if(printable.opt)print("!!!!MTMCMC models already estimated!!!!")
}else
{
res.par <- parallelize(X = vect,FUN = .self$fitmodel)
}
p.select.y <- array(data = 0, dim = max.cpu)
for(mod_id in 1:max.cpu)
{
if(cluster)
{
fm<-res.par[[mod_id]]
if(is.null(fm)&&(is.na(res.par[[mod_id]]$waic)))
{
varcand<-varcurb
if(printable.opt)print("locMTMCMC Model Fit Error!?")
next
}
}
varcand<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand<-res.par[[mod_id]]$waic
mlikcand<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
if((mlikcand>mlikglob)) #update the parameter of interest
{
if(printable.opt)print(paste("locMTMCMC update waic.glob = ", waiccand))
if(printable.opt)print(paste("locMTMCMC update waic.glob.mlik = ", mlikglob))
mlikglob<-mlikcand
waicglob<-waiccand
varglob<-varcand
if(cluster)
modglob<-fm
}
g1 <- waiccur
if(waiccur == Inf)
{
g1 = 1
}
p.select.y[mod_id]<-(mlikcand + vect[[mod_id]]$log.mod.switchback.prob+log(lambda(c = cc, alpha = aa, g1 = -g1, g2 = -waiccand,g.domain.pos = FALSE))) # correct for different criteria later
if(is.na(p.select.y[mod_id]))
p.select.y[mod_id] <- 0
if(is.infinite(p.select.y[mod_id]) || p.select.y[mod_id]>100000000)
{
#if(printable.opt)print(paste("very large log.w.y detected ",p.select.y[mod_id]))
p.select.y[mod_id] <- 100000000
}
}
max.p.select.y <- max(p.select.y)
p.select.y<-p.select.y-max.p.select.y
if(printable.opt)print(paste("max log.w.y is ",max.p.select.y,"normilized log.w.n.y is ", paste(p.select.y,collapse = ", ")))
ID<-sample.int(n = max.cpu,size = 1,prob = exp(p.select.y))
if(printable.opt)print(paste("cand ",ID," selected"))
varcand<-vect[[ID]]$varcur
if(cluster)
{
waiccand<-res.par[[ID]]$waic
mlikcand<-res.par[[ID]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
#p.Q.cand<- p.select.y[ID]/sum(p.select.y)
if(printable.opt)print("do reverse step")
p.select.z <- array(data = 0.01, dim = max.cpu)
if(max.cpu!=1)
{
vect1<-buildmodel(max.cpu = max.cpu -1,varcur.old = varcand,statid = model$statid,switch.type = switch.type, min.N = min.N, max.N = max.N)
cluster<-TRUE
flag1<-0
for(mod_id in 1:(max.cpu-1))
{
if(is.null(vect1[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==(max.cpu-1))
{
cluster<-FALSE
if(printable.opt)print("!!!!MTMCMC reverse models already estimated!!!!")
}else
{
res.par.back <- parallelize(X = vect1,FUN = .self$fitmodel)
}
for(mod_id in 1:(max.cpu-1))
{
if(cluster)
{
if(is.null(fm)&&(is.na(res.par.back[[mod_id]]$waic)))
{
if(printable.opt)print("locMTMCMC Model Fit Error!?")
next
}
}
varcand.b<-vect1[[mod_id]]$varcur
if(cluster)
{
waiccand.b<-res.par.back[[mod_id]]$waic
mlikcand.b<-res.par.back[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand.b)+1
waiccand.b<-statistics1[iidd,2]
mlikcand.b<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand.b,collapse = "")
waiccand.b<-values(hashStat[iidd])[2]
mlikcand.b<-values(hashStat[iidd])[1]
}
if((mlikcand.b>mlikglob))
{
if(printable.opt)print(paste("locMTMCMC update waic.glob = ", waiccand.b))
if(printable.opt)print(paste("locMTMCMC update waic.glob.mlik = ", mlikcand.b))
mlikglob<-mlikcand.b
waicglob<-waiccand.b
varglob<-varcand.b
if(cluster)
modglob<-fm
}
g1 = waiccand
if(waiccand == Inf)
{
g1 = 1
}
p.select.z[mod_id]<-(mlikcand.b+vect1[[mod_id]]$log.mod.switchback.prob+(lambda(c = cc, alpha = aa, g1 = -g1, g2 = -waiccand.b,g.domain.pos = FALSE))) # correct for different criteria later
if(is.na(p.select.z[mod_id]))
p.select.z[mod_id]=0
if(is.infinite(p.select.z[mod_id]) || p.select.z[mod_id] > 100000000)
{
#if(printable.opt)print(paste("very large log.w.y detected ",p.select.z[mod_id]))
p.select.z[mod_id] <- 100000000
}
}
}
if( waiccur == Inf)
{
g1 = 1
}
p.select.z[max.cpu] <- (mlikcur+vect[[ID]]$log.mod.switch.prob+(lambda(c = cc, alpha = aa, g1 = -g1, g2 = -waiccand,g.domain.pos = FALSE)))
if(is.na(p.select.z[mod_id]))
p.select.z[mod_id]=0
if(is.infinite(p.select.z[mod_id]) || p.select.z[mod_id] > 100000000)
{
#if(printable.opt)print(paste("very large log.w.y detected ",p.select.z[mod_id]))
p.select.z[mod_id] <- 100000000
}
max.p.select.z <- max(p.select.z)
p.select.z<-p.select.z-max.p.select.z
if(printable.opt)print(paste("max log.w.z is ",max.p.select.z,"normilized log.w.n.z is ", paste(p.select.z,collapse = ", ")))
if(log(runif(n = 1,min = 0,max = 1)) < (log(sum(exp(p.select.y)))-log(sum(exp(p.select.z)))) + max.p.select.y - max.p.select.z )
{
mlikcur<-mlikcand
if(printable.opt)print(paste("locMTMCMC update ratcur = ", mlikcand))
if(printable.opt)print(paste("locMTMCMC accept move with ", waiccand))
varcur<-varcand
waiccur<-waiccand
}
}),abort = function(){fm<-fmb;closeAllConnections();options(error=traceback); onerr<-TRUE})
}
#if(printable.opt)print("FINISH LOCAL MTMCMC")
#!#if(printable.opt)print(points)
if(model$reverse == FALSE)
{
if(is.null(varcur))
{
#if(printable.opt)print("No moves acceoted in the procedure")
varcur<-varcand
waiccur<-waiccand
varcur<-varcand
}
vect<-buildmodel(max.cpu = 1,varcur.old = varcur,statid = model$statid,switch.type = type.randomize,min.N = min.N.randomize,max.N = max.N.randomize)
varcur<-vect[[1]]$varcur
#if(printable.opt)print(varcur)
cluster<-TRUE
if(is.null(vect[[1]]$formula))
{
cluster<-FALSE
if(printable.opt)print("!!!!MTMCMC reverse models already estimated!!!!")
}else
{
mod<-fitmodel(vect[[1]])
}
if(cluster)
{
waiccur<-mod$waic
mlikcur<-mod$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcur)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcur,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
# incorporate what happens for the backward optimization
model.prob<-vect[[1]]$log.mod.switch.prob
model.prob.fix<-vect[[1]]$log.mod.switchback.prob
}else # incorporate what happens for the reverse move
{
if(is.null(varcur))
{
#if(printable.opt)print("No moves acceoted in the reverse procedure")
varcur<-varcand
waiccur<-waiccand
}
model.probs<-calculate.move.logprobabilities(varold = varcur, varnew = model$varold,switch.type = type.randomize,min.N = min.N.randomize,max.N = max.N.randomize)
model.prob<-model.probs$log.switch.forw.prob
model.prob.fix<-model.probs$log.switch.back.prob
}
if(is.null(varcur))
{
#if(printable.opt)print("NO VARCUR OBTAINED")
varcur<-i
waiccur<-Inf
varcur<-model$varold
}
return(list(varcur = varcur, waiccur = waiccur, mlikcur = mlikcur, log.prob.cur = model.prob,log.prob.fix = model.prob.fix, varglob = varglob, waicglob = waicglob, mlikglob = mlikglob, modglob = modglob))
},
#local simulated annealing optimization
learnlocalSA=function(model)
{
t.min<-SA.param$t.min
t<-SA.param$t.init
dt<-SA.param$dt
M<-SA.param$M
varcand<-model$varcur
varcurb<-model$varcur
varcur<-model$varcur
varglob<-model$varcur
varglob<-NULL
modglob<-NULL
probcur<-1
probrevcur<-1
first.prob <- 1
fm<-NULL
fmb<-NULL
mlikcur<- model$mlikcur
waiccur<-model$waiccur
# estimate large jump in a reverse move
# estimate large jump in a reverse move
if((model$reverse && !model$sa2) || is.infinite(mlikcur))
{
vectbg<-buildmodel(max.cpu = 1,varcur.old = varcur,statid = model$statid,switch.type=8, min.N = min.N,max.N = max.N)
if(!is.null(vectbg[[1]]$formula))
{
bgmod <- lapply(X = vectbg,FUN = .self$fitmodel)
waiccur<-bgmod[[1]]$waic
mlikcur<-bgmod[[1]]$mlik
}
else if(exists("statistics1"))
{
iidd<-bittodec(varcur)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcur,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
}
if(printable.opt)print(paste("Begin with ", mlikcur))
mlikglob<- mlikcur
mlikcand<- mlikcur
waiccand<- waiccur
waicglob<- waiccur
waiccur<- waiccur
while(t>t.min)
{
if(printable.opt)print(paste("anneal to ",t))
t.new<-t*exp(-dt)
if(model$reverse == TRUE && t.new <= t.min)
{
M<-M -1
}
for(m in 1:M)
{
withRestarts(tryCatch({
mmax.cpu = max.cpu
if(model$switch.type == 5)
{
mmax.cpu = Nvars - sum(varcur)
}else if(model$switch.type == 6)
{
mmax.cpu = sum(varcur)
}
if(mmax.cpu == 0)
mmax.cpu = 1
vect<-buildmodel(max.cpu = mmax.cpu,varcur.old = varcur,statid = model$statid,switch.type=model$switch.type, min.N = min.N,max.N = max.N)
cluster<-TRUE
flag1<-0
for(mod_id in 1:mmax.cpu)
{
if(is.null(vect[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==mmax.cpu)
{
cluster<-FALSE
if(printable.opt)print("!!!!SA Models already estimated!!!!")
}else
{
res.par <- parallelize(X = vect,FUN = .self$fitmodel)
}
for(mod_id in 1:mmax.cpu)
{
if(cluster)
{
fmb<-fm
fm<-res.par[[mod_id]]
waiccand<-Inf
if(is.null(fm)&&(is.na(res.par[[mod_id]]$waic)))
{
varcand<-varcurb
if(printable.opt)print("SA Model Fit Error!?")
next
}
}
varcand<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand<-res.par[[mod_id]]$waic
mlikcand<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-stri_paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
if(objective==0)
{
objcand<-waiccand
objcur<-waiccur
objglob<-waicglob
}else
{
objcand<- -mlikcand
objcur<- -mlikcur
objglob<- -mlikglob
}
if(t == SA.param$t.init && mod_id == 1 && m == 2)
{
delta<-objcand - objcur
first.prob <- vect[[mod_id]]$log.mod.switchback.prob + log(punif(q = exp(x = delta/t),min = 0,max = 1))
}
if(objcand<objcur)
{
if(printable.opt)print(paste("SA accept move with ", objcand))
waiccur<-waiccand
varcur<-varcand
mlikcur<-mlikcand
if(objcand<objglob)
{
waicglob<-waiccand
varglob<-varcand
mlikglob<-mlikcand
if(cluster)
modglob<-fm
if(printable.opt)print(paste("SA update global optima with", objcand))
}
}else
{
delta<-objcand - objcur
if(runif(n = 1,min = 0,max = 1) <= exp(x = -delta/t))
{
model.probs<-calculate.move.logprobabilities(varold = varcur, varnew = varcand,switch.type = model$switch.type,min.N = min.N,max.N = max.N)
probcur<-model.probs$log.switch.forw.prob
probrevcur<-model.probs$log.switch.back.prob
waiccur<-waiccand
varcur<-varcand
mlikcur<-mlikcand
if(printable.opt)print(paste("SA accept move with ", objcand))
}
}
}
}),abort = function(){varcur<-varcurb; fm<-fmb;closeAllConnections();options(error=traceback); onerr<-TRUE})
}
t<-t.new
}
t<-t/exp(-dt)
if(model$reverse == FALSE)
{
model.prob<-log(punif(q = exp(x = -delta/t),min = 0,max = 1)) + probcur # log(P(Mk,Mk-1))
model.prob.fix<-log(punif(q = exp(x = delta/t),min = 0,max = 1)) + probrevcur # log(P(Mk-1,Mk))
if(model$sa2 == TRUE)
{
model.prob.fix<-model.prob.fix + first.prob # correcting for the term for local improvements of type 3.
}
}else # incorporate what happens for the reverse move
{
if(is.null(varcur))
{
if(printable.opt)print("No moves accepted in the reverse procedure")
varcur<-model$varcur
objcur<-model$objcur
}
delta<-objcur-model$objold
model.probs<-calculate.move.logprobabilities(varold = varcur, varnew = model$varold, switch.type = model$switch.type,min.N = min.N,max.N = max.N)
model.prob<-punif(q = exp(x = -delta/t),min = 0,max = 1,log.p = TRUE) + model.probs$log.switch.forw.prob
model.prob.fix<-punif(q = exp(x = delta/t),min = 0,max = 1,log.p = TRUE) + model.probs$log.switch.back.prob
if(model.prob==-Inf)
{
model.prob<- -100000000
}
if(model.prob.fix==-Inf)
{
model.prob.fix<- -100000000
}
}
return(list(varcur = varcur, waiccur = waiccur, mlikcur = mlikcur, log.prob.cur = model.prob,log.prob.fix = model.prob.fix, varglob = varglob, waicglob = waicglob, mlikglob = mlikglob, modglob = modglob))
},
#forward selection procedure
forward_selection=function(model)
{
if(printable.opt)print("begin forward selection procedure")
varcand<-model$varcur
varcurb<-model$varcur
varglob<-varcand
mlikglob<- model$mlikcur
mlikcur<- model$mlikcur
waiccand<- model$waiccur
waicglob<-model$waiccur
waiccur<-model$waiccur
waiccurb<-model$waiccur
varglob<-NULL
modglob<-NULL
fm<-NULL
fmb<-NULL
ub<-bittodec(array(1,length(varcurb)))
layer<-length(which(varcurb == 0))
mlikcur<- model$mlikcur
waiccur<-model$waiccur
# estimate large jump in a reverse move
# estimate large jump in a reverse move
if(is.infinite(mlikcur))
{
vectbg<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = model$statid,switch.type=8, min.N = min.N,max.N = max.N)
if(!is.null(vectbg[[1]]$formula))
{
bgmod <- lapply(X = vectbg,FUN = .self$fitmodel)
waiccur<-bgmod[[1]]$waic
mlikcur<-bgmod[[1]]$mlik
}
else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}
else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
if(!is.na(mlikcur) && !is.na(waiccur) )
{
mlikglob<- mlikcur
mlikcur<- mlikcur
waiccand<- waiccur
waicglob<- waiccur
waiccur<- waiccur
waiccurb<- waiccur
}
}
while(layer>0)
{
withRestarts(tryCatch({
if(printable.opt)print(paste("proceed with layer",layer))
if(printable.opt)print(paste("current solution is",as.character(varcand)))
vect<-buildmodel(max.cpu = layer,varcur.old = varcurb,statid = model$statid, switch.type = 5,min.N = min.N, max.N = max.N)
if(printable.opt)print(paste("finish preparing models at layer",layer))
cluster<-TRUE
flag1<-0
for(mod_id in 1:layer)
{
if(is.null(vect[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==layer)
{
cluster<-FALSE
if(printable.opt)print("!!!!forward Models already estimated!!!!")
}else
{
res.par <- parallelize(X = vect,FUN = .self$fitmodel)
}
if(printable.opt)print(paste("end forward optimizing at layer",layer))
for(mod_id in 1:layer)
{
if(cluster){
fmb<-fm
fm<-res.par[[mod_id]]
waiccand<-Inf
if(is.null(fm)&&(is.na(res.par[[mod_id]]$waic)))
{
varcand<-varcurb
if(printable.opt)print("forward Model Fit Error!?")
next
}
}
varcand<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand<-res.par[[mod_id]]$waic
mlikcand<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
if(objective==0)
{
objcand<-waiccand
objcur<-waiccur
objglob<-waicglob
}else
{
objcand<- -mlikcand
objcur<- -mlikcur
objglob<- -mlikglob
}
if(objcand<=objcur || mod_id ==1)
{
if(printable.opt)print(paste("forward accept with ", objcand))
objcur<-objcand
varcurb<-varcand
waiccur<-waiccand
varcur<-varcand
mlikcur<-mlikcand
if(objcur<objglob)
{
objglob<-objcur
waicglob<-waiccand
varglob<-varcand
mlikglob<-mlikcand
if(!is.null(fm))
modglob<-fm
if(printable.opt)print(paste("forward global optima with ", objcand))
}
}
# else
# {
# if(waiccand<=waiccur)
# {
# waiccur<-waiccand
# varcur<-varcand
# }
#
# }
}
if(objcur!=objglob)
{
if(model$locstop)
{
break
}else
{
varcurb<-varcur
}
}
}),abort = function(){varcur<-varcurb; fm<-fmb;closeAllConnections();options(error=traceback); onerr<-TRUE})
layer<-layer-1
}
model.prob<-1
model.prob.fix<-1
return(list(varcur = varglob, waiccur = waicglob, mlikcur = mlikglob, log.prob.cur = model.prob,log.prob.fix = model.prob.fix, varglob = varglob, waicglob = waicglob, mlikglob = mlikglob, modglob = modglob))
},
#backward selection procedure
backward_selection=function(model)
{
#if(printable.opt)print("begin backward selection procedure")
varcand<-model$varcur
varcurb<-model$varcur
varglob<-varcand
mlikglob<- model$mlikcur
mlikcur<- model$mlikcur
waiccur<- model$waiccur
waicglob<-model$waiccur
varglob<-NULL
modglob<-NULL
waiccurb<- model$waiccur
fm<-NULL
fmb<-NULL
ub<-bittodec(array(1,length(varcurb)))
layer<-length(which(varcurb == 1))
if(is.infinite(mlikcur))
{
vectbg<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = model$statid,switch.type=8, min.N = min.N,max.N = max.N)
if(!is.null(vectbg[[1]]$formula))
{
bgmod <- lapply(X = vectbg,FUN = .self$fitmodel)
waiccur<-bgmod[[1]]$waic
mlikcur<-bgmod[[1]]$mlik
}
else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
if(!is.na(mlikcur) && !is.na(waiccur) )
{
mlikglob<- mlikcur
mlikcur<- mlikcur
waiccand<- waiccur
waicglob<- waiccur
waiccur<- waiccur
waiccurb<- waiccur
}
}
while(layer>0)
{
withRestarts(tryCatch({
if(printable.opt)print(paste("backward proceed with layer",layer))
if(printable.opt)print(paste("current backward solution is",as.character(varcand)))
vect<-buildmodel(max.cpu = layer,varcur.old = varcurb,statid = model$statid, switch.type = 6,min.N = min.N, max.N = max.N)
if(printable.opt)print(paste("finish backward preparing models at layer",layer))
cluster<-TRUE
flag1<-0
for(mod_id in 1:layer)
{
if(is.null(vect[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==layer)
{
cluster<-FALSE
if(printable.opt)print("!!!!backward Models already estimated!!!!")
}else
{
res.par <- parallelize(X = vect,FUN = .self$fitmodel)
}
if(printable.opt)print(paste("end backward optimizing at layer",layer))
for(mod_id in 1:layer)
{
if(cluster){
fmb<-fm
fm<-res.par[[mod_id]]
waiccand<-Inf
if(is.null(fm)&&(is.na(res.par[[mod_id]]$waic)))
{
varcand<-varcurb
if(printable.opt)print("backward Model Fit Error!?")
next
}
}
varcand<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand<-res.par[[mod_id]]$waic
mlikcand<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
if(objective==0)
{
objcand<-waiccand
objcur<-waiccur
objglob<-waicglob
}else
{
objcand<- -mlikcand
objcur<- -mlikcur
objglob<- -mlikglob
}
if(objcand<=objcur|| mod_id ==1)
{
if(printable.opt)print(paste("backward accept with ", objcand))
objcur<-objcand
varcurb<-varcand
waiccur<-waiccand
varcur<-varcand
mlikcur<-mlikcand
if(objcur<objglob)
{
objglob<-objcur
waicglob<-waiccand
varglob<-varcand
mlikglob<-mlikcand
if(!is.null(fm))
modglob<-fm
if(printable.opt)print(paste("backward global optima with ", objcand))
}
}
}
if(objcur!=objglob)
{
if(model$locstop)
{
break
}else
{
varcurb<-varcur
}
}
}),abort = function(){varcur<-varcurb; fm<-fmb;closeAllConnections();options(error=traceback); onerr<-TRUE})
layer<-layer-1
}
model.prob<-1
model.prob.fix<-1
return(list(varcur = varglob, waiccur = waicglob, mlikcur = mlikglob, log.prob.cur = model.prob,log.prob.fix = model.prob.fix, varglob = varglob, waicglob = waicglob, mlikglob = mlikglob, modglob = modglob))
},
#full selection procedure
full_selection=function(model)
{
if(printable.opt)print(paste("begin full selection procedure!","Careful, ",2^Nvars," models have to be estimated"))
if(Nvars>30)
if(printable.opt)print("Finishing the procedure might well take forever!")
varcand<-array(0,Nvars)
varcurb<-varcand
varglob<-varcand
varglob<-NULL
modglob<-NULL
mlikglob<- model$mlikcur
mlikcur<- model$mlikcur
waiccand<- model$waiccur
waicglob<-model$waiccur
waiccur<-model$waiccur
waiccurb<-model$waiccur
fm<-NULL
fmb<-NULL
ubs<-as.integer(bittodec(array(1,Nvars)) + 1)
ub<-model$ub
totit<-as.integer(ubs/ub) + 1
if(model$totalit<totit)
{
totit<-model$totalit
}
if(is.infinite(mlikcur))
{
vectbg<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = model$statid,switch.type=8, min.N = min.N,max.N = max.N)
if(!is.null(vectbg[[1]]$formula))
{
bgmod <- lapply(X = vectbg,FUN = .self$fitmodel)
waiccur<-bgmod[[1]]$waic
mlikcur<-bgmod[[1]]$mlik
}
else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
if(!is.na(waiccur)&&!is.na(mlikcur))
{
mlikglob<- mlikcur
mlikcand<- mlikcur
waiccand<- waiccur
waicglob<- waiccur
waiccur<- waiccur
waiccurb<- waiccur
}
}
for(i in 1:totit)
{
if(ub*i>ubs)
{
ub<-ubs - ub*(i-1)-1
if(printable.opt)print(paste("last ",ub," iterations to complete"))
varcurb<-varcand
}
withRestarts(tryCatch({
vect<-buildmodel(max.cpu = ub,varcur.old = varcurb,statid = model$statid,switch.type = 7, shift.cpu = model$ub*(i-1),min.N = min.N,max.N = max.N)
if(printable.opt)print(paste("proceed with full ecumeration"))
if(printable.opt)print(paste("current solution is",as.character(varcand)))
cluster<-TRUE
flag1<-0
for(mod_id in 1:ub)
{
if(is.null(vect[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==ub)
{
cluster<-FALSE
if(printable.opt)print("!!!!full models already estimated!!!!")
}else
{
res.par <- parallelize(X = vect,FUN = .self$fitmodel)
}
if(printable.opt)print(paste("end optimizing full ecumeration"))
for(mod_id in 1:ub)
{
if(cluster){
fmb<-fm
fm<-res.par[[mod_id]]
waiccand<-Inf
if(is.null(fm)&&(is.na(res.par[[mod_id]]$waic)))
{
varcand<-varcurb
if(printable.opt)print("full Model Fit Error!?")
next
}
}
varcand<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand<-res.par[[mod_id]]$waic
mlikcand<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
if(objective==0)
{
objcand<-waiccand
objcur<-waiccur
objglob<-waicglob
}else
{
objcand<- -mlikcand
objcur<- -mlikcur
objglob<- -mlikglob
}
if(objcand<=objcur)
{
if(printable.opt)print(paste("full accept with ", objcand))
objcur<-objcand
varcurb<-varcand
waiccur<-waiccand
varcur<-varcand
mlikcur<-mlikcand
if(objcur<objglob)
{
objglob<-objcur
waicglob<-waiccand
varglob<-varcand
mlikglob<-mlikcand
if(!is.null(fm))
modglob<-fm
if(printable.opt)print(paste("full global optima with ", objcand))
}
}
varcurb<-varcand
}
#waiccurb<-waiccur
}),abort = function(){varcur<-varcurb; fm<-fmb;closeAllConnections();options(error=traceback); onerr<-TRUE})
}
# if(length(which(varcur == 1))==(Nvars-1))
# {
# vectbg<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = model$statid,switch.type=8, min.N = min.N,max.N = max.N)
# if(!is.null(vectbg[[1]]$formula))
# {
# bgmod <- lapply(X = vectbg,FUN = .self$fitmodel)
# waiccand<-bgmod[[1]]$waic
# mlikcand<-bgmod[[1]]$mlik
# }
# else
# {
# iidd<-bittodec(varcur)+1
# waiccand<-statistics1[iidd,2]
# mlikcand<-statistics1[iidd,1]
# }
# if(objective==0)
# {
# objcand<-waiccand
# objcur<-waiccur
# objglob<-waicglob
# }else
# {
# objcand<- -mlikcand
# objcur<- -mlikcur
# objglob<- -mlikglob
# }
#
#
# if(objcand<=objcur)
# {
# if(printable.opt)print(paste("full accept with ", objcand))
# objcur<-objcand
# varcurb<-varcand
# waiccur<-waiccand
# varcur<-varcand
# mlikcur<-mlikcand
#
# if(objcur<objglob)
# {
# objglob<-objcur
# waicglob<-waiccand
# varglob<-varcand
# mlikglob<-mlikcand
# if(!is.null(fm))
# modglob<-fm
#
# if(printable.opt)print(paste("full global optima with ", objcand))
# }
# }
# }
#
model.prob<-1
model.prob.fix<-1
return(list(varcur = varglob, waiccur = waicglob, mlikcur = mlikglob, log.prob.cur = model.prob,log.prob.fix = model.prob.fix, varglob = varglob, waicglob = waicglob, mlikglob = mlikglob, modglob = modglob))
},
#forward backward random dance
forw_backw_walk = function(model)
{
varcur<-rbinom(n = Nvars,size = 1,prob = runif(n = 1,min = 0,max = model$p1))
mlikcur<- -Inf
waiccur<- Inf
for(i in 1:model$steps)
{
fff<-forward_selection(list(varcur=rbinom(n = Nvars,size = 1,prob = runif(n = 1,min = 0,max = model$p1)),mlikcur=-Inf,waiccur =Inf,locstop = FALSE,statid=-1))
if(objective ==1)
{
if(fff$mlikglob>mlikcur)
{
mlikcur<-fff$mlikglob
varcur<-fff$varglob
waiccur<-fff$waicglob
}
}
else
{
if(fff$waicglob<waiccur)
{
mlikcur<-fff$mlikglob
varcur<-fff$varglob
waiccur<-fff$waicglob
}
}
set.seed(i*model$steps)
bbb<-backward_selection(list(varcur=rbinom(n = Nvars,size = 1,prob = runif(n = 1,min = model$p1,max = 1)),mlikcur=-Inf,waiccur =Inf,locstop = FALSE,statid=-1))
if(objective ==1)
{
if(bbb$mlikglob>mlikcur)
{
mlikcur<-bbb$mlikglob
varcur<-bbb$varglob
waiccur<-bbb$waicglob
}
}
else
{
if(bbb$waicglob<waiccur)
{
mlikcur<-bbb$mlikglob
varcur<-bbb$varglob
waiccur<-bbb$waicglob
}
}
}
if(model$reverse == FALSE)
{
vect<-buildmodel(max.cpu = 1,varcur.old = varcur,statid = -1,switch.type = type.randomize,min.N = min.N.randomize,max.N = max.N.randomize)
varcur<-vect[[1]]$varcur
#if(printable.opt)print(varcur)
cluster<-TRUE
if(is.null(vect[[1]]$formula))
{
cluster<-FALSE
if(printable.opt)print("!!!!Back Forw reverse model already estimated!!!!")
}else
{
mod <- lapply(X = vect, FUN = fitmodel)
}
if(cluster)
{
waiccur<-mod[[1]]$waic
mlikcur<-mod[[1]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcur)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcur,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
# incorporate what happens for the backward optimization
model.prob<-vect[[1]]$log.mod.switch.prob
model.prob.fix<-vect[[1]]$log.mod.switchback.prob
}else # incorporate what happens for the reverse move
{
model.probs<-calculate.move.logprobabilities(switch.type = type.randomize,varold = varcur, varnew = model$varold,min.N = min.N.randomize,max.N = max.N.randomize)
model.prob<-model.probs$log.switch.forw.prob
model.prob.fix<-model.probs$log.switch.back.prob
}
return(list(varcur = varcur, waiccur = waiccur, mlikcur = mlikcur, log.prob.cur = model.prob,log.prob.fix = model.prob.fix, varglob = varcur, waicglob = waiccur, mlikglob = mlikcur))
},
#local greedy optimization
learnlocalND=function(model)
{
# Step.nd
varcand<-model$varcur
varglob<-model$varcur
varcurb<-model$varcur
mlikcand<- model$mlikcur
waiccand<-model$waiccur
modglob<-NULL
fm<-NULL
fmb<-NULL
opt.achieved<-FALSE
# estimate large jump in a reverse move
if(model$reverse || is.infinite(mlikcand))
{
vectbg<-buildmodel(max.cpu = 1,varcur.old = varcand,statid = model$statid,switch.type=8, min.N = min.N,max.N = max.N)
if(!is.null(vectbg[[1]]$formula))
{
bgmod <- lapply(X = vectbg,FUN = .self$fitmodel)
waiccand<-bgmod[[1]]$waic
mlikcand<-bgmod[[1]]$mlik
}
else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
}
if(printable.opt)print(paste("Begin with ",mlikcand))
mlikglob<- mlikcand
mlikcand<- mlikcand
waiccand<- waiccand
waicglob<- waiccand
waiccur<- waiccand
buf.M.nd <- M.nd
if(model$switch.type == 5)
{
buf.M.nd = Nvars - sum(varcurb)
}else if(model$switch.type == 6)
{
buf.M.nd = sum(varcurb)
}
if(buf.M.nd == 0)
buf.M.nd = 1
if(M.nd<buf.M.nd)
buf.M.nd<-M.nd
for(iterat in 1:buf.M.nd)
{
withRestarts(tryCatch({
# statistics <- describe(statistics)
mmax.cpu = max.cpu
if(model$switch.type == 5)
{
mmax.cpu = Nvars - sum(varcurb)
}else if(model$switch.type == 6)
{
mmax.cpu = sum(varcurb)
}
if(mmax.cpu == 0)
mmax.cpu = 1
vect<-buildmodel(max.cpu = mmax.cpu,varcur.old = varcurb,statid = model$statid, switch.type = model$switch.type,min.N = min.N,max.N = max.N)
cluster<-TRUE
flag1<-0
for(mod_id in 1:mmax.cpu)
{
if(is.null(vect[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==mmax.cpu)
{
cluster<-FALSE
if(printable.opt)print("!!!!Greedy Models already estimated!!!!")
}else
{
res.par <- parallelize(X = vect,FUN = .self$fitmodel)
}
for(mod_id in 1:mmax.cpu)
{
varcand1<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand1<-res.par[[mod_id]]$waic
mlikcand1<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand1)+1
waiccand1<-statistics1[iidd,2]
mlikcand1<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand1,collapse = "")
waiccand1<-values(hashStat[iidd])[2]
mlikcand1<-values(hashStat[iidd])[1]
}
if(objective==0)
{
objcand<-waiccand1
objcur<-waiccand
objglob<-waicglob
}
else
{
objcand<- -mlikcand1
objcur<- -mlikcand
objglob<- -mlikglob
}
if(objcand<objcur || mod_id ==1)
{
varcand<-varcand1
waiccand<-waiccand1
mlikcand<-mlikcand1
if(printable.opt)print(paste("GREEDY update local optima with ", objcand))
if(cluster)
fm<-res.par[[mod_id]]
}
}
#if(printable.opt)print(waiccand)
if(objective==0)
{
objcand<-waiccand1
objcur<-waiccand
objglob<-waicglob
}
else
{
objcand<- -mlikcand1
objcur<- -mlikcand
objglob<- -mlikglob
}
if(objcur<objglob)
{
waicglob<-waiccand
varglob<-varcand
varcurb<-varcand
mlikglob<-mlikcand
if(cluster)
modglob<-fm
if(printable.opt)print(paste("GREEDY update global optima with ", objcur))
}
}),abort = function(){opt.achieved <- TRUE; fm<-fmb;closeAllConnections();options(error=traceback); onerr<-TRUE})
if(objcur!=objglob)
{
if(locstop.nd)
{
break
}else
{
varcurb<-varcand
}
}
}
#!#if(printable.opt)print(points)
if(model$reverse == FALSE)
{
vect<-buildmodel(max.cpu = 1,varcur.old = varcand,statid = model$statid,switch.type = type.randomize,min.N = min.N.randomize,max.N = max.N.randomize)
varcur<-vect[[1]]$varcur
#if(printable.opt)print(varcur)
cluster<-TRUE
if(is.null(vect[[1]]$formula))
{
cluster<-FALSE
if(printable.opt)print("!!!!Greedy reverse model already estimated!!!!")
}else
{
mod <- lapply(X = vect, FUN = fitmodel)
}
if(cluster)
{
waiccur<-mod[[1]]$waic
mlikcur<-mod[[1]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcur)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcur,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
# incorporate what happens for the backward optimization
model.prob<-vect[[1]]$log.mod.switch.prob
model.prob.fix<-vect[[1]]$log.mod.switchback.prob
}else # incorporate what happens for the reverse move
{
model.probs<-calculate.move.logprobabilities(switch.type = type.randomize,varold = varcand, varnew = model$varold,min.N = min.N.randomize,max.N = max.N.randomize)
model.prob<-model.probs$log.switch.forw.prob
model.prob.fix<-model.probs$log.switch.back.prob
varcur <- varcand
waiccur <- waiccand
mlikcur <- mlikcand
}
return(list(varcur = varcur, waiccur = waiccur, mlikcur = mlikcur, log.prob.cur = model.prob,log.prob.fix = model.prob.fix, varglob = varglob, waicglob = waicglob, mlikglob = mlikglob, modglob = modglob))
},
#global emjmcmc procedure for model selection (hyper heuristic logic in terms of COP)
modejumping_mcmc=function(glob.model)
{
stm <- proc.time()
if(printable.opt)print("Begin model selection EMJMCMC2016 procedure")
set.seed(runif(n = 1, min = 1, max = seed), kind = NULL, normal.kind = NULL)
acc_moves<-1
accept_old<-1
distrib_of_proposals <- glob.model$distrib_of_proposals
distrib_of_neighbourhoods <- glob.model$distrib_of_neighbourhoods
# do the search and simulations accross the modes
g.results[4,1]<- 0
g.results[4,2]<- 0
if(glob.model$presearch)
{
forward_selection(list(varcur=rep(0,length(fparam.example)),mlikcur=-Inf,waiccur =Inf,locstop = glob.model$locstop,statid=-1))
backward_selection(list(varcur=rep(1,length(fparam.example)),mlikcur=-Inf,waiccur =Inf,locstop = glob.model$locstop,statid=-1))
if(exists("statistics1")&&recalc.margin < 2^Nvars)
{
p.add <<- as.array(post_proceed_results(statistics1)$p.post)
}
else if(exists("hashStat")&&recalc.margin < 2^Nvars)
{
p.add <<- as.array(post_proceed_results_hash(hashStat)$p.post)
}
}else
{
p.add<<-array(data = 0.1,Nvars)
p.post<-array(data = 0.1,Nvars)
vec<-rbinom(n = Nvars,size = 1,prob = 0.0000001) # generate an initial solution
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
}
waiccur<-Inf
waicglob<-Inf
mlikcur<- -Inf
mlikglob<- -Inf
ratcur<- -Inf
#set up initial parameters
if(is.null(glob.model$varcur))
{
if((!is.na(g.results[1,2]))&&g.results[1,2]>0)
{
vec<-dectobit(g.results[1,2]-1)
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
waiccur<-g.results[2,1]
waicglob<- g.results[2,1]
mlikcur<- g.results[1,1]
mlikglob<- g.results[1,1]
ratcur<- g.results[1,1]
print(paste("initial solution is set with mlik of ",mlikcur))
}else{
vec<-rbinom(n = Nvars,size = 1,prob = 0.5) # generate an initial solution
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
}
}else if(length(glob.model$varcur[which(glob.model$varcur %in% c(0,1))])==Nvars)
{
varcur<-glob.model$varcur
}
else
{
if(printable.opt)print("Incorrect initial solution set be the user, a random one is generated")
vec<-rbinom(n = Nvars,size = 1,prob = 0.5) # generate an initial solution
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
}
varcurb<-varcur
varglob<-varcur
modglob<-NULL
p1 = array(data = 0.0001,dim = Nvars)
p2 = array(data = 0.9999,dim = Nvars)
j<-0
j.a<-0
p.post<-array(data = 1,dim = Nvars)
waiccur<-Inf
waicglob<-Inf
mlikcur<- -Inf
mlikglob<- -Inf
ratcur<- -Inf
fm<-NULL
eps.emp<-normprob(p1,p2)
max.cpu.buf<-max.cpu
delta.time <- 0
LocImprove<-0
LocNeighbor<-0
max.cpu.buf<-max.cpu.glob
while((eps.emp>=glob.model$eps || j<= glob.model$maxit || j <= glob.model$burnin) && delta.time < glob.model$max.time && g.results[4,1]<= glob.model$trit && g.results[4,2]<= glob.model$trest)
{
p1<-p.post/acc_moves
set.seed(runif(n = 1, min = 1, max = seed*100), kind = NULL, normal.kind = NULL)
LocImprove <- (sample.int(n = 5,size = 1,prob = distrib_of_proposals) - 1)
LocNeighbor<-(sample.int(n = 7,size = 1,prob = distrib_of_neighbourhoods[LocImprove+1,]))
switch.type.glob.buf = LocNeighbor
switch.type.buf = LocNeighbor
if(LocNeighbor == 7)
{
switch.type.glob.buf = 9
switch.type.buf = 9
}
#if(printable.opt)print(LocImprove)
j<-j+1
j.a<-j.a+1
if(j%%glob.model$print.freq == 0)
{
print(paste(j," iterations completed up to now after ",delta.time," cpu minutes"," best MLIK found ",g.results[1,1] ," current mlik found ",mlikcur, "current acceptance ratio ",acc_moves/j.a))
}
if(j%%100==0)
seed = runif(n = 1,min = 0,max = 100000)
# the small part of the code to be upgraded at least slightly
if(allow_offsprings %in% c(1,2) && j%%mutation_rate == 0 && (j<=last.mutation || Nvars!=Nvars.max))
{
if(Nvars>Nvars.max || j==mutation_rate)
{
#do the stuff here
if(j==mutation_rate)
fparam.pool<<-c(fparam.pool,filtered)
to.del <- which(p.add < p.allow.tree)
if(length(to.del)==Nvars)
to.del<-to.del[-sample.int(n = Nvars,size = sample.int(n=Nvars-1,size = 1),prob = p.add+p.epsilon)]
if(length(to.del)<Nvars-Nvars.max)
{
tdl.id<-order(p.add,decreasing = T)
to.del<-to.del[-tdl.id[1:Nvars.max]]
}
print("Data filtered! Insignificant variables deleted!")
# keysarr <- as.array(keys(hashStat))
# keysarr.new<-NULL
# values.new<-values(hashStat)
# for(id.replace in to.del){
# for(jjj in 1:length(keysarr))
# {
# if(!stri_sub(keysarr[jjj],from = id.replace, to = id.replace)=="1")
# {
# keysarr.new<-c(keysarr.new,stri_sub(keysarr[jjj],from = 1, to = Nvars.max))
# }
# else
# {
#
# }
# }
# }
# keysarr.new<-unique(keysarr.new)
if(length(to.del)>0)
{
clear(hashStat)
#rm(hashStat)
gc()
#hashStat<<-hash(keys=keysarr.new,values=as.list(data.frame((values.new))))
hashStat<<-hash()
fparam<<-fparam[-to.del]
Nvars<<-length(fparam)
Nvars.init<<-Nvars
p.add<<-p.add[-to.del]
p.post<-array(data = 1,dim = Nvars)
#print(paste("mutation happended ",proposal," tree added"))
varcurb<-varcurb[1:Nvars]
varcand<-varcurb[1:Nvars]
varglob<-varcurb[1:Nvars]
p1 <- array(0,dim = (Nvars))
p2 <- array(1,dim = (Nvars))
acc_moves<-1
j.a<-1
}
}
else
{
if(Nvars>=Nvars.max)
{
idmut<-(which(p.add[(Nvars.init+1):Nvars] <= p.allow.replace) + Nvars.init)
lidmut<-length(idmut) #maximal number of covariates that can die out
if(lidmut>0)
{
p.del<-(lidmut - sum(p.add[idmut]))/lidmut
lidmut<-rbinom(n = 1,size = lidmut,prob = p.del)
}
}else
{
idmut<-(Nvars+1):Nvars.max
lidmut<-Nvars.max-Nvars
}
for(idel in 1:lidmut){
p.del<-1-(sum(p.add))/Nvars
mother<-ifelse(runif(n = 1,min = 0,max = 1)<=p.del,fparam[which(rmultinom(n = 1,size = 1,prob = p.add/2)==1)],fparam[runif(n = 1,min = 1,max=Nvars.init)])
ltreem<-stri_length(mother)
mother<-stri_sub(mother,from=2, to = ltreem)
if(allow_offsprings==1)
sjm<-sum(stri_count_fixed(str = mother, pattern = c("&","|")))
else
sjm<-sum(stri_count_fixed(str = mother, pattern = c("+","*")))
if(sjm<=max.tree.size)
{
#p.del<-1-(sum(p.add))/Nvars
father<-ifelse(runif(n = 1,min = 0,max = 1)<=p.del,fparam.pool[runif(n = 1,min = 1,max=length(fparam.pool))],fparam[which(rmultinom(n = 1,size = 1,prob = p.add/2)==1)])
ltreef<-stri_length(father)
father<-stri_sub(father,from=2, to = ltreef)
if(allow_offsprings==1)
sjf<-sum(stri_count_fixed(str = father, pattern = c("&","|")))
else
sjf<-sum(stri_count_fixed(str = father, pattern = c("+","*")))
if(sjm+sjf+1<=max.tree.size)
{
if(allow_offsprings==1)
{
if(!grepl(father, mother,fixed = T)&&!grepl(mother, father,fixed = T))
{
proposal<-stri_paste(paste(ifelse(runif(n = 1,min = 0,max = 1)<p.nor,"I((1-","I(("),mother,sep = ""),paste(ifelse(runif(n = 1,min = 0,max = 1)<p.nor,"(1-","("),father,"))",sep = ""),sep = ifelse(runif(n = 1,min = 0,max = 1)<p.and,")&",")|"))
}
else
{
if(max(sjm,sjf)>1)
{
t.d<-sample.int(size = 1,n = (max(sjm,sjf)+1))
if(sjm>=sjf)
{
loc<-c(1,stri_locate_all(str = mother,regex = "\\&|\\||\\*|\\+")[[1]][,1],stri_length(mother))
proposal<-stri_paste(stri_sub(mother,from = 1,to = loc[t.d]-1),stri_sub(mother,from = (loc[t.d+1]+(t.d==1)),to = stri_length(mother)))
}else
{
loc<-c(1,stri_locate_all(str = father,regex = "\\&|\\||\\*|\\+")[[1]][,1],stri_length(father))
proposal<-stri_paste(stri_sub(father,from = 1,to = loc[t.d]-1),stri_sub(father,from = (loc[t.d+1]+(t.d==1)),to = stri_length(father)))
}
diffs<-(stri_count_fixed(str = proposal, pattern = "(")-stri_count_fixed(str = proposal, pattern = ")"))
if(diffs>0)
proposal<-stri_paste(proposal,stri_paste(rep(")",diffs),collapse = ""),collapse = "")
if(diffs<0)
proposal<-stri_paste(stri_paste(rep("(",-diffs),collapse = ""),proposal,collapse = "")
proposal<-stri_paste("I",proposal)
#print(paste("&&&&&&",mother,"ssss",father))
}
else
proposal<-stri_paste("I",mother)
}
#proposal<-stri_paste("I",mother)
}
else
{
proposal<-stri_paste(paste(ifelse(runif(n = 1,min = 0,max = 1)<p.nor,"I(","I(-"),mother,sep = ""),paste("(",father,"))",sep = ""),sep = ifelse(runif(n = 1,min = 0,max = 1)<p.and,"*","+"))
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
while((proposal %in% fparam))
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
}
}
else
{
t.d<-sample.int(size = 1,n = (max(sjm,sjf)+1))
if(sjm>=sjf)
{
loc<-c(1,stri_locate_all(str = mother,regex = "\\&|\\||\\*|\\+")[[1]][,1],stri_length(mother))
proposal<-stri_paste(stri_sub(mother,from = 1,to = loc[t.d]-1),stri_sub(mother,from = (loc[t.d+1]+(t.d==1)),to = stri_length(mother)))
}else
{
loc<-c(1,stri_locate_all(str = father,regex = "\\&|\\||\\*|\\+")[[1]][,1],stri_length(father))
proposal<-stri_paste(stri_sub(father,from = 1,to = loc[t.d]-1),stri_sub(father,from = (loc[t.d+1]+(t.d==1)),to = stri_length(father)))
}
diffs<-(stri_count_fixed(str = proposal, pattern = "(")-stri_count_fixed(str = proposal, pattern = ")"))
if(diffs>0)
proposal<-stri_paste(proposal,stri_paste(rep(")",diffs),collapse = ""),collapse = "")
if(diffs<0)
proposal<-stri_paste(stri_paste(rep("(",-diffs),collapse = ""),proposal,collapse = "")
proposal<-stri_paste("I",proposal)
#print(paste("!!!!!",mother,"ssss",father))
}
#maybe check correlations here
if( (!(proposal %in% fparam)) && Nvars<Nvars.max)
{
#if(cor())
fparam<<-c(fparam,proposal)
Nvars<<-as.integer(Nvars+1)
p.add<<-as.array(c(p.add,p.allow.replace))
p.post<-as.array(c(p.post,1))
if(printable.opt)
print(paste("mutation happended ",proposal," tree added"))
}
else if(!(proposal %in% fparam))
{
to.del<-(which(p.add[(Nvars.init+1):Nvars]< p.allow.replace)+ Nvars.init)
lto.del<-length(x = to.del)
if(lto.del>0)
{
id.replace <- to.del[round(runif(n = 1,min = 1,max = lto.del))]
if(printable.opt)
print(paste("mutation happended ",proposal," tree replaced ", fparam[id.replace]))
fparam[id.replace]<<-proposal
keysarr <- as.array(keys(hashStat))
p.add[id.replace]<<-p.allow.replace
for(jjj in 1:length(keysarr))
{
if(stri_sub(keysarr[jjj],from = id.replace, to = id.replace)=="1")
{
del(x = keysarr[jjj],hash = hashStat)
}
}
}
}
}
}
varcurb<-c(varcurb,array(1,dim = (Nvars -length(varcurb))))
varcand<-c(varcand,array(1,dim = (Nvars -length(varcand))))
varglob<-c(varglob,array(1,dim = (Nvars -length(varglob))))
p.post<- array(1,dim = (Nvars))
p1 = c(p1,array(0,dim = (Nvars -length(p1))))
p2 = c(p1,array(1,dim = (Nvars -length(p1))))
acc_moves<-1
j.a<-1
}
} else if(allow_offsprings == 3 && j%%mutation_rate == 0 && (j<=last.mutation || Nvars!=Nvars.max))
{
#if(latnames[1]!="")
# perform preliminary filtration here
if(Nvars>Nvars.max || j==mutation_rate)
{
#pool.cor.prob = T
#do the stuff here
if(j==mutation_rate)
{
fparam.pool<<-unique(c(fparam.pool,filtered))
if(!pool.cor.prob)
pool.probs<-array(data = 1/length(fparam.pool),dim = length(fparam.pool))
else{
fobserved.cleaned<-fobserved
fobserved.cleaned<-stri_replace(str = fobserved.cleaned,fixed = "I(",replacement = "")
fobserved.cleaned<-stri_replace(str = fobserved.cleaned,fixed = ")",replacement = "")
fparam.pool.cleaned<-fparam.pool
fparam.pool.cleaned<-stri_replace(str = fparam.pool.cleaned,fixed = "I(",replacement = "")
fparam.pool.cleaned<-stri_replace(str = fparam.pool.cleaned,fixed = ")",replacement = "")
pool.probs<-abs(cor(estimator.args$data[[fobserved.cleaned]],estimator.args$data[,which(fparam.pool.cleaned %in% names(estimator.args$data))]))+p.epsilon
rm(fobserved.cleaned)
rm(fparam.pool.cleaned)
#print(pool.probs[1:100])
}
}
to.del <- which(p.add < p.allow.tree)
if(length(to.del)==Nvars)
to.del<-to.del[-sample.int(n = Nvars,size = sample.int(n=Nvars-1,size = 1),prob = p.add+p.epsilon)]
if(length(to.del)<Nvars-Nvars.max)
{
tdl.id<-order(p.add,decreasing = T)
to.del<-to.del[-tdl.id[1:Nvars.max]]
}
print("Data filtered! Insignificant variables deleted!")
if(length(to.del)>0)
{
clear(hashStat)
#rm(hashStat)
#gc()
#hashStat<<-hash(keys=keysarr.new,values=as.list(data.frame((values.new))))
#rm(hashStat)
hashStat<<-hash()
#clear(hashStat)
#hashStat<<-hash()
fparam<<-fparam[-to.del]
#if(!keep.origin)
# pool.probs[which(fparam.pool %in% fparam)]<-1
Nvars<<-length(fparam)
Nvars.init<<-Nvars
p.add<<-p.add[-to.del]
p.post<-array(data = 1,dim = Nvars)
#print(paste("mutation happended ",proposal," tree added"))
varcurb<-varcurb[-to.del]
varcand<-varcurb[-to.del]
varglob<-varcurb[-to.del]
p1 <- array(0,dim = (Nvars))
p2 <- array(1,dim = (Nvars))
acc_moves<-1
j.a<-1
}
}
else
{
if(Nvars>=Nvars.max)
{
if(keep.origin)
{
idmut<-(which(p.add[(Nvars.init+1):Nvars] <= p.allow.replace) + Nvars.init)
lidmut<-length(idmut) #maximal number of covariates that can die out
if(lidmut>0)
{
p.del<-(lidmut - sum(p.add[idmut]))/lidmut
lidmut<-rbinom(n = 1,size = lidmut,prob = p.del)
}
}else{
idmut<-which(p.add <= p.allow.replace)
lidmut<-length(idmut) #maximal number of covariates that can die out
if(lidmut>0)
{
p.del<-(lidmut - sum(p.add[idmut]))/lidmut
lidmut<-rbinom(n = 1,size = lidmut,prob = p.del)
}
}
#if(lidmut>0)
#{
# p.del<-(lidmut - sum(p.add[idmut]))/lidmut
# lidmut<-rbinom(n = 1,size = lidmut,prob = p.del)
#}
}else
{
idmut<-(Nvars+1):Nvars.max
lidmut<-Nvars.max-Nvars
}
# now having chosen the candidates to be deleted we can propose new variables
idel<-1
repsd = 1
while(idel <= lidmut && repsd <=lidmut*100){
repsd = repsd +1
#gen.prob<-c(1,1,1,1,1)#just uniform for now
action.type <- sample.int(n = 5,size = 1,prob = gen.prob)
if(action.type==1)
{
# mutation (add a leave not in the search space)
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1,prob = pool.probs)]
}else if(action.type==2){
# crossover type of a proposal
# generate a mother
#actvars<-which(varcurb==1)
mother<-ifelse(runif(n = 1,min = 0,max = 1)<=pool.cross,fparam[sample.int(n =Nvars, size =1,prob = p.add+p.epsilon)],fparam.pool[sample.int(n = length(fparam.pool),size =1,prob = pool.probs)])
ltreem<-stri_length(mother)
mother<-stri_sub(mother,from=1, to = ltreem)
#sjm<-sum(stri_count_fixed(str = mother, pattern = c("+","*")))
# generate a father
father<-ifelse(runif(n = 1,min = 0,max = 1)<=pool.cross,fparam[sample.int(n = Nvars, size =1,prob = p.add+p.epsilon)],fparam.pool[sample.int(n = length(fparam.pool),size =1,prob = pool.probs)])
ltreef<-stri_length(father)
father<-stri_sub(father,from=1, to = ltreef)
#sjf<-sum(stri_count_fixed(str = father, pattern = c("+","*")))
proposal<-stri_paste("I(",stri_paste(mother,father,sep="*"),")",sep = "")
}else if(action.type==3){
proposal<-ifelse(runif(n = 1,min = 0,max = 1)<=pool.cross,fparam[sample.int(n = Nvars,size =1, prob = p.add+p.epsilon)],fparam.pool[sample.int(n = length(fparam.pool),size =1,prob = pool.probs)])
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
}else if(action.type==4){
# select a subset for the projection
spad = sum(p.add)
actvars <- which(rbinom(n = length(fparam),size = 1,prob = p.add/spad+p.epsilon)==1)
if(length(actvars)<=1)
{
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
}else{
capture.output(withRestarts(tryCatch({
#print(as.formula(stri_paste(fobserved,"~ 1 +",paste0(fparam[actvars],collapse = "+"))))
# get the projection coefficients as the posterior mode of the fixed effects
if(deep.method == 1){
bet.act <- do.call(.self$estimator, c(estimator.args,as.formula(stri_paste(fobserved,"~ 1 +",paste0(fparam[actvars],collapse = "+")))))$summary.fixed$mean
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
bet.act<-round(bet.act, digits = 8)
bet.act<-stri_paste("m(",bet.act,",",sep = "")
# make a projection
bet.act<-stri_paste(bet.act,c("1",fparam[actvars]),")",sep = "")
bet.act<-stri_paste("I(",bet.act,")",sep = "")
proposal<-stri_paste("I(",stri_paste(bet.act,collapse = "+"),")",collapse = "")
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
#print(proposal)
}else if(deep.method == 2){
cursigma = sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)]
bet.act = gnlr(y=data.example[[fobserved]],
distribution = estimator.args$distribution,
mu = as.formula(stri_paste("~",estimator.args$link,"(",cursigma,"(","b0 +",paste0("b",1:length(actvars),"*",fparam[actvars],collapse = "+"),"))")),
pmu = rep(0,length(actvars)+1))$coefficients
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
#bet.act<-round(bet.act, digits = 2)
bet.act<-round(bet.act, digits = 8)
bet.act<-stri_paste("m(",bet.act,",",sep = "")
# make a projection
bet.act<-stri_paste(bet.act,c("1",fparam[actvars]),")",sep = "")
bet.act<-stri_paste("I(",bet.act,")",sep = "")
proposal<-stri_paste("I(",stri_paste(bet.act,collapse = "+"),")",collapse = "")
proposal<-stri_paste("I(",cursigma,"(",proposal,"))",sep = "")
}else if(deep.method == 3){
cursigma = sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)]
forstr = stri_paste("~",estimator.args$link,"(",cursigma,"(","m(0,1) +",paste0("m(",rnorm(length(actvars),0,1),",",fparam[actvars],")",collapse = "+"),"))")
forstr = stri_replace_all_fixed(str = forstr,pattern = c("m(-"),replacement = "m(")
forstr = stri_replace_all_fixed(str = forstr,pattern = c("m("),replacement = "m(b_")
#print(as.formula(forstr))
nlrr = gnlr(y=data.example[[fobserved]],
distribution = estimator.args$distribution,
mu = as.formula(forstr),
pmu = rnorm(stri_count_fixed(str = forstr,pattern = "m("),0,0.0001))#$coefficients
beg.rep = stri_locate_all(str = forstr,fixed = "m(b")[[1]][,2]
end.rep = stri_locate_all(str = forstr,fixed = "," )[[1]][,2]
bet.act = nlrr$coefficients
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
bet.act<-round(bet.act, digits = 8)
torepl = stri_sub(str = forstr,from = beg.rep,to = end.rep)
for(i in 1:length(bet.act))
forstr = stri_replace_all_fixed(str = forstr,pattern =torepl[i],replacement = stri_paste(bet.act[i],","))
forstr = stri_replace_all_fixed(str = forstr,pattern =paste0("~",estimator.args$link),replacement = "I")
proposal<-forstr
}
else{
bet.act <- rnorm(n = (length(actvars)+1),mean = 0,sd = 1)
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
bet.act<-round(bet.act, digits = 8)
bet.act<-stri_paste("m(",bet.act,",",sep = "")
# make a projection
bet.act<-stri_paste(bet.act,c("1",fparam[actvars]),")",sep = "")
bet.act<-stri_paste("I(",bet.act,")",sep = "")
proposal<-stri_paste("I(",stri_paste(bet.act,collapse = "+"),")",collapse = "")
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
}
}, error = function(err) {
#print(err)
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
},finally = {
proposal = proposal
})))
#print(proposal)
if(is.na(proposal))
{
print(fparam[actvars])
print(actvars)
print(bet.act)
}
}
}else if(action.type==5)
{
#reduce an operator fparam[idel]
#print("reduction")
#print(idel)
if(idel>length(fparam))
{
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
}else{
cpm<-sum(stri_count_fixed(str = fparam[idel], pattern = c("*")))
if(length(cpm)==0)
cpm<-0
if(cpm>0)
{
t.d<-sample.int(size = 1,n = (cpm))
#print(fparam[idel])
loc<-c(1,stri_locate_all(str = fparam[idel],regex = "\\*")[[1]][,1],stri_length(fparam[idel]))
proposal<-stri_paste(stri_sub(fparam[idel],from = 1,to = loc[t.d]-1+2*(t.d==1)),stri_sub(fparam[idel],from = (loc[t.d+1]+(t.d==1)),to = stri_length(fparam[idel])))
if(runif(n = 1,min = 0,max = 1)<del.sigma){
dsigmas<-sample.int(size = 1,n = length(sigmas))
if(sigmas[dsigmas]!="")
proposal<-stri_replace_all_fixed(replacement = "",str = proposal,pattern = sigmas[dsigmas])
}
so<-stri_count_fixed(str = proposal, pattern="(")
sc<-stri_count_fixed(str = proposal, pattern=")")
#print(proposal)
if(sc>so){
proposal<-stri_paste(stri_paste("I",rep("(",sc-so), collapse = ''),proposal)
}else if(sc<so)
proposal<-stri_paste(proposal,stri_paste(rep(")",so-sc),collapse = ''))
#print(proposal)
}else{
proposal<-fparam[idel]
}
}
}
sj<-(stri_count_fixed(str = proposal, pattern = "*"))
sj<-sj+(stri_count_fixed(str = proposal, pattern = "+"))
sj<-sj+sum(stri_count_fixed(str = proposal, pattern = sigmas))
sj<-sj+1
if(length(sj)==0)
{
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
sj <- 0
}else if(is.na(proposal)||is.na(sj))
{
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
sj <- 0
}
else if(sj>max.tree.size)
{
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
}
add<-T
ids.lat<-integer(0)
if(latnames[1]!="")
{
ids.lat<-which(fparam %in% latnames)
if(sum(stri_count_fixed(str = proposal,pattern = latnames))>0)
add<-F
}
if(length(ids.lat)==0)
ids.lat<-Nvars.max +1
#print(add)
#print(proposal)
if(proposal %in% latnames)
{
if((proposal %in% fparam[ids.lat]))
add<-F
}else{
if(add){
withRestarts(tryCatch(capture.output({
bet.act <- do.call(.self$estimator, c(estimator.args,as.formula(stri_paste(fobserved,"~ 1 +",paste0(c(fparam[-ids.lat],proposal),collapse = "+")))))$summary.fixed$mean
if(is.na(bet.act[length(fparam[-ids.lat])+2])&& (action.type!=4&&gen.prob[2]==0||gen.prob[2]!=0))
{
add<-F
}else
{
idel<-idel+1
}
}, error = function(err) {
add<-F
},finally = {}
)))
}
}
#print(add)
#print("next")
if(add & Nvars<Nvars.max)# alternative restricted to correlation: if((max(cor(eval(parse(text = proposal),envir = data.example),sapply(fparam, function(x) eval(parse(text=x),envir = data.example))))<0.9999) && Nvars<Nvars.max)
{
fparam<<-c(fparam,proposal)
Nvars<<-as.integer(Nvars+1)
p.add<<-as.array(c(p.add,p.allow.replace))
p.post<-as.array(c(p.post,1))
if(printable.opt)
print(paste("mutation happended ",proposal," tree added"))
}
else if(add)#alternative restricted to correlation: if(max(abs(cor(eval(parse(text = proposal),envir = data.example),sapply(fparam, function(x) eval(parse(text=x),envir = data.example)))))<0.9999)
{
#if(action.type==4)
# print(proposal)
if(keep.origin){
to.del<-(which(p.add[(Nvars.init+1):Nvars]< p.allow.replace)+ Nvars.init)
lto.del<-length(x = to.del)
}else{
to.del<-which(p.add < p.allow.replace)
lto.del<-length(x = to.del)
}
#to.del<-(which(p.add[(Nvars.init+1):Nvars]< p.allow.replace)+ Nvars.init)
#lto.del<-length(x = to.del)
if(lto.del>0)
{
id.replace <- to.del[round(runif(n = 1,min = 1,max = lto.del))]
if(printable.opt)
print(paste("mutation happended ",proposal," tree replaced ", fparam[id.replace]))
fparam[id.replace]<<-proposal
keysarr <- as.array(keys(hashStat))
p.add[id.replace]<<-p.allow.replace
for(jjj in 1:length(keysarr))
{
if(stri_sub(keysarr[jjj],from = id.replace, to = id.replace)=="1")
{
del(x = keysarr[jjj],hash = hashStat)
}
}
}
}
}
}
if(p.add.default<1)
p.add<<-array(p.add.default,Nvars)
varcurb<-c(varcurb,array(1,dim = (Nvars -length(varcurb))))
varcand<-c(varcand,array(1,dim = (Nvars -length(varcand))))
varglob<-c(varglob,array(1,dim = (Nvars -length(varglob))))
p.post<- array(1,dim = (Nvars))
p1 = c(p1,array(0,dim = (Nvars -length(p1))))
p2 = c(p1,array(1,dim = (Nvars -length(p1))))
acc_moves<-1
j.a<-1
}else if(allow_offsprings == 4 && j%%mutation_rate == 0 && (j<=last.mutation || Nvars!=Nvars.max))
{
add.buf<-F
# perform preliminary filtration here
if(Nvars>Nvars.max || j==mutation_rate)
{
on.suggested <- 1
preaccepted<-F
#do the stuff here
if(j==mutation_rate)
{
fparam.pool<<-unique(c(fparam.pool,filtered))
if(!pool.cor.prob)
pool.probs<-array(data = 1/length(fparam.pool),dim = length(fparam.pool))
else{
fobserved.cleaned<-fobserved
fobserved.cleaned<-stri_replace(str = fobserved.cleaned,fixed = "I(",replacement = "")
fobserved.cleaned<-stri_replace(str = fobserved.cleaned,fixed = ")",replacement = "")
fparam.pool.cleaned<-fparam.pool
fparam.pool.cleaned<-stri_replace(str = fparam.pool.cleaned,fixed = "I(",replacement = "")
fparam.pool.cleaned<-stri_replace(str = fparam.pool.cleaned,fixed = ")",replacement = "")
pool.probs<-abs(cor(estimator.args$data[[fobserved.cleaned]],estimator.args$data[,which(fparam.pool.cleaned %in% names(estimator.args$data))]))+p.epsilon
rm(fobserved.cleaned)
rm(fparam.pool.cleaned)
#print(pool.probs[1:100])
}
}
to.del <- which(p.add < p.allow.tree)
if(length(to.del)==Nvars)
to.del<-to.del[-sample.int(n = Nvars,size = sample.int(n=Nvars-1,size = 1),prob = p.add+p.epsilon)]
if(length(to.del)<Nvars-Nvars.max)
{
tdl.id<-order(p.add,decreasing = T)
to.del<-to.del[-tdl.id[1:Nvars.max]]
}
print("Data filtered! Insignificant variables deleted!")
if(length(to.del)>0)
{
clear(hashStat)
#rm(hashStat)
#gc()
#hashStat<<-hash(keys=keysarr.new,values=as.list(data.frame((values.new))))
clear(hashStat)
#hashStat<<-hash()
fparam<<-fparam[-to.del]
if(!keep.origin)
pool.probs[which(fparam.pool %in% fparam)]<-1
Nvars<<-length(fparam)
Nvars.init<<-Nvars
p.add<<-p.add[-to.del]
p.post<-array(data = 1,dim = Nvars)
#print(paste("mutation happended ",proposal," tree added"))
varcurb<-varcurb[-to.del]
varcand<-varcurb[-to.del]
varglob<-varcurb[-to.del]
p1 <- array(0,dim = (Nvars))
p2 <- array(1,dim = (Nvars))
acc_moves<-1
j.a<-1
super.backward = F
}
}
else
{
if(Nvars>=Nvars.max)
{
# delete those that are not in the active model with probability 0.5 each
if(keep.origin)
{
idmut<-(which(p.add[(Nvars.init+1):Nvars] <= p.allow.replace) + Nvars.init)
lidmut<-length(idmut) #maximal number of covariates that can die out
if(lidmut>0)
{
p.del<-(lidmut - sum(p.add[idmut]))/lidmut
lidmut<-rbinom(n = 1,size = lidmut,prob = p.del)
}
}else{
idmut<-which(p.add <= p.allow.replace)
lidmut<-length(idmut) #maximal number of covariates that can die out
if(lidmut>0)
{
p.del<-(lidmut - sum(p.add[idmut]))/lidmut
lidmut<-rbinom(n = 1,size = lidmut,prob = p.del)
}
}
#mod.id.old<-runif(n = 1000,min = 1,max = 2^Nvars)
if(on.suggested%%2==1){
if(preaccepted)
{
log.mod.switch.prob.back<-sum(abs(varcurb.buf-varcurb))
eqal.things<-which(varcurb.buf==varcurb)
log.mod.switch.prob.back<-log.mod.switch.prob.back+length(which(fparam[eqal.things]!=tmp.buf.1[eqal.things]))
log.mod.switch.prob.back<-log.mod.switch.prob.back^prand
if(printable.opt) print(paste0("afteracceptance ratio ",log.mod.switch.prob.back/log.mod.switch.prob))
if(runif(1,0,1)<=log.mod.switch.prob.back/log.mod.switch.prob)
{
if(printable.opt) print("preaccepted mutation is accepted")
mlikcur<-mlikcur.buf.2
varcurb<-varcurb.buf.2
fparam<<-tmp.buf.2
p.add<<-p.add.buf.2
}else
{
if(printable.opt) print("preaccepted mutation rejected")
fparam<<-tmp.buf.1
p.add<<-p.add.buf.1
mlikcur<-mlikcur.buf
varcurb<-varcurb.buf
}
preaccepted<-F
}
tmp.buf<-fparam[which(varcurb==1)]
tmp.buf.1<-fparam
p.add.buf.1<-p.add
# hashStat.buf.1<-copy(hashStat)
vect<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = -1,min.N = Nvars,max.N = Nvars,switch.type = 9)
res.par <- lapply(X = vect,FUN = .self$fitmodel)
mlikcur<-res.par[[1]]$mlik
varcurb<-vect[[1]]$varcur
mlikcur.buf<-mlikcur
varcurb.buf<-varcurb
if(printable.opt) print("OLDMOD")
mso=(mlikcur)#(sum(unlist(lapply(res.par, function(x) exp(x$mlik)))))
if(printable.opt) print(mso)
}else if(on.suggested%%2==0){
#tmp.buf2<-fparam[which(varcurb==1)]
tmp.buf.2<-fparam
p.add.buf.2<-p.add
vect<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = -1,min.N = Nvars,max.N = Nvars,switch.type = 9)
log.mod.switch.prob<-vect[[1]]$log.mod.switch.prob
res.par <- lapply(X = vect,FUN = .self$fitmodel)
#print(mlikcur)
mlikcur<-res.par[[1]]$mlik
varcurb<-vect[[1]]$varcur
vect<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = -1,min.N = Nvars,max.N = Nvars,switch.type = 9)
log.mod.switch.prob<-vect[[1]]$log.mod.switch.prob
res.par <- lapply(X = vect,FUN = .self$fitmodel)
#print(mlikcur)
mlikcur<-res.par[[1]]$mlik
varcurb<-vect[[1]]$varcur
mlikcur.buf.2<-mlikcur
varcurb.buf.2<-varcurb
msn=(mlikcur)#(sum(unlist(lapply(res.par, function(x) exp(x$mlik)))))
if(printable.opt) print("NEWMOD")
if(printable.opt) print(msn)
if(msn == Inf && mso == Inf ||msn == 0 && mso == 0)
{
msn<-1
mso<-1
}#*log((sum(tmp.buf%in%fparam)==length(tmp.buf)))
if(log(runif(1,0,1))>=((msn)-(mso)))
{
if(printable.opt)print("proposal is rejected")
fparam<<-tmp.buf.1
p.add<<-p.add.buf.1
mlikcur<-mlikcur.buf
varcurb<-varcurb.buf
preaccepted<-F
#on.suggested<-on.suggested+1
}else{
if(printable.opt)print("mutation is preaccepted")
#fparam<<-tmp.buf.1
#p.add<<-p.add.buf.1
#lidmut<-0
preaccepted<-T
}
}
on.suggested<-on.suggested+1
}else
{
idmut<-(Nvars+1):Nvars.max
lidmut<-Nvars.max-Nvars
}
# now having chosen the candidates to be deleted we can propose new variables
idel<-1
while(idel <= lidmut){
#gen.prob<-c(1,1,1,1,1)#just uniform for now
action.type <- sample.int(n = 5,size = 1,prob = gen.prob)
if(action.type==1)
{
# mutation (add a leave not in the search space)
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1,prob = pool.probs)]
}else if(action.type==2){
# crossover type of a proposal
# generate a mother
#actvars<-which(varcurb==1)
mother<-ifelse(runif(n = 1,min = 0,max = 1)<=pool.cross,fparam[sample.int(n =Nvars, size =1,prob = p.add+p.epsilon)],fparam.pool[sample.int(n = length(fparam.pool),size =1,prob = pool.probs)])
ltreem<-stri_length(mother)
mother<-stri_sub(mother,from=1, to = ltreem)
#sjm<-sum(stri_count_fixed(str = mother, pattern = c("+","*")))
# generate a father
father<-ifelse(runif(n = 1,min = 0,max = 1)<=pool.cross,fparam[sample.int(n = Nvars, size =1,prob = p.add+p.epsilon)],fparam.pool[sample.int(n = length(fparam.pool),size =1,prob = pool.probs)])
ltreef<-stri_length(father)
father<-stri_sub(father,from=1, to = ltreef)
#sjf<-sum(stri_count_fixed(str = father, pattern = c("+","*")))
proposal<-stri_paste("I(",stri_paste(mother,father,sep="*"),")",sep = "")
}else if(action.type==3){
proposal<-ifelse(runif(n = 1,min = 0,max = 1)<=pool.cross,fparam[sample.int(n = Nvars,size =1, prob = p.add+p.epsilon)],fparam.pool[sample.int(n = length(fparam.pool),size =1,prob = pool.probs)])
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
}else if(action.type==4){
# select a sparse subset for the projection
spad = sum(p.add)
actvars <- which(rbinom(n = length(fparam),size = 1,prob = p.add/spad+p.epsilon)==1)
#actvars <- which(rbinom(n = Nvars,size = 1,prob = p.add+p.epsilon)==1)
if(length(actvars)<=1)
{
proposal <- fparam[1]
}else{
capture.output(withRestarts(tryCatch({
#print(as.formula(stri_paste(fobserved,"~ 1 +",paste0(fparam[actvars],collapse = "+"))))
# get the projection coefficients as the posterior mode of the fixed effects
if(deep.method == 1){
bet.act <- do.call(.self$estimator, c(estimator.args,as.formula(stri_paste(fobserved,"~ 1 +",paste0(fparam[actvars],collapse = "+")))))$summary.fixed$mean
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
bet.act<-round(bet.act, digits = 8)
bet.act<-stri_paste("m(",bet.act,",",sep = "")
# make a projection
bet.act<-stri_paste(bet.act,c("1",fparam[actvars]),")",sep = "")
bet.act<-stri_paste("I(",bet.act,")",sep = "")
proposal<-stri_paste("I(",stri_paste(bet.act,collapse = "+"),")",collapse = "")
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
#print(proposal)
}else if(deep.method == 2){
cursigma = sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)]
bet.act = gnlr(y=data.example[[fobserved]],
distribution = estimator.args$distribution,
mu = as.formula(stri_paste("~",estimator.args$link,"(",cursigma,"(","b0 +",paste0("b",1:length(actvars),"*",fparam[actvars],collapse = "+"),"))")),
pmu = rep(0,length(actvars)+1))$coefficients
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
#bet.act<-round(bet.act, digits = 2)
bet.act<-round(bet.act, digits = 8)
bet.act<-stri_paste("m(",bet.act,",",sep = "")
# make a projection
bet.act<-stri_paste(bet.act,c("1",fparam[actvars]),")",sep = "")
bet.act<-stri_paste("I(",bet.act,")",sep = "")
proposal<-stri_paste("I(",stri_paste(bet.act,collapse = "+"),")",collapse = "")
proposal<-stri_paste("I(",cursigma,"(",proposal,"))",sep = "")
}else if(deep.method == 3){
cursigma = sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)]
forstr = stri_paste("~",estimator.args$link,"(",cursigma,"(","m(0,1) +",paste0("m(",rnorm(length(actvars),0,1),",",fparam[actvars],")",collapse = "+"),"))")
forstr = stri_replace_all_fixed(str = forstr,pattern = c("m(-"),replacement = "m(")
forstr = stri_replace_all_fixed(str = forstr,pattern = c("m("),replacement = "m(b_")
#print(as.formula(forstr))
nlrr = gnlr(y=data.example[[fobserved]],
distribution = estimator.args$distribution,
mu = as.formula(forstr),
pmu = rnorm(stri_count_fixed(str = forstr,pattern = "m("),0,0.0001))#$coefficients
beg.rep = stri_locate_all(str = forstr,fixed = "m(b")[[1]][,2]
end.rep = stri_locate_all(str = forstr,fixed = "," )[[1]][,2]
bet.act = nlrr$coefficients
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
bet.act<-round(bet.act, digits = 8)
torepl = stri_sub(str = forstr,from = beg.rep,to = end.rep)
for(i in 1:length(bet.act))
forstr = stri_replace_all_fixed(str = forstr,pattern =torepl[i],replacement = stri_paste(bet.act[i],","))
forstr = stri_replace_all_fixed(str = forstr,pattern =paste0("~",estimator.args$link),replacement = "I")
proposal<-forstr
}
else{
bet.act <- rnorm(n = (length(actvars)+1),mean = 0,sd = 1)
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
bet.act<-round(bet.act, digits = 8)
bet.act<-stri_paste("m(",bet.act,",",sep = "")
# make a projection
bet.act<-stri_paste(bet.act,c("1",fparam[actvars]),")",sep = "")
bet.act<-stri_paste("I(",bet.act,")",sep = "")
proposal<-stri_paste("I(",stri_paste(bet.act,collapse = "+"),")",collapse = "")
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
}
}, error = function(err) {
#print(err)
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
},finally = {
proposal = proposal
})))
#print(proposal)
if(is.na(proposal))
{
print(fparam[actvars])
print(actvars)
print(bet.act)
}
}
}else if(action.type==5)
{
#reduce an operator fparam[idel]
#print("reduction")
#print(idel)
if(idel>length(fparam))
{
proposal<-fparam[1]
}else{
cpm<-sum(stri_count_fixed(str = fparam[idel], pattern = c("*")))
if(length(cpm)==0)
cpm<-0
if(cpm>0)
{
t.d<-sample.int(size = 1,n = (cpm))
#print(fparam[idel])
loc<-c(1,stri_locate_all(str = fparam[idel],regex = "\\*")[[1]][,1],stri_length(fparam[idel]))
proposal<-stri_paste(stri_sub(fparam[idel],from = 1,to = loc[t.d]-1+2*(t.d==1)),stri_sub(fparam[idel],from = (loc[t.d+1]+(t.d==1)),to = stri_length(fparam[idel])))
if(runif(n = 1,min = 0,max = 1)<del.sigma){
dsigmas<-sample.int(size = 1,n = length(sigmas))
if(sigmas[dsigmas]!="")
proposal<-stri_replace_all_fixed(replacement = "",str = proposal,pattern = sigmas[dsigmas])
}
so<-stri_count_fixed(str = proposal, pattern="(")
sc<-stri_count_fixed(str = proposal, pattern=")")
#print(proposal)
if(sc>so){
proposal<-stri_paste(stri_paste("I",rep("(",sc-so), collapse = ''),proposal)
}else if(sc<so)
proposal<-stri_paste(proposal,stri_paste(rep(")",so-sc),collapse = ''))
#print(proposal)
}else{
proposal<-fparam[idel]
}
}
}
sj<-(stri_count_fixed(str = proposal, pattern = "*"))
sj<-sj+(stri_count_fixed(str = proposal, pattern = "+"))
sj<-sj+sum(stri_count_fixed(str = proposal, pattern = sigmas))
sj<-sj+1
if(sj>max.tree.size || length(sj)==0)
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
if(is.na(proposal))
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
add<-T
tryCatch(capture.output({
bet.act <- do.call(.self$estimator, c(estimator.args,as.formula(stri_paste(fobserved,"~ 1 +",paste0(c(fparam,proposal),collapse = "+")))))$summary.fixed$mean
if(is.na(bet.act[length(fparam)+2]))
{
add<-F
}else
{
idel<-idel+1
}
}, error = function(err) {
add<-F
}))
if(add & Nvars<Nvars.max)# alternative restricted to correlation: if((max(cor(eval(parse(text = proposal),envir = data.example),sapply(fparam, function(x) eval(parse(text=x),envir = data.example))))<0.9999) && Nvars<Nvars.max)
{
fparam<<-c(fparam,proposal)
Nvars<<-as.integer(Nvars+1)
p.add<<-as.array(c(p.add,p.allow.replace))
p.post<-as.array(c(p.post,1))
#if(printable.opt)
if(printable.opt) print(paste("mutation happended ",proposal," tree added"))
}
else if(add)#alternative restricted to correlation: if(max(abs(cor(eval(parse(text = proposal),envir = data.example),sapply(fparam, function(x) eval(parse(text=x),envir = data.example)))))<0.9999)
{
if(keep.origin){
to.del<-(which(p.add[(Nvars.init+1):Nvars]< p.allow.replace)+ Nvars.init)
lto.del<-length(x = to.del)
}else{
to.del<-which(p.add < p.allow.replace)
lto.del<-length(x = to.del)
}
if(lto.del>0)
{
id.replace <- to.del[round(runif(n = 1,min = 1,max = lto.del))]
#if(printable.opt)
#print(paste("mutation suggested ",proposal," tree replaced ", fparam[id.replace]))
fparam[id.replace]<<-proposal
keysarr <- as.array(keys(hashStat))
p.add[id.replace]<<-p.allow.replace
for(jjj in 1:length(keysarr))
{
if(stri_sub(keysarr[jjj],from = id.replace, to = id.replace)=="1")
{
del(x = keysarr[jjj],hash = hashStat)
}
}
}
}
}
}
varcurb<-c(varcurb,array(1,dim = (Nvars -length(varcurb))))
varcand<-c(varcand,array(1,dim = (Nvars -length(varcand))))
varglob<-c(varglob,array(1,dim = (Nvars -length(varglob))))
p.post<- array(1,dim = (Nvars))
p1 = c(p1,array(0,dim = (Nvars -length(p1))))
p2 = c(p1,array(1,dim = (Nvars -length(p1))))
acc_moves<-1
j.a<-1
}else if(allow_offsprings > 0 && j%%mutation_rate == 0 && j>last.mutation)
{
recalc.margin = 2^Nvars
}
#withRestarts(tryCatch({
varcur<-varcurb
if(LocImprove<=3)
{
vect<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = 4 + LocImprove,min.N = min.N.glob,max.N = max.N.glob,switch.type = switch.type.glob.buf)
max.cpu.buf = 1
}else
{
vect<-buildmodel(max.cpu = max.cpu.glob,varcur.old = varcurb,statid = 4 + LocImprove,min.N = min.N,max.N = max.N,switch.type = switch.type.glob.buf)
max.cpu.buf = max.cpu.glob
}
cluster<-TRUE
flag1<-0
for(mod_id in 1:max.cpu.buf)
{
if(is.null(vect[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==max.cpu.glob)
{
cluster<-FALSE
if(printable.opt)print("!!!!Models already estimated!!!!")
}else
{
if(max.cpu.glob > 1)
res.par <- parallelize(X = vect,FUN = .self$fitmodel)
else
res.par <- lapply(X = vect,FUN = .self$fitmodel)
}
if(LocImprove>3)
{
if(printable.opt)print("!!!!Proceed with no local improvements!!!!")
p.select.y <- array(data = 0, dim = max.cpu.glob)
for(mod_id in 1:max.cpu.glob)
{
if(cluster)
{
fm<-res.par[[mod_id]]
if(is.null(fm)&&(is.na(res.par[[mod_id]]$waic)))
{
varcand<-varcurb
if(printable.opt)print("GlobMTMCMC Model Fit Error!?")
next
}
}
varcand<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand<-res.par[[mod_id]]$waic
mlikcand<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
if((mlikcand>mlikglob)) #update the parameter of interest
{
if(printable.opt)print(paste("GlobMTMCMC update waic.glob = ", waiccand))
if(printable.opt)print(paste("GlobMTMCMC update mlik.glob = ", mlikglob))
mlikglob<-mlikcand
waicglob<-waiccand
varglob<-varcand
if(cluster)
modglob<-fm
}
g1 <- waiccur
if(waiccur == Inf)
{
g1 = 1
}
p.select.y[mod_id]<-(mlikcand + vect[[mod_id]]$log.mod.switchback.prob+log(lambda(c = cc, alpha = aa, g1 = -g1, g2 = -waiccand,g.domain.pos = FALSE))) # correct for different criteria later
if(is.na(p.select.y[mod_id]))
p.select.y[mod_id] <- 0
if(is.infinite(p.select.y[mod_id]) || p.select.y[mod_id]>100000000)
{
#if(printable.opt)print(paste("very large log.w.y detected ",p.select.y[mod_id]))
p.select.y[mod_id] <- 100000000
}
}
max.p.select.y <- max(p.select.y)
p.select.y<-p.select.y-max.p.select.y
if(printable.opt)print(paste("max log.w.y is ",max.p.select.y,"normilized log.w.n.y is ", paste(p.select.y,collapse = ", ")))
ID<-sample.int(n = max.cpu.glob,size = 1,prob = exp(p.select.y))
if(printable.opt)print(paste("cand ",ID," selected"))
varcand<-vect[[ID]]$varcur
if(cluster)
{
waiccand<-res.par[[ID]]$waic
mlikcand<-res.par[[ID]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
#p.Q.cand<- p.select.y[ID]/sum(p.select.y)
if(printable.opt)print("do reverse step")
p.select.z <- array(data = 0.01, dim = max.cpu.glob)
if(max.cpu.glob!=1)
{
if(switch.type.glob.buf==5)
cstm<-6
else if(switch.type.glob.buf==6)
{
cstm<-5
}
else
{
cstm <- switch.type.glob.buf
}
vect1<-buildmodel(max.cpu = max.cpu.glob -1,varcur.old = varcand,statid = 4 + LocImprove,switch.type = cstm, min.N = min.N, max.N = max.N)
cluster<-TRUE
flag1<-0
for(mod_id in 1:(max.cpu.glob-1))
{
if(is.null(vect1[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==(max.cpu.glob-1))
{
cluster<-FALSE
if(printable.opt)print("!!!!MTMCMC reverse models already estimated!!!!")
}else
{
res.par.back <- parallelize(X = vect1,FUN = .self$fitmodel)
}
for(mod_id in 1:(max.cpu.glob-1))
{
if(cluster)
{
if(is.null(fm)&&(is.na(res.par.back[[mod_id]]$waic)))
{
if(printable.opt)print("locMTMCMC Model Fit Error!?")
next
}
}
varcand.b<-vect1[[mod_id]]$varcur
if(cluster)
{
waiccand.b<-res.par.back[[mod_id]]$waic
mlikcand.b<-res.par.back[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand.b)+1
waiccand.b<-statistics1[iidd,2]
mlikcand.b<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand.b,collapse = "")
waiccand.b<-values(hashStat[iidd])[2]
mlikcand.b<-values(hashStat[iidd])[1]
}
if((mlikcand.b>mlikglob))
{
if(printable.opt)print(paste("GlobMTMCMC update waic.glob = ", waiccand.b))
if(printable.opt)print(paste("GlobMTMCMC update mlik.glob = ", mlikcand.b))
mlikglob<-mlikcand.b
waicglob<-waiccand.b
varglob<-varcand.b
if(cluster)
modglob<-fm
}
g1 = waiccand
if(waiccand == Inf)
{
g1 = 1
}
p.select.z[mod_id]<-(mlikcand.b+vect1[[mod_id]]$log.mod.switchback.prob+(lambda(c = cc, alpha = aa, g1 = -g1, g2 = -waiccand.b,g.domain.pos = FALSE))) # correct for different criteria later
if(is.na(p.select.z[mod_id]))
p.select.z[mod_id]=0
if(is.infinite(p.select.z[mod_id]) || p.select.z[mod_id] > 100000000)
{
#if(printable.opt)print(paste("very large log.w.y detected ",p.select.z[mod_id]))
p.select.z[mod_id] <- 100000000
}
}
}
if( waiccur == Inf)
{
g1 = 1
}
p.select.z[max.cpu.glob] <- (mlikcur+vect[[ID]]$log.mod.switch.prob+(lambda(c = cc, alpha = aa, g1 = -g1, g2 = -waiccand,g.domain.pos = FALSE)))
if(is.na(p.select.z[mod_id]))
p.select.z[mod_id]=0
if(is.infinite(p.select.z[mod_id]) || p.select.z[mod_id] > 100000000)
{
#if(printable.opt)print(paste("very large log.w.y detected ",p.select.z[mod_id]))
p.select.z[mod_id] <- 100000000
}
max.p.select.z <- max(p.select.z)
p.select.z<-p.select.z-max.p.select.z
if(printable.opt)print(paste("max log.w.z is ",max.p.select.z,"normilized log.w.n.z is ", paste(p.select.z,collapse = ", ")))
if(log(runif(n = 1,min = 0,max = 1)) < (log(sum(exp(p.select.y)))-log(sum(exp(p.select.z)))) + max.p.select.y - max.p.select.z )
{
mlikcur<-mlikcand
ratcur<-mlikcand
if(printable.opt)print(paste("global MTMCMC update ratcur = ", mlikcand))
if(printable.opt)print(paste("global MTMCMC accept move with ", waiccand))
varcurb<-varcand
waiccur<-waiccand
id<-bittodec(varcurb)+1
acc_moves<-acc_moves+1
if(j<glob.model$burnin)
{
distrib_of_proposals[5]<-distrib_of_proposals[5]+1
}else
{
if(exists("statistics1"))
{
statistics1[id,14]<-statistics1[id,14] + 1
statistics1[id,4]<-statistics1[id,4] + 1
}
p.post<- (p.post + varcurb)
}
}else if(j<glob.model$burnin && distrib_of_proposals[5]>0)
{
distrib_of_proposals[5]<-distrib_of_proposals[5] - 1
}
}else
{
if(cluster)
{
fm<-res.par[[mod_id]]
if(is.null(fm)&&(is.na(res.par[[mod_id]]$waic)))
{
varcand<-varcurb
if(printable.opt)print("EMJMCMC Model Fit Error!?")
next
}
}
varcand<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand<-res.par[[mod_id]]$waic
mlikcand<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
varcur<-varcand
}
# try local improvements
if(LocImprove<=3)
{
# sa improvements
if(LocImprove == 0 || LocImprove == 3)
{
if(printable.opt)print("Try SA imptovements")
buf.change <- array(data = 1,dim = Nvars)
buf.change[which(varcur - varcurb!=0)]=0
#buf.opt[floor(runif(n = n.size,min = 1,max = Nvars+0.999999))] = 1
if(objective ==0)
{
objold<-waiccur
objcur<-waiccand
}else
{
objold<- -mlikcur
objcur<- -mlikcand
}
model = list(statid = 4 + LocImprove, switch.type = switch.type.buf, change = buf.change,mlikcur = mlikcur,
varcur = varcur,varold = varcurb, objcur = objcur,objold = objold, sa2 = ifelse(LocImprove == 3,TRUE,FALSE) ,reverse=FALSE)
SA.forw<-learnlocalSA(model)
ratcand<-SA.forw$mlikcur
if(LocImprove == 0)
{
ids = which(buf.change == 1)
model$varcur <- SA.forw$varcur
model$waiccur<-SA.forw$waiccur
model$varcur[ids] = 1 - model$varcur[ids]
model$mlikcur<- -Inf
model$waiccur<- Inf
#estimate the jump!!!
if(objective ==0)
{
model$objold<-waiccur
}else
{
model$objold<- -ratcand
}
model$reverse = TRUE
if(switch.type.buf==5)
{
model$switch.type <- 6
}
else if(switch.type.buf==6)
{
model$switch.type <- 5
}
SA.back<-learnlocalSA(model)
}
if(LocImprove == 0)
{
thact<-sum(ratcand, - ratcur, - SA.forw$log.prob.cur,SA.forw$log.prob.fix,SA.back$log.prob.cur, - SA.back$log.prob.fix,na.rm=T)
if(log(runif(n = 1,min = 0,max = 1))<=thact)
{
ratcur<-ratcand
mlikcur<-ratcand
if(printable.opt)print(paste("update ratcur through SA = ", ratcur))
varcurb<-SA.forw$varcur
acc_moves<-acc_moves+1
id<-bittodec(varcurb)+1
if(j<glob.model$burnin)
{
distrib_of_proposals[1]<-distrib_of_proposals[1]+1
}else
{
if(exists("statistics1")){
statistics1[id,10]<-statistics1[id,10] + 1
statistics1[id,4]<-statistics1[id,4] + 1
}
p.post<- (p.post + varcurb)
}
}else if(j<glob.model$burnin && distrib_of_proposals[1]>0)
{
distrib_of_proposals[1]<-distrib_of_proposals[1] - 1
}
if((SA.back$mlikglob<mlikglob))
{
if(printable.opt)print(paste("update waic.glob sa.back = ", SA.back$waicglob))
if(printable.opt)print(paste("update waic.glob.mlik sa.back= ", SA.back$mlikglob))
waicglob<-SA.back$waicglob
varglob<-SA.back$varglob
modglob<-SA.back$modglob
}
}else
{
thact<-sum(ratcand, - ratcur, - SA.forw$log.prob.cur,SA.forw$log.prob.fix,vect[[mod_id]]$log.mod.switchback.prob, - vect[[mod_id]]$log.mod.switch.prob,na.rm=T)
if(log(runif(n = 1,min = 0,max = 1))<=thact)
{
ratcur<-ratcand
mlikcur<-ratcand
if(printable.opt)print(paste("update ratcur through SA = ", ratcur))
varcurb<-SA.forw$varcur
id<-bittodec(varcurb)+1
acc_moves<-acc_moves+1
if(j<glob.model$burnin)
{
distrib_of_proposals[4]<-distrib_of_proposals[4]+1
}else
{
if(exists("statistics1")){
statistics1[id,13]<-statistics1[id,13] + 1
statistics1[id,4]<-statistics1[id,4] + 1
}
p.post<- (p.post + varcurb)
}
}else if(j<glob.model$burnin && distrib_of_proposals[4]>0)
{
distrib_of_proposals[4]<-distrib_of_proposals[4] - 1
}
}
if((SA.forw$mlikglob<mlikglob))
{
if(printable.opt)print(paste("update waic.glob sa.forw = ", SA.forw$waicglob))
if(printable.opt)print(paste("update waic.glob.mlik sa.forw = ", SA.forw$mlikglob))
waicglob<-SA.forw$waicglob
varglob<-SA.forw$varglob
modglob<-SA.forw$modglob
}
}else if(LocImprove == 1)
{
if(printable.opt)print("Try MTMCMC imptovements")
buf.change <- array(data = 1,dim = Nvars)
buf.change[which(varcur - varcurb!=0)]=0
#buf.opt[floor(runif(n = n.size,min = 1,max = Nvars+0.999999))] = 1
model = list(statid = 4 + LocImprove,reverse = FALSE, change = buf.change,mlikcur = mlikcur,waiccur = waiccur,
varcur = varcur,varold = varcurb)
MTMCMC.forw<-learnlocalMCMC(model)
ids = which(buf.change == 1)
model$varcur <- MTMCMC.forw$varcur
model$varcur[ids] = 1 - model$varcur[ids]
model$mlikcur<- -Inf
model$waiccur<- Inf
model$reverse = TRUE
#if(printable.opt)print("learn reverse local MTMCMC")
MTMCMC.back<-learnlocalMCMC(model)
#if(printable.opt)print("finish reverse local MTMCMC")
MTMCMC.p.forw<-MTMCMC.forw$log.prob.cur
MTMCMC.p.back<-MTMCMC.back$log.prob.fix
ratcand<-MTMCMC.forw$mlikcur
#if(log(runif(n = 1,min = 0,max = 1))<=(ratcand - ratcur - MTMCMC.forw$log.prob.cur + MTMCMC.forw$log.prob.fix + MTMCMC.back$log.prob.cur - MTMCMC.back$log.prob.fix))
thact<-sum(ratcand, - ratcur, - MTMCMC.forw$log.prob.cur,MTMCMC.forw$log.prob.fix,MTMCMC.back$log.prob.cur,- MTMCMC.back$log.prob.fix,na.rm=T)
if(log(runif(n = 1,min = 0,max = 1))<=thact)
{
ratcur<-ratcand
mlikcur<-ratcand
#if(printable.opt)print(paste("update ratcur through MTMCMC = ", ratcur))
varcurb<-MTMCMC.forw$varcur
acc_moves<-acc_moves+1
id<-bittodec(varcurb)+1
if(j<glob.model$burnin)
{
distrib_of_proposals[2]<-distrib_of_proposals[2]+1
}else
{
if(exists("statistics1")){
statistics1[id,11]<-statistics1[id,11] + 1
statistics1[id,4]<-statistics1[id,4] + 1
}
p.post<- (p.post + varcurb)
}
}else if(j<glob.model$burnin && distrib_of_proposals[2]>1)
{
distrib_of_proposals[2]<-distrib_of_proposals[2] - 1
}
if((MTMCMC.forw$mlikglob<mlikglob))
{
#if(printable.opt)print(paste("update waic.glob MTMCMC.forw = ", MTMCMC.forw$waicglob))
#if(printable.opt)print(paste("update waic.glob.mlik MTMCMC.forw = ", MTMCMC.forw$mlikglob))
waicglob<-MTMCMC.forw$waicglob
varglob<-MTMCMC.forw$varglob
modglob<-MTMCMC.forw$modglob
}
if((MTMCMC.back$mlikglob<mlikglob))
{
#if(printable.opt)print(paste("update waic.glob MTMCMC.back = ", MTMCMC.back$waicglob))
#if(printable.opt)print(paste("update waic.glob.mlik MTMCMC.back= ", MTMCMC.back$mlikglob))
waicglob<-MTMCMC.back$waicglob
varglob<-MTMCMC.back$varglob
modglob<-MTMCMC.back$modglob
}
}else if(LocImprove == 2)
{
if(printable.opt)print("Try greedy heuristic imptovements")
buf.change <- array(data = 1,dim = Nvars)
buf.change[which(varcur - varcurb!=0)]=0
#buf.opt <- buf.change
#buf.opt[floor(runif(n = n.size,min = 1,max = Nvars+0.999999))] = 1
if(objective ==0)
{
objold<-waiccur
objcur<-waiccand
}else
{
objold<- -mlikcur
objcur<- -mlikcand
}
model = list(statid = 4 + LocImprove, change = buf.change,
varcur = varcur,varold = varcurb, switch.type = switch.type.buf,mlikcur = mlikcur,objcur = objcur, objold = objold, reverse=FALSE)
GREEDY.forw<-learnlocalND(model)
ids = which(buf.change == 1)
model$varcur <- GREEDY.forw$varcur
model$varcur[ids] = 1 - model$varcur[ids]
model$mlikcur<- -Inf
model$waiccur<- Inf
model$reverse = TRUE
ratcand<-GREEDY.forw$mlikcur
if(objective ==0)
{
model$objold<-waiccur
}else
{
model$objold<- -ratcand
}
if(switch.type.buf==5)
{
model$switch.type <- 6
}
else if(switch.type.buf==6)
{
model$switch.type <- 5
}
GREEDY.back<-learnlocalND(model)
GREEDY.p.forw<-GREEDY.forw$log.prob.cur
GREEDY.p.back<-GREEDY.back$log.prob.fix
#if(log(runif(n = 1,min = 0,max = 1))<=(ratcand - ratcur - GREEDY.forw$log.prob.cur + GREEDY.forw$log.prob.fix + GREEDY.back$log.prob.cur - GREEDY.back$log.prob.fix))
thact<-sum(ratcand, - ratcur, - GREEDY.forw$log.prob.cur,GREEDY.forw$log.prob.fix,GREEDY.back$log.prob.cur,-GREEDY.back$log.prob.fix,na.rm=T)
if(log(runif(n = 1,min = 0,max = 1))<=thact)
{
ratcur<-ratcand
mlikcur<-ratcand
if(printable.opt)print(paste("update ratcur through ND = ", ratcur))
varcurb<-GREEDY.forw$varcur
acc_moves<-acc_moves+1
id<-bittodec(varcurb)+1
if(j<glob.model$burnin)
{
distrib_of_proposals[3]<-distrib_of_proposals[3]+1
}else
{
if(exists("statistics1")){
statistics1[id,12]<-statistics1[id,12] + 1
statistics1[id,4]<-statistics1[id,4] + 1
}
p.post<- (p.post + varcurb)
}
}else if(j<glob.model$burnin && distrib_of_proposals[3]>1)
{
distrib_of_proposals[3]<-distrib_of_proposals[3] - 1
}
if((GREEDY.forw$mlikglob<mlikglob))
{
if(printable.opt)print(paste("update waic.glob ND.forw = ", GREEDY.forw$waicglob))
if(printable.opt)print(paste("update waic.glob.mlik ND.forw = ", GREEDY.forw$mlikglob))
waicglob<-GREEDY.forw$waicglob
varglob<-GREEDY.forw$varglob
modglob<-GREEDY.forw$modglob
}
if((GREEDY.back$mlikglob<mlikglob))
{
if(printable.opt)print(paste("update waic.glob ND.back = ", GREEDY.back$waicglob))
if(printable.opt)print(paste("update waic.glob.mlik ND.back= ", GREEDY.back$mlikglob))
waicglob<-GREEDY.back$waicglob
varglob<-GREEDY.back$varglob
modglob<-GREEDY.back$modglob
}
}
}
#}),abort = function(){if(printable.opt)print("error");varcur<-varcurb;closeAllConnections();options(error=traceback); onerr<-TRUE})
if(thin_rate!=-1)
{
if(acc_moves == accept_old && j>glob.model$burnin && j%%as.integer(thin_rate)==0) #carry out smart thinning
{
if(!is.null(varcurb))
{
p.post<- (p.post + varcurb)
thin_count <- thin_count +1
id<-bittodec(varcurb)+1
if(exists("statistics1"))
{
statistics1[id,4]<-statistics1[id,4] + 1
}
}
}
}
accept_old <- acc_moves
p2<-p.post/acc_moves
if(j>glob.model$burnin && (recalc.margin >= 2^Nvars) && sum(p2)!=0)
{
p.add <<- as.array(p2)
}
eps.emp<-normprob(p1,p2)
etm <- proc.time()
delta.time <- (etm[3] - stm[3])/60.0
}
if(is.null(modglob))
{
vect<-buildmodel(max.cpu = 1,varcur.old = varglob,statid = 3, switch.type = 8)
res.par <- lapply(X = vect, FUN = fitmodel)
modglob<-res.par[[1]]$fm
}
#!#print the results
if(printable.opt)print(paste(j," iterations completed in total"))
#if(printable.opt)print(paste("WAIC.glob = ", waicglob))
etm <- proc.time()
tt<-(etm[3]-stm[3])/60.0
acc_ratio <- acc_moves/j.a
if(printable.opt)print(paste(j," moves proposed in total, ", acc_moves," of them accepted, acceptance ratio is ",acc_ratio))
if(printable.opt)print(paste("posterior distribution ofproposals is", distrib_of_proposals))
if(exists("statistics1"))
{
bayes.res<-post_proceed_results(statistics1)
m.post<-statistics1[,4]/j.a
}else if(exists("hashStat"))
{
bayes.res<-post_proceed_results_hash(hashStat)
m.post<-NULL
}
else
{
bayes.res<-NULL
m.post<-NULL
}
return(list(model=modglob, vars=varglob, waic = waicglob, mlik = mlikglob, time=(tt), freqs = distrib_of_proposals, acc_ratio = acc_ratio, p.post = p.post/acc_moves, m.post = m.post, p.post.freq = p.post, eps=eps.emp, bayes.results = bayes.res))
},
#save big.data results, if the latter are available
save_results_csv = function(statistics1, filename)
{
write.big.matrix(x = statistics1,filename = filename)
},
#vizualize the results graphically if the latter are available
visualize_results = function(statistics1, template, mds_size, crit,draw_dist = FALSE)
{
ids = NULL
if(crit$mlik){
ids<-c(ids,which(statistics1[,1]==-100000))
ids<-c(ids,which(statistics1[,1]==-Inf))}
#ids<-c(ids,which(statistics1[,1]>0))
if(crit$waic){
ids<-c(ids,which(statistics1[,2]==Inf))
ids<-c(ids,which(statistics1[,3]==Inf))}
if(crit$dic){
ids<-c(ids,which(is.na(statistics1[,3])))}
if(length(ids)!=0)
{
if(crit$mlik)
mlik.lim<-c(min(statistics1[-ids,1],na.rm = TRUE),max(statistics1[-ids,1],na.rm = TRUE))
if(crit$waic)
waic.lim<-c(min(statistics1[-ids,2],na.rm = TRUE),max(statistics1[-ids,2],na.rm = TRUE))
if(crit$dic)
dic.lim<-c(min(statistics1[-ids,3],na.rm = TRUE),max(statistics1[-ids,3],na.rm = TRUE))
}else
{
if(crit$mlik)
mlik.lim<-c(min(statistics1[,1],na.rm = TRUE),max(statistics1[,1],na.rm = TRUE))
if(crit$waic)
waic.lim<-c(min(statistics1[,2],na.rm = TRUE),max(statistics1[,2],na.rm = TRUE))
if(crit$dic)
dic.lim<-c(min(statistics1[,3],na.rm = TRUE),max(statistics1[,3],na.rm = TRUE))
}
norm<-0.5*sqrt(sum(statistics1[,4],na.rm = TRUE))
if(crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_legend.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_legend.jpg",sep = ""))
plot(xlab = "posterior probability of a visit found", ylab="visit type",c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(7,7,7,-1,-1,-1,-1),ylim = c(0,9), xlim=c(0,1),pch=19, col = 7,cex= c(2,2,2,0,0,0,0))
points(c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(6,6,6,-1,-1,-1,-1),pch=8, col = 5,cex= c(1,2,3,0,0,0,0))
points(c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(1,1,1,-1,-1,-1,-1),pch=2, col = 2,cex= c(1,2,3,0,0,0,0))
points(c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(2,2,2,-1,-1,-1,-1),pch=3, col = 3,cex= c(1,2,3,0,0,0,0))
points(c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(3,3,3,-1,-1,-1,-1),pch=4, col = 4,cex= c(1,2,3,0,0,0,0))
points(c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(4,4,4,-1,-1,-1,-1),pch=6, col = 6,cex=c(1,2,3,0,0,0,0))
points(c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(5,5,5,-1,-1,-1,-1),pch=1, col = 1,cex= c(1,2,3,0,0,0,0))
points(c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(8,8,8,-1,-1,-1,-1),pch=19, col = 2,cex= c(2,2,2,0,0,0,0))
legend(x = 0.35,y = 1.5,legend = "- SA 1 local optimization accepted",bty="n" )
legend(x = 0.35,y = 2.5,legend = "- MTMCMC local optimization accepted",bty="n" )
legend(x = 0.35,y = 3.5,legend = "- GREEDY local optimization accepted",bty="n" )
legend(x = 0.35,y = 4.5,legend = "- SA 2 local optimization accepted",bty="n" )
legend(x = 0.35,y = 5.5,legend = "- NO local optimization accepted",bty="n" )
legend(x = 0.35,y = 6.5,legend = "- Totally accepted",bty="n" )
legend(x = 0.35,y = 7.5,legend = "- Totally explored",bty="n" )
legend(x = 0.35,y = 8.5,legend = "- Bayes formula based posterior",bty="n" )
dev.off()
if(printable.opt)print(paste("drawing ",workdir,template,"_mlik.jpg",sep = ""))
jpeg(file=paste(workdir,template,"_mlik.jpg",sep = ""))
plot(ylim = mlik.lim, xlab = "model_id", ylab="MLIK" , statistics1[,1],pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,1],pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,1],pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,1],pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,1],pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,1],pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,1],pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$waic)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_waic.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_waic.jpg",sep = ""))
plot(ylim = waic.lim, xlab = "model_id", ylab="WAIC" ,statistics1[,2],pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,2],pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,2],pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,2],pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,2],pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,2],pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,2],pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$dic)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_dic.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_dic.jpg",sep = ""))
plot(ylim = dic.lim, xlab = "model_id", ylab="DIC" ,statistics1[,3],pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,3],pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,3],pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,3],pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,3],pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,3],pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,3],pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$waic && crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_mlik-waic.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_mlik-waic.jpg",sep = ""))
plot(ylim = mlik.lim, xlim = waic.lim,xlab = "WAIC", ylab="MLIK" ,statistics1[,2],statistics1[,1], pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,2],statistics1[,1],pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,2],statistics1[,1],pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,2],statistics1[,1],pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,2],statistics1[,1],pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,2],statistics1[,1],pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,2],statistics1[,1],pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$dic && crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_mlik-dic.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_mlik-dic.jpg",sep = ""))
plot(ylim = mlik.lim, xlim = dic.lim,xlab = "DIC", ylab="MLIK" ,statistics1[,3],statistics1[,1], pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,3],statistics1[,1],pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,3],statistics1[,1],pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,3],statistics1[,1],pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,3],statistics1[,1],pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,3],statistics1[,1],pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,3],statistics1[,1],pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$dic && crit$waic)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_waic-dic.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_waic-dic.jpg",sep = ""))
plot(ylim = waic.lim, xlim = dic.lim,xlab = "WAIC", ylab="DIC" ,statistics1[,3],statistics1[,2], pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,3],statistics1[,2],pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,3],statistics1[,2],pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,3],statistics1[,2],pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,3],statistics1[,2],pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,3],statistics1[,2],pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,3],statistics1[,2],pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
norm1<-(sum(statistics1[,4],na.rm = TRUE))
xyz<-which(!is.na(statistics1[,1]))
xyz<-intersect(xyz,which(statistics1[,1]!=-10000))
moddee<-which(statistics1[,1]==max(statistics1[,1],na.rm = TRUE))[1]
zyx<-array(data = NA,dim = 2 ^(Nvars)+1)
nconsum<-sum(exp(-statistics1[moddee,1]+statistics1[xyz,1]),na.rm = TRUE)
if( nconsum > 0)
{
zyx[xyz]<-exp(statistics1[xyz,1]-statistics1[moddee,1])/nconsum
y.post.lim<-c(0,max(zyx[xyz]))
}else{
zyx[xyz]<-statistics1[xyz,3]/norm1
y.post.lim<-c(0,NaN)
}
if(is.nan(y.post.lim[2]))
y.post.lim[2]<-max(statistics1[,3]/norm1,na.rm = TRUE)
if(is.nan(y.post.lim[2]))
y.post.lim[2]<-1
if(crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_Pr(MID).jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_Pr(MID).jpg",sep = ""))
plot(xlab = "model_id", ylab="Pr(M(model_id)ID)",ylim = y.post.lim, statistics1[,4]/norm1,pch=19, col = 7,cex= 3*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,4]/norm1,pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,4]/norm1,pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,4]/norm1,pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,4]/norm1,pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,4]/norm1,pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,4]/norm1,pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
points(zyx,pch=20, col = 2,cex= 2)
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$waic && crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_waic-Pr(MID).jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_waic-Pr(MID).jpg",sep = ""))
plot(xlim = waic.lim, ylim = y.post.lim,xlab = "WAIC(M)", ylab="Pr(MID)",statistics1[,2],statistics1[,4]/norm1, pch=19, col = 7,cex= 3*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,2],statistics1[,4]/norm1,pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,2],statistics1[,4]/norm1,pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,2],statistics1[,4]/norm1,pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,2],statistics1[,4]/norm1,pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,2],statistics1[,4]/norm1,pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,2],statistics1[,4]/norm1,pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
points(statistics1[,2],zyx,pch=20, col = 2,cex= 2)
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$dic && crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_dic-Pr(MID).jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_dic-Pr(MID).jpg",sep = ""))
plot(xlim = dic.lim, ylim = y.post.lim,xlab = "dic(M)", ylab="Pr(MID)",statistics1[,3],statistics1[,4]/norm1, pch=19, col = 7,cex= 3*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,3],statistics1[,4]/norm1,pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,3],statistics1[,4]/norm1,pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,3],statistics1[,4]/norm1,pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,3],statistics1[,4]/norm1,pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,3],statistics1[,4]/norm1,pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,3],statistics1[,4]/norm1,pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
points(statistics1[,3],zyx,pch=20, col = 2,cex= 2)
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$mlik)
{
jpeg(file=paste(workdir,template,"_mlik-Pr(MID).jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
plot(xlim = mlik.lim,ylim = y.post.lim, xlab = "MLIK", ylab="Pr(MID)",statistics1[,1],statistics1[,4]/norm1, pch=19, col = 7,cex= 3*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,1],statistics1[,4]/norm1,pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/statistics1[,3]*3 +1,0))
points(statistics1[,1],statistics1[,4]/norm1,pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/statistics1[,4]*3 +1,0))
points(statistics1[,1],statistics1[,4]/norm1,pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/statistics1[,4]*3 +1,0))
points(statistics1[,1],statistics1[,4]/norm1,pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/statistics1[,4]*3 +1,0))
points(statistics1[,1],statistics1[,4]/norm1,pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/statistics1[,4]*3 +1,0))
points(statistics1[,1],statistics1[,4]/norm1,pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/statistics1[,4]*3 +1,0))
points(statistics1[,1],zyx,pch=20, col = 2,cex= 2)
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(draw_dist)
{
if(printable.opt)print("Calculating distance matrix, may take a significant amount of time, may also produce errors if your machine does not have enough memory")
capture.output({withRestarts(tryCatch(capture.output({
lldd<-2^(Nvars)+1
moddee<-which(zyx==max(zyx,na.rm = TRUE))
iidr<-which(statistics1[moddee,1]==max(statistics1[moddee,1],na.rm = TRUE))
iidr<-which(statistics1[moddee[iidr],3]==max(statistics1[moddee[iidr],3],na.rm = TRUE))
moddee<-moddee[iidr]
if(length(moddee)>1)
moddee<-moddee[1]
vec<-dectobit.alt(moddee-1)
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
df = data.frame(varcur)
for(i in 1:(lldd-1))
{
if(i==moddee)
{
next
}else
{
vec<-dectobit.alt(i-1)
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
df<-cbind(df,varcur)
#colnames(x = df)[i] <- paste("solution ",i)
}
}
df<-t(df)
x<-dist(x = df,method = "binary")
dists<-c(0,x[1:lldd-1])
#length(dists)
#which(dists==0)
})), abort = function(){onerr<-TRUE})})
if(crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_distance-mlik.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_distance-MLIK.jpg",sep = ""))
plot(xlab = "x = |M* - M| = distance from the main mode", ylab="MLIK(M)",ylim = mlik.lim,y=c(statistics1[moddee,1],statistics1[-moddee,1]),x=dists,pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(y=c(statistics1[moddee,1],statistics1[-moddee,1]),x=dists,pch=8, col = ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,5,0),cex= ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,c(statistics1[moddee,4],statistics1[-moddee,4])/norm+1,0))
points(y=c(statistics1[moddee,1],statistics1[-moddee,1]),x=dists,pch=2, col = ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,2,0),cex= ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,c(statistics1[moddee,10],statistics1[-moddee,10])/norm+1,0))
points(y=c(statistics1[moddee,1],statistics1[-moddee,1]),x=dists,pch=3, col = ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,3,0),cex= ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,c(statistics1[moddee,11],statistics1[-moddee,11])/norm+1,0))
points(y=c(statistics1[moddee,1],statistics1[-moddee,1]),x=dists,pch=4, col = ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,4,0),cex= ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,c(statistics1[moddee,12],statistics1[-moddee,12])/norm+1,0))
points(y=c(statistics1[moddee,1],statistics1[-moddee,1]),x=dists,pch=6, col = ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,6,0),cex= ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,c(statistics1[moddee,13],statistics1[-moddee,13])/norm+1,0))
points(y=c(statistics1[moddee,1],statistics1[-moddee,1]),x=dists,pch=1, col = ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,1,0),cex= ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,c(statistics1[moddee,14],statistics1[-moddee,14])/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$waic)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_distance-waic.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_distance-waic.jpg",sep = ""))
plot(xlab = "x = |M* - M| = distance from the main mode", ylab="WAIC(M)",ylim = waic.lim,y=c(statistics1[moddee,2],statistics1[-moddee,2]),x=dists,pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(y=c(statistics1[moddee,2],statistics1[-moddee,2]),x=dists,pch=8, col = ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,5,0),cex= ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,c(statistics1[moddee,4],statistics1[-moddee,4])/norm+1,0))
points(y=c(statistics1[moddee,2],statistics1[-moddee,2]),x=dists,pch=2, col = ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,2,0),cex= ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,c(statistics1[moddee,10],statistics1[-moddee,10])/norm+1,0))
points(y=c(statistics1[moddee,2],statistics1[-moddee,2]),x=dists,pch=3, col = ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,3,0),cex= ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,c(statistics1[moddee,11],statistics1[-moddee,11])/norm+1,0))
points(y=c(statistics1[moddee,2],statistics1[-moddee,2]),x=dists,pch=4, col = ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,4,0),cex= ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,c(statistics1[moddee,12],statistics1[-moddee,12])/norm+1,0))
points(y=c(statistics1[moddee,2],statistics1[-moddee,2]),x=dists,pch=6, col = ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,6,0),cex= ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,c(statistics1[moddee,13],statistics1[-moddee,13])/norm+1,0))
points(y=c(statistics1[moddee,2],statistics1[-moddee,2]),x=dists,pch=1, col = ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,1,0),cex= ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,c(statistics1[moddee,14],statistics1[-moddee,14])/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$dic)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_distance-dic.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_distance-dic.jpg",sep = ""))
plot(xlab = "x = |M* - M| = distance from the main mode", ylab="DIC(M)",ylim = dic.lim,y=c(statistics1[moddee,3],statistics1[-moddee,3]),x=dists,pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(y=c(statistics1[moddee,3],statistics1[-moddee,3]),x=dists,pch=8, col = ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,5,0),cex= ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,c(statistics1[moddee,4],statistics1[-moddee,4])/norm+1,0))
points(y=c(statistics1[moddee,3],statistics1[-moddee,3]),x=dists,pch=2, col = ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,2,0),cex= ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,c(statistics1[moddee,10],statistics1[-moddee,10])/norm+1,0))
points(y=c(statistics1[moddee,3],statistics1[-moddee,3]),x=dists,pch=3, col = ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,3,0),cex= ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,c(statistics1[moddee,11],statistics1[-moddee,11])/norm+1,0))
points(y=c(statistics1[moddee,3],statistics1[-moddee,3]),x=dists,pch=4, col = ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,4,0),cex= ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,c(statistics1[moddee,12],statistics1[-moddee,12])/norm+1,0))
points(y=c(statistics1[moddee,3],statistics1[-moddee,3]),x=dists,pch=6, col = ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,6,0),cex= ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,c(statistics1[moddee,13],statistics1[-moddee,13])/norm+1,0))
points(y=c(statistics1[moddee,3],statistics1[-moddee,3]),x=dists,pch=1, col = ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,1,0),cex= ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,c(statistics1[moddee,14],statistics1[-moddee,14])/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_distance-Pr(MID).jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_distance-Pr(MID).jpg",sep = ""))
plot(xlab = "x = |M* - M| = distance from the main mode",ylim = y.post.lim, ylab="Pr(MID)",y=c(statistics1[moddee,4],statistics1[-moddee,4])/norm1,x=dists,pch=19, col = 7,cex= 3*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(y=c(statistics1[moddee,4],statistics1[-moddee,4])/norm1,x=dists,pch=8, col = ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,5,0),cex= ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,c(statistics1[moddee,4],statistics1[-moddee,4])/norm+1,0))
points(y=c(statistics1[moddee,4],statistics1[-moddee,4])/norm1,x=dists,pch=2, col = ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,2,0),cex= ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,c(statistics1[moddee,10],statistics1[-moddee,10])/norm+1,0))
points(y=c(statistics1[moddee,4],statistics1[-moddee,4])/norm1,x=dists,pch=3, col = ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,3,0),cex= ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,c(statistics1[moddee,11],statistics1[-moddee,11])/norm+1,0))
points(y=c(statistics1[moddee,4],statistics1[-moddee,4])/norm1,x=dists,pch=4, col = ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,4,0),cex= ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,c(statistics1[moddee,12],statistics1[-moddee,12])/norm+1,0))
points(y=c(statistics1[moddee,4],statistics1[-moddee,4])/norm1,x=dists,pch=6, col = ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,6,0),cex= ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,c(statistics1[moddee,13],statistics1[-moddee,13])/norm+1,0))
points(y=c(statistics1[moddee,4],statistics1[-moddee,4])/norm1,x=dists,pch=1, col = ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,1,0),cex= ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,c(statistics1[moddee,14],statistics1[-moddee,14])/norm+1,0))
points(y= c(zyx[moddee],zyx[-moddee]),x=dists,pch=20, col = 2,cex= 2)
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_mds-Pr(MID).jpg",sep = ""))
if(printable.opt)print("Calculating distance matrix, may take a significant amount of time, may also produce errors if your machine does not have enough memory")
capture.output({withRestarts(tryCatch(capture.output({
# further address subset of the set of the best solution of cardinality 1024
if(lldd>mds_size)
{
lldd<-mds_size
quant<-(sort(statistics1[,1],decreasing = TRUE)[lldd+1])
indmds<-which(statistics1[,1]>quant)
length(indmds)
}else{
quant<- -Inf
indmds<-1:(lldd)
}
vec<-dectobit.alt(moddee-1)
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
df = data.frame(varcur)
for(i in 1:(lldd-1))
{
if(i==moddee)
{
next
}else
{
vec<-dectobit.alt(indmds[i]-1)
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
df<-cbind(df,varcur)
#colnames(x = df)[i] <- paste("solution ",i)
}
}
df<-t(df)
x<-dist(x = df,method = "binary")
dists<-c(0,x[1:lldd-1])
fit.mds <- cmdscale(d = x,eig=FALSE, k=2) # k is the number of dim
#fit.mds # view results
x.mds <- fit.mds[,1]
y.mds <- fit.mds[,2]
jpeg(file=paste(workdir,template,"_mds_map_posteriors.jpg",sep = ""))
plot(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=2,pch = 10,cex= c(zyx[moddee],zyx[setdiff(indmds, moddee)])*50,0)
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=2,pch = 10,cex= c(zyx[moddee],zyx[setdiff(indmds, moddee)])*50,0)
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=7,pch = 19,cex= 0.4)
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=1,pch = 19,cex= 0.01)
dev.off()
})), abort = function(){onerr<-TRUE})})
}
}
},
#calculates posterior probabilities based on a current search
post_proceed_results = function(statistics1)
{
xyz<-which(!is.na(statistics1[,1]))
g.results[4,2] <- length(xyz)
xyz<-intersect(xyz,which(statistics1[,1]!=-10000))
moddee<-which(statistics1[,1]==max(statistics1[,1],na.rm = TRUE))[1]
zyx<-array(data = NA,dim = length(statistics1[,1]))
nconsum<-sum(exp(-statistics1[moddee,1]+statistics1[xyz,1]),na.rm = TRUE)
if( nconsum > 0)
{
zyx[xyz]<-exp(statistics1[xyz,1]-statistics1[moddee,1])/nconsum
}else{
nnnorm<-sum(statistics1[xyz,4],na.rm = T)
if(nnnorm==0)
nnnorm <- 1
zyx[xyz]<-statistics1[xyz,4]/nnnorm
}
statistics1[,15]<-zyx
lldd<-2^(Nvars)+1
p.post<-array(data = 0,dim = Nvars)
for(i in xyz)
{
vec<-dectobit(i-1)
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
p.post <- (p.post + varcur*statistics1[i,15])
}
if(!exists("p.post")||is.null(p.post)||sum(p.post,na.rm = T)==0 || sum(p.post,na.rm = T)>Nvars)
{
p.post <- array(data = 0.5,dim = Nvars)
}
return(list(p.post = p.post, m.post = zyx, s.mass = sum(exp(statistics1[xyz,1]),na.rm = TRUE)))
},
post_proceed_results_hash = function(hashStat)
{
if(save.beta)
{
if(allow_offsprings==0||Nvars>Nvars.max)
{
if(fparam[1]=="Const")
{
linx<-Nvars + 3
}else
{
linx<-Nvars + 1 + 3
}
}else
{
if(fparam[1]=="Const")
{
linx<-Nvars.max + 3
}else
{
linx<-Nvars.max + 1 + 3
}
}
}else
{
linx <- 3
}
lHash<-length(hashStat)
mliks <- values(hashStat)[which((1:(lHash * linx)) %% linx == 1)]
xyz<-which(mliks!=-10000)
g.results[4,2] <- lHash
moddee<-which( mliks ==max( mliks ,na.rm = TRUE))[1]
zyx<-array(data = NA,dim = lHash)
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
if( nconsum > 0)
{
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}else{
diff<-0-mliks[moddee]
mliks<-mliks+diff
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}
keysarr <- as.array(keys(hashStat))
p.post<-array(data = 0,dim = Nvars)
for(i in 1:lHash)
{
if(is.na(zyx[i]))
{
del(x = keysarr[i],hash = hashStat)
next
}
#vec<-dectobit(strtoi(keysarr[i], base = 0L)-1) # we will have to write some function that would handle laaaaargeee integers!
varcur<- as.integer(strsplit(keysarr[i],split = "")[[1]])
if(length(which(is.na(varcur)))>0)
{
del(x = keysarr[i],hash = hashStat)
next
}
if(length(varcur)>Nvars)
varcur<-varcur[1:Nvars]
p.post <- (p.post + varcur*zyx[i])
}
if(!exists("p.post") || is.null(p.post) || sum(p.post,na.rm = T)==0 || sum(p.post,na.rm = T)>Nvars)
{
p.post <- array(data = 0.5,dim = Nvars)
}
#values(hashStat)[which((1:(lHash * linx)) %%linx == 4)]<-zyx
return(list(p.post = p.post, m.post = zyx, s.mass = sum(exp(mliks),na.rm = TRUE)))
},
calculate_quality_measures = function(vect,n,truth)
{
rmse.pi <- array(data = 0,Nvars)
bias.pi <- array(data = 0,Nvars)
for(i in 1:n)
{
bias.pi <- (bias.pi + (vect[,i]-truth))
rmse.pi <- (rmse.pi + (vect[,i]^2+truth^2 - 2*vect[,i]*truth))
}
bias.pi <- bias.pi/n
rmse.pi <- rmse.pi/n
return(list(bias.pi = bias.pi, rmse.pi = rmse.pi))
},
forecast=function(covariates,nvars,link.g)
{
ids<-which(!is.na(statistics1[,15]))
res<-0
for(i in ids)
{
res<-res + statistics1[i,15]*link.g(sum(statistics1[i,16:nvars]*covariates,na.rm = T))
}
return(list(forecast=res))
},
forecast.matrix=function(covariates,link.g)
{
res<-NULL
ncases <- dim(covariates)[1]
formula.cur<-as.formula(paste(fparam[1],"/2 ~",paste0(fparam,collapse = "+")))
nvars <- Nvars
if(save.beta)
{
if(exists("statistics1"))
{
ids<-which(!is.na(statistics1[,15]))
lids<-length(ids)
statistics1[ids,(17:(nvars+16))][which(is.na(statistics1[ids,(17:(nvars+16))]))]<-0
res<-t(statistics1[ids,15])%*%g(statistics1[ids,(16:(nvars+16))]%*%t(model.matrix(object = formula.cur,data = covariates)))
}else if(exists("hashStat"))
{
if(allow_offsprings==0)
{
if(fparam[1]=="Const")
{
linx<-Nvars + 3
}else
{
linx<-Nvars + 1 + 3
}
}else
{
if(fparam[1]=="Const")
{
linx<-Nvars.max + 3
}else
{
linx<-Nvars.max + 1 + 3
}
}
lHash<-length(hashStat)
mliks <- values(hashStat)[which((1:(lHash * linx)) %% linx == 1)]
betas <- values(hashStat)[which((1:(lHash * linx)) %% linx == 4)]
for(i in 1:(Nvars-1))
{
betas<-cbind(betas,values(hashStat)[which((1:(lHash * linx)) %% linx == (4+i))])
}
betas<-cbind(betas,values(hashStat)[which((1:(lHash * linx)) %% linx == (0))])
betas[which(is.na(betas))]<-0
xyz<-which(mliks!=-10000)
g.results[4,2] <- lHash
moddee<-which( mliks ==max( mliks ,na.rm = TRUE))[1]
zyx<-array(data = NA,dim = lHash)
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
if( nconsum > 0)
{
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}else{
diff<-0-mliks[moddee]
mliks<-mliks+diff
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}
res<-t(zyx)%*%g(betas%*%t(model.matrix(object = formula.cur,data = covariates)))
}
}else
{
warning("No betas were saved. Prediction is impossible. Please change the search parameters and run the search again.")
}
return(list(forecast=res))
},
forecast.matrix.na=function(covariates,link.g,betas,mliks.in)
{
formula2<-as.formula(paste(fparam[1],"/2 ~ -1+",paste0(fparam,collapse = "+")))
current.na.action <- options('na.action')
options(na.action='na.pass')
covariates<- as.data.frame(model.matrix(object = formula2,data = covariates,na.action=na.include))
options('na.action'= current.na.action$na.action)
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "I",replacement = "Z")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "(",replacement = "o")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = ")",replacement = "c")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "+",replacement = "p")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "-",replacement = "m")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "*",replacement = "M")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "|",replacement = "a")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "&",replacement = "A")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = ",",replacement = "k")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = " ",replacement = "")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "\n",replacement = "")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "cFALSE",replacement = "c")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "cTRUE",replacement = "c")
fparam.tmp<-stri_replace_all(str = fparam,fixed = "I",replacement = "Z")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = "(",replacement = "o")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = ")",replacement = "c")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = "+",replacement = "p")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = "-",replacement = "m")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = ",",replacement = "k")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = "*",replacement = "M")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = "|",replacement = "a")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = "&",replacement = "A")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = " ",replacement = "")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = "\n",replacement = "")
formula.cur<-as.formula(paste(fparam.tmp[1],"/2 ~",paste0(fparam.tmp,collapse = "+")))
na.ids<-matrix(data = 0,nrow = dim(covariates)[1],ncol = dim(covariates)[2])
na.ids[which(is.na(covariates))]<-1
na.bc<-colSums(na.ids)
ids.betas<-NULL
res.na<-array(NA, dim(covariates)[1])
for(i in which(na.bc>0))
{
if(((names(covariates)[i] %in% fparam.tmp)||(paste0("Zo",names(covariates)[i],"c",collapse = "")%in%fparam.tmp)))
{
ids.betas<-c(ids.betas,which(fparam.tmp==names(covariates)[i] | fparam.tmp == paste0("Zo",names(covariates)[i],"c",collapse = "")))
next
}
else
{
na.ids[which(is.na(covariates[,i])),i]<-0
na.bc[i]<-0
}
}
na.br<-rowSums(na.ids)
lv.br<-sort(unique(na.br))
if(lv.br[1]==0)
{
ids<-which(na.br==0)
mliks<-mliks.in
xyz<-which(mliks!=-10000)
moddee<-which( mliks ==max( mliks ,na.rm = TRUE))[1]
zyx<-array(data = NA,dim = length(mliks))
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
betas1<-betas
betas1[which(is.na(betas1))]<-0
if( nconsum > 0)
{
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}else{
diff<-0-mliks[moddee]
mliks<-mliks+diff
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}
covariates1<- covariates[ids,]
res<-t(zyx)%*%g(betas1%*%t(model.matrix(object = as.formula(formula.cur),data = covariates1)))
res.na[ids]<-res
rm(mliks)
rm(res)
rm(zyx)
rm(xyz)
rm(covariates1)
rm(betas1)
}
k.b<-0
for(i in which(na.bc>0))
{
k.b<-k.b+1
w.ids<-which(!is.na(betas[,(ids.betas[k.b]+1)]))
for(j in lv.br)
{
if(j==0)
next
ids<-((which(na.ids[,i]==1 & na.br==j & is.na(res.na))))
if(length(ids)==0)
next
var.del <- NULL
for(iii in which(na.bc>0))
{
if(iii==i)
next
if(sum(na.ids[ids,iii])>0)
{
var.del<-(which(fparam.tmp==names(covariates)[iii] | fparam.tmp == paste0("I(",names(covariates)[iii],")",collapse = "")))
if(length(var.del>0))
{
w.ids<-union(w.ids,which(!is.na(betas[,(var.del+1)])))
}
}
}
mliks<-mliks.in[-w.ids]
if(length(mliks)==0)
{
warning("not enough models for bagging in prediction. please train the model longer!")
return(-1)
}
xyz<-which(mliks!=-10000)
moddee<-which( mliks ==max( mliks ,na.rm = TRUE))[1]
zyx<-array(data = NA,dim = length(mliks))
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
betas1<-betas[-w.ids,]
betas1[which(is.na(betas1))]<-0
if( nconsum > 0)
{
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}else{
diff<-0-mliks[moddee]
mliks<-mliks+diff
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}
covariates1<- as.matrix(covariates[ids,])
covariates1[which(is.na(covariates1))]<-0
covariates1<-as.data.frame(covariates1)
res<-t(zyx)%*%g(betas1%*%t(model.matrix(object = formula.cur,data = covariates1)))
res.na[ids]<-res
rm(mliks)
rm(zyx)
rm(xyz)
rm(res)
rm(covariates1)
}
}
return(list(forecast = res.na))
},
forecast.matrix.na.fast=function(covariates,link.g,betas,mliks.in)
{
formula.cur<-as.formula(paste(fparam[1],"/2 ~",paste0(fparam,collapse = "+")))
na.ids<-matrix(data = 0,nrow = dim(covariates)[1],ncol = dim(covariates)[2])
na.ids[which(is.na(covariates))]<-1
na.bc<-colSums(na.ids)
ids.betas<-NULL
res.na<-array(NA, dim(covariates)[1])
for(i in which(na.bc>0))
{
if(((names(covariates)[i] %in% fparam)||(paste0("I(",names(covariates)[i],")",collapse = "")%in%fparam)))
{
ids.betas<-c(ids.betas,which(fparam==names(covariates)[i] | fparam == paste0("I(",names(covariates)[i],")",collapse = "")))
next
}
else
{
na.ids[which(is.na(covariates[,i])),i]<-0
na.bc[i]<-0
}
}
na.br<-rowSums(na.ids)
lv.br<-sort(unique(na.br))
if(lv.br[1]==0)
{
ids<-which(na.br==0)
mliks<-mliks.in
xyz<-which(mliks!=-10000)
moddee<-which( mliks ==max( mliks ,na.rm = TRUE))[1]
zyx<-array(data = NA,dim = lHash)
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
betas1<-betas
betas1[which(is.na(betas1))]<-0
if( nconsum > 0)
{
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}else{
diff<-0-mliks[moddee]
mliks<-mliks+diff
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}
covariates1<- covariates[ids,]
res<-t(zyx)%*%g(betas1%*%t(model.matrix(object = formula.cur,data = covariates1)))
res.na[ids]<-res
rm(mliks)
rm(res)
rm(zyx)
rm(xyz)
rm(covariates1)
rm(betas1)
}
ids<-(which(is.na(res.na)))
for(iii in which(na.bc>0))
{
if(sum(na.ids[ids,iii])>0)
{
var.del<-(which(fparam==names(covariates)[iii] | fparam == paste0("I(",names(covariates)[iii],")",collapse = "")))
if(length(var.del>0))
{
w.ids<-union(w.ids,which(!is.na(betas[,(var.del+1)])))
}
}
}
mliks<-mliks.in[-w.ids]
if(length(mliks)==0)
{
warning("not enough models for bagging in prediction. please train the model longer!")
return(-1)
}
xyz<-which(mliks!=-10000)
moddee<-which( mliks ==max( mliks ,na.rm = TRUE))[1]
zyx<-array(data = NA,dim = length(mliks))
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
betas1<-betas[-w.ids,]
betas1[which(is.na(betas1))]<-0
if( nconsum > 0)
{
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}else{
diff<-0-mliks[moddee]
mliks<-mliks+diff
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}
covariates1<- as.matrix(covariates[ids,])
covariates1[which(is.na(covariates1))]<-0
covariates1<-as.data.frame(covariates1)
res<-t(zyx)%*%g(betas1%*%t(model.matrix(object = formula.cur,data = covariates1)))
res.na[ids]<-res
rm(mliks)
rm(zyx)
rm(xyz)
rm(res)
rm(covariates1)
return(list(forecast = res.na))
}
)
)
options(bigmemory.typecast.warning=FALSE)
aliaksah/EMJMCMC2016 documentation built on July 27, 2023, 5:48 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions runemjmcmc parall.gmj do.call.emjmcmc simplifyposteriors simplify.formula estimate.glm parallelize estimate.gamma.cpen estimate.inla.poisson estimate.inla estimate.bas.lm erf sigmoid estimate.bigm estimate.speedglm estimate.elnet estimate.logic.lm pinferunemjmcmc mcgmjpse mcgmjpar LogicRegr estimate.logic.lm.jef estimate.logic.lm.tCCH estimate.logic.bern.tCCH estimate.logic.bern runpar.infer simplifyposteriors.infer estimate.logic.lm estimate.logic.lm.tCCH estimate.logic.bern.tCCH estimate.logic.bern estimate.logic.glm factorial estimate.bas.glm m
Documented in do.call.emjmcmc erf estimate.bas.glm estimate.bas.lm estimate.bigm estimate.elnet estimate.glm estimate.inla estimate.logic.glm estimate.logic.lm estimate.speedglm factorial LogicRegr m parallelize parall.gmj pinferunemjmcmc runemjmcmc sigmoid simplify.formula simplifyposteriors
#rm(list = ls(all = TRUE))
#install the following packages if required!
if(!("sp" %in% rownames(installed.packages())))
install.packages("sp")
if(!("INLA" %in% rownames(installed.packages())))
install.packages("INLA", repos=c(getOption("repos"), INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE)
if(!("bigmemory" %in% rownames(installed.packages())))
install.packages("bigmemory")
if(!("ade4" %in% rownames(installed.packages())))
install.packages("ade4")
if(!("hash" %in% rownames(installed.packages())))
install.packages("hash")
if(!("speedglm" %in% rownames(installed.packages())))
install.packages("speedglm")
if(!("stringi" %in% rownames(installed.packages())))
install.packages("stringi")
if(!("biglm" %in% rownames(installed.packages())))
install.packages("biglm")
if(!("glmnet" %in% rownames(installed.packages())))
install.packages("glmnet")
if(!("BAS" %in% rownames(installed.packages())))
install.packages("https://github.com/aliaksah/EMJMCMC2016/blob/master/examples/BAS%20archive/BAS_0.91.tar.gz?raw=true", repos = NULL)
if(!("BAS" %in% rownames(installed.packages())))
install.packages("BAS")
if(!("MASS" %in% rownames(installed.packages())))
install.packages("MASS")
if(!("parallel" %in% rownames(installed.packages())))
install.packages("parallel")
if(!("stats" %in% rownames(installed.packages())))
install.packages("stats")
#if(!("inline" %in% rownames(installed.packages())))
# install.packages("inline")
if(!("RCurl" %in% rownames(installed.packages())))
install.packages("RCurl")
if(!("gnlm" %in% rownames(installed.packages())))
install.packages("gnlm")
#library(inline)
library(gnlm)
library(glmnet)
library(biglm)
library(hash)
library(sp)
library(INLA)
library(parallel)
library(bigmemory)
library(MASS)
library(ade4)
library(BAS)# should be version 0.9 !!!! otherwise some dependencies might not work!
library(stringi)
require(stats)
#includes <- '#include <sys/wait.h>'
#code <- 'int wstat; while (waitpid(-1, &wstat, WNOHANG) > 0) {};'
#wait <- cfunction(body=code, includes=includes, convention='.C')
m<-function(a,b)a*b
estimate.bas.glm <- function(formula, data, family, prior, logn)
{
#only poisson and binomial families are currently adopted
X <- model.matrix(object = formula,data = data)
out <- bayesglm.fit(x = X, y = data[,1], family=family,coefprior=prior)
# use dic and aic as bic and aic correspondinly
return(list(mlik = out$logmarglik,waic = -(out$deviance + 2*out$rank) , dic = -(out$deviance + logn*out$rank),summary.fixed =list(mean = coefficients(out))))
}
factorial<-function(x) ifelse(x<=170,gamma(abs(x) + 1),gamma(171))
estimate.logic.glm <- function(formula, data, family, n, m, r = 1)
{
X <- model.matrix(object = formula,data = data)
out <- bayesglm.fit(x = X, y = data[,51], family=family,coefprior=aic.prior())
p <- out$rank
fmla.proc<-as.character(formula)[2:3]
fobserved <- fmla.proc[1]
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam <-stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj<-(stri_count_fixed(str = fparam, pattern = "&"))
sj<-sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj<-sj+1
Jprior <- sum(log(factorial(sj)/((m^sj)*2^(2*sj-2))))
mlik = (-(out$deviance + log(n)*(out$rank)) + 2*(Jprior))/2+n
if(mlik==-Inf)
mlik = -10000
return(list(mlik = mlik,waic = -(out$deviance + 2*out$rank) , dic = -(out$deviance + log(n)*out$rank),summary.fixed =list(mean = coefficients(out))))
}
#define the function estimating parameters of a given Bernoulli logic regression with Jeffrey's prior
estimate.logic.bern = function(formula = NULL, data, family = binomial(), n=1000, m=50, r = 1,k.max=21)
{
if(length(formula)==0)
return(list(mlik = -10000 + rnorm(1,0,1),waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
if(is.na(formula))
return(list(mlik = -10000 + rnorm(1,0,1),waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
out = glm(formula = formula,data = data, family=family)
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc=as.character(formula)[2:3]
fobserved = fmla.proc[1]
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
Jprior = sum(log(factorial(sj)/((m^sj)*2^(2*sj-2))))
mlik = (-(out$deviance + log(n)*(out$rank)) + 2*(Jprior))/2+n
if(mlik==-Inf)
mlik = -10000
return(list(mlik = mlik,waic = -(out$deviance + 2*out$rank) , dic = -(out$deviance + log(n)*out$rank),summary.fixed =list(mean = coefficients(out))))
}
#define the function estimating parameters of a given Bernoulli logic regression with robust g prior
estimate.logic.bern.tCCH = function(formula = NULL,y.id = 51, data, n=1000, m=50, r = 1, p.a = 1, p.b = 2, p.r = 1.5, p.s = 0, p.v=-1, p.k = 1,k.max=21)
{
if(length(formula)==0)
return(list(mlik = -10000 + rnorm(1,0,1),waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
if(is.na(formula))
return(list(mlik = -10000 + rnorm(1,0,1),waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
X = scale(model.matrix(object = formula,data = data),center = T,scale = F)
X[,1] = 1
fmla.proc=as.character(formula)[2:3]
out = glm(formula = as.formula(paste0(fmla.proc[1],"~X+0")),data=data,family = binomial())
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
beta=coef(out)[-1]
if(length(which(is.na(beta)))>0)
{
return(list(mlik = -10000 + rnorm(1,0,1),waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
p.v = (n+1)/(p+1)
sout = summary(out)
J.a.hat = 1/sout$cov.unscaled[1,1]
if(length(beta)>0&&length(beta)==(dim(sout$cov.unscaled)[1]-1)&&length(which(is.na(beta)))==0)
{
Q = t(beta)%*%solve(sout$cov.unscaled[-1,-1])%*%beta
}else{
return(list(mlik = -10000 + rnorm(1,0,1),waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
Jprior = sum(log(factorial(sj)/((m^sj)*2^(2*sj-2))))
mlik = (logLik(out)- 0.5*log(J.a.hat) - 0.5*p*log(p.v) -0.5*Q/p.v + log(beta((p.a+p)/2,p.b/2)) + log(phi1(p.b/2,p.r,(p.a+p.b+p)/2,(p.s+Q)/2/p.v,1-p.k))+Jprior + p*log(r)+n)
if(is.na(mlik)||mlik==-Inf)
mlik = -10000+ rnorm(1,0,1)
return(list(mlik = mlik,waic = AIC(out) , dic = BIC(out),summary.fixed =list(mean = coefficients(out))))
}
#define the function estimating parameters of a given Gaussian logic regression with robust g prior
estimate.logic.lm.tCCH = function(formula = NULL, data, n=1000, m=50, r = 1, p.a = 1, p.b = 2, p.r = 1.5, p.s = 0, p.v=-1, p.k = 1,k.max=21)
{
if(is.null(formula))
return(list(mlik = -10000,waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
fmla.proc=as.character(formula)[2:3]
fobserved = fmla.proc[1]
if(fmla.proc[2]=="-1")
return(list(mlik = -10000,waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
out = lm(formula = formula,data = data)
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
Jprior = prod(factorial(sj)/((m^sj)*2^(2*sj-2)))
p.v = (n+1)/(p+1)
R.2 = summary(out)$r.squared
mlik = (-0.5*p*log(p.v) -0.5*(n-1)*log(1-(1-1/p.v)*R.2) + log(beta((p.a+p)/2,p.b/2)) - log(beta(p.a/2,p.b/2)) + log(phi1(p.b/2,(n-1)/2,(p.a+p.b+p)/2,p.s/2/p.v,R.2/(p.v-(p.v-1)*R.2))) - hypergeometric1F1(p.b/2,(p.a+p.b)/2,p.s/2/p.v,log = T)+log(Jprior) + p*log(r)+n)
if(mlik==-Inf||is.na(mlik)||is.nan(mlik))
mlik = -10000
return(list(mlik = mlik,waic = AIC(out)-n , dic = BIC(out)-n,summary.fixed =list(mean = coef(out))))
}
#define the function estimating parameters of a given Gaussian logic regression with Jeffrey's prior
estimate.logic.lm = function(formula= NULL, data, n, m, r = 1,k.max=21)
{
if(is.null(formula))
return(list(mlik = -10000,waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
out = lm(formula = formula,data = data)
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc=as.character(formula)[2:3]
fobserved = fmla.proc[1]
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
Jprior = prod(factorial(sj)/((m^sj)*2^(2*sj-2)))
mlik = (-BIC(out)+2*log(Jprior) + 2*p*log(r)+n)/2
if(mlik==-Inf)
mlik = -10000
return(list(mlik = mlik,waic = AIC(out)-n , dic = BIC(out)-n,summary.fixed =list(mean = coef(out))))
}
#define the function simplifying logical expressions at the end of the search
simplifyposteriors.infer=function(X,posteriors,th=0.0000001,thf=0.5, resp)
{
todel = which(posteriors[,2]<th)
if(length(todel)>0)
posteriors=posteriors[-todel,]
rhash=hash()
for(i in 1:length(posteriors[,1]))
{
expr=posteriors[i,1]
#print(expr)
res=model.matrix(data=X,object = as.formula(paste0(resp,"~",expr)))
res[,1]=res[,1]-res[,2]
ress=c(stri_flatten(res[,1],collapse = ""),stri_flatten(res[,2],collapse = ""),posteriors[i,2],expr)
ress[1] = stri_sub(ress[1],from = 1,to = 9999)
if(!(ress[1] %in% values(rhash)||(ress[2] %in% values(rhash))))
rhash[[ress[1]]]=ress
else
{
if(ress[1] %in% keys(rhash))
{
rhash[[ress[1]]][3]= (as.numeric(rhash[[ress[1]]][3]) + as.numeric(ress[3]))
if(stri_length(rhash[[ress[1]]][4])>stri_length(expr))
rhash[[ress[1]]][4]=expr
}
else
{
rhash[[ress[2]]][3]= (as.numeric(rhash[[ress[2]]][3]) + as.numeric(ress[3]))
if(stri_length(rhash[[ress[2]]][4])>stri_length(expr))
rhash[[ress[2]]][4]=expr
}
}
}
res=as.data.frame(t(values(rhash)[c(3,4),]))
res$V1=as.numeric(as.character(res$V1))
tokeep = which(res$V1>thf)
if(length(tokeep)>0)
{
res=res[tokeep,]
}else
warning(paste0("No features with posteriors above ",thf,". Returning everything"))
res=res[order(res$V1, decreasing = T),]
clear(rhash)
rm(rhash)
tokeep = which(res[,1]>1)
if(length(tokeep)>0)
res[tokeep,1]=1
colnames(res)=c("posterior","feature")
rownames(res) = NULL
return(res)
}
#define a function performing the map step for a given thread
runpar.infer=function(vect)
{
ret = NULL
tryCatch({
set.seed(as.integer(vect$cpu))
do.call(runemjmcmc, vect[1:(length(vect)-5)])
vals=values(hashStat)
fparam=mySearch$fparam
cterm=max(vals[1,],na.rm = T)
ppp=mySearch$post_proceed_results_hash(hashStat = hashStat)
post.populi=sum(exp(values(hashStat)[1,][1:vect$NM]-cterm),na.rm = T)
betas = NULL
mliks = NULL
if(vect$save.beta){
#get the modes of beta coefficients for the explored models
Nvars=mySearch$Nvars
linx =mySearch$Nvars+4
lHash=length(hashStat)
mliks = values(hashStat)[which((1:(lHash * linx)) %% linx == 1)]
betas = values(hashStat)[which((1:(lHash * linx)) %% linx == 4)]
for(i in 1:(Nvars-1))
{
betas=cbind(betas,values(hashStat)[which((1:(lHash * linx)) %% linx == (4+i))])
}
betas=cbind(betas,values(hashStat)[which((1:(lHash * linx)) %% linx == (0))])
}
preds = NULL
if(vect$predict)
{
preds=mySearch$forecast.matrix.na(link.g = vect$link, covariates = (vect$test),betas = betas,mliks.in = mliks)$forecast
}
ret = list(post.populi = post.populi, p.post = ppp$p.post, cterm = cterm, preds = preds, fparam = fparam, betas = betas, mliks = mliks )
if(length(cterm)==0){
vect$cpu=as.integer(vect$cpu)+as.integer(runif(1,1,10000))
if(vect$cpu<50000)
ret = runpar.infer(vect)
else
ret = NULL
}
},error = function(err){
print(paste0("error in thread", vect[length(vect)]))
print(err)
vect$cpu=as.integer(vect$cpu)+as.integer(runif(1,1,10000))
if(vect$cpu<50000)
ret = runpar.infer(vect)
else
ret =err
},finally = {
#clear(hashStat)
#rm(hashStat)
#rm(vals)
gc()
return(ret)
})
}
#define the function estimating parameters of a given Bernoulli logic regression with Jeffrey's prior
estimate.logic.bern = function(formula, data, family = binomial(), n=1000, m=50, r = 1,k.max=21)
{
if(is.null(formula))
return(list(mlik = -10000 + rnorm(1,0,1),waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
out = glm(formula = formula,data = data, family=family)
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc=as.character(formula)[2:3]
fobserved = fmla.proc[1]
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
Jprior = sum(log(factorial(sj)/((m^sj)*2^(2*sj-2))))
mlik = (-(out$deviance + log(n)*(out$rank)) + 2*(Jprior))/2+n
if(mlik==-Inf)
mlik = -10000
return(list(mlik = mlik,waic = -(out$deviance + 2*out$rank) , dic = -(out$deviance + log(n)*out$rank),summary.fixed =list(mean = coefficients(out))))
}
#define the function estimating parameters of a given Bernoulli logic regression with robust g prior
estimate.logic.bern.tCCH = function(formula = NULL,y.id = 51, data, n=1000, m=50, r = 1, p.a = 1, p.b = 2, p.r = 1.5, p.s = 0, p.v=-1, p.k = 1,k.max=21)
{
if(is.null(formula))
return(list(mlik = -10000 + rnorm(1,0,1),waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
X = scale(model.matrix(object = formula,data = data),center = T,scale = F)
X[,1] = 1
fmla.proc=as.character(formula)[2:3]
out = glm(formula = as.formula(paste0(fmla.proc[1],"~X+0")),data=data,family = binomial())
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
beta=coef(out)[-1]
if(length(which(is.na(beta)))>0)
{
return(list(mlik = -10000 + rnorm(1,0,1),waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
p.v = (n+1)/(p+1)
sout = summary(out)
J.a.hat = 1/sout$cov.unscaled[1,1]
if(length(beta)>0&&length(beta)==(dim(sout$cov.unscaled)[1]-1)&&length(which(is.na(beta)))==0)
{
Q = t(beta)%*%solve(sout$cov.unscaled[-1,-1])%*%beta
}else{
return(list(mlik = -10000 + rnorm(1,0,1),waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
Jprior = sum(log(factorial(sj)/((m^sj)*2^(2*sj-2))))
mlik = (logLik(out)- 0.5*log(J.a.hat) - 0.5*p*log(p.v) -0.5*Q/p.v + log(beta((p.a+p)/2,p.b/2)) + log(phi1(p.b/2,p.r,(p.a+p.b+p)/2,(p.s+Q)/2/p.v,1-p.k))+Jprior + p*log(r)+n)
if(is.na(mlik)||mlik==-Inf)
mlik = -10000+ rnorm(1,0,1)
return(list(mlik = mlik,waic = AIC(out) , dic = BIC(out),summary.fixed =list(mean = coefficients(out))))
}
#define the function estimating parameters of a given Gaussian logic regression with robust g prior
estimate.logic.lm.tCCH = function(formula = NULL, data, n=1000, m=50, r = 1, p.a = 1, p.b = 2, p.r = 1.5, p.s = 0, p.v=-1, p.k = 1,k.max=21)
{
if(is.null(formula))
return(list(mlik = -10000,waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
fmla.proc=as.character(formula)[2:3]
fobserved = fmla.proc[1]
if(fmla.proc[2]=="-1")
return(list(mlik = -10000,waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
out = lm(formula = formula,data = data)
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
Jprior = prod(factorial(sj)/((m^sj)*2^(2*sj-2)))
p.v = (n+1)/(p+1)
R.2 = summary(out)$r.squared
mlik = (-0.5*p*log(p.v) -0.5*(n-1)*log(1-(1-1/p.v)*R.2) + log(beta((p.a+p)/2,p.b/2)) - log(beta(p.a/2,p.b/2)) + log(phi1(p.b/2,(n-1)/2,(p.a+p.b+p)/2,p.s/2/p.v,R.2/(p.v-(p.v-1)*R.2))) - hypergeometric1F1(p.b/2,(p.a+p.b)/2,p.s/2/p.v,log = T)+log(Jprior) + p*log(r)+n)
if(mlik==-Inf||is.na(mlik)||is.nan(mlik))
mlik = -10000
return(list(mlik = mlik,waic = AIC(out)-n , dic = BIC(out)-n,summary.fixed =list(mean = coef(out))))
}
#define the function estimating parameters of a given Gaussian logic regression with Jeffrey's prior
estimate.logic.lm.jef = function(formula= NULL, data, n, m, r = 1,k.max=21)
{
if(is.null(formula))
return(list(mlik = -10000,waic =10000 , dic = 10000,summary.fixed =list(mean = 1)))
out = lm(formula = formula,data = data)
p = out$rank
if(p>k.max)
{
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = 0)))
}
fmla.proc=as.character(formula)[2:3]
fobserved = fmla.proc[1]
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]=stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam =stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj=(stri_count_fixed(str = fparam, pattern = "&"))
sj=sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj=sj+1
Jprior = prod(factorial(sj)/((m^sj)*2^(2*sj-2)))
mlik = (-BIC(out)+2*log(Jprior) + 2*p*log(r)+n)/2
if(mlik==-Inf)
mlik = -10000
return(list(mlik = mlik,waic = AIC(out)-n , dic = BIC(out)-n,summary.fixed =list(mean = coef(out))))
}
LogicRegr = function(formula, data, family = "Gaussian",prior = "J",report.level = 0.5, d = 20, cmax = 5, kmax = 20, p.and = 0.9, p.not = 0.05, p.surv = 0.1,ncores = -1, n.mods = 1000 ,advanced = list(presearch = T,locstop = F ,estimator = estimate.logic.bern.tCCH,estimator.args = list(data = data.example,n = 1000, m = 50,r=1),recalc_margin = 250, save.beta = F,interact = T,relations = c("","lgx2","cos","sigmoid","tanh","atan","erf"),relations.prob =c(0.4,0.0,0.0,0.0,0.0,0.0,0.0),interact.param=list(allow_offsprings=1,mutation_rate = 300,last.mutation = 5000, max.tree.size = 1, Nvars.max = 100,p.allow.replace=0.9,p.allow.tree=0.2,p.nor=0.2,p.and = 1),n.models = 10000,unique = T,max.cpu = 4,max.cpu.glob = 4,create.table = F,create.hash = T,pseudo.paral = T,burn.in = 50,outgraphs=F,print.freq = 1000,advanced.param = list(
max.N.glob=as.integer(10),
min.N.glob=as.integer(5),
max.N=as.integer(3),
min.N=as.integer(1),
printable = F)))
{
data.example = data
advanced$formula = formula
advanced$data = data
advanced$interact.param$Nvars.max = d
advanced$interact.param$ max.tree.size= cmax - 1
advanced$interact.param$p.and = p.and
advanced$interact.param$p.nor = p.not
advanced$interact.param$p.allow.tree = p.surv
if(!prior %in% c("J","G"))
{
warning("Wrong prior supplied. J (for Jeffrey's) and G (for robust g) priors are allowd only. Setting J as default.")
prior = "J"
}
if(!family %in% c("Gaussian","Bernoulli"))
{
warning("Wrong familty supplied. Gaussian and Bernoulli families are allowd only. Setting Gaussian as default.")
family = "Gaussian"
}
if(family == "Gaussian")
{
if(prior == "J")
{
advanced$estimator = estimate.logic.lm.jef
advanced$estimator.args = list(data = data, n = dim(data)[1], m =stri_count_fixed(as.character(formula)[3],"+"),k.max = kmax)
}else{
advanced$estimator = estimate.logic.lm.tCCH
advanced$estimator.args = list(data = data, n = dim(data)[1], m =stri_count_fixed(as.character(formula)[3],"+"),k.max = kmax)
}
}else{
if(prior == "J")
{
advanced$estimator = estimate.logic.bern
advanced$estimator.args = list(data = data, n = dim(data)[1], m =stri_count_fixed(as.character(formula)[3],"+"),k.max = kmax)
}else{
advanced$estimator = estimate.logic.bern.tCCH
advanced$estimator.args = list(data = data, n = dim(data)[1], m =stri_count_fixed(as.character(formula)[3],"+"),k.max = kmax)
}
}
if(ncores<1)
ncores = detectCores()
return(pinferunemjmcmc(n.cores = ncores,report.level = report.level, simplify = T, num.mod.best = n.mods, predict = F, runemjmcmc.params = advanced))
}
mcgmjpar = function(X,FUN,mc.cores) mclapply(X= X,FUN = FUN,mc.preschedule = T,mc.cores = mc.cores)
mcgmjpse = function(X,FUN,mc.cores) lapply(X,FUN)
pinferunemjmcmc = function(n.cores = 4, mcgmj = mcgmjpar, report.level = 0.5, simplify = F, num.mod.best = 1000, predict = F, test.data = 1, link.function = function(z)z, runemjmcmc.params)
{
if(predict)
{
runemjmcmc.params$save.beta = T
if(length(test.data)==0)
{
warning("Test data is not provided. No predictions will be made!")
}
}
params = list(runemjmcmc.params)[rep(1,n.cores)]
for(i in 1:n.cores)
{
params[[i]]$test = test.data
params[[i]]$link = link.function
params[[i]]$predict = predict
params[[i]]$NM = num.mod.best
params[[i]]$cpu=i
}
M = n.cores
#results = runpar.infer(params[[1]])
results=mcgmj(X = params,FUN = runpar.infer,mc.cores = n.cores)
#print(results)
#clean up
gc()
#prepare the data structures for final analysis of the runs
compmax = runemjmcmc.params$interact.param$Nvars.max + 1
resa=array(data = 0,dim = c(compmax,M*3))
post.popul = array(0,M)
max.popul = array(0,M)
nulls=NULL
not.null=1
#check which threads had non-zero exit status
for(k in 1:M)
{
if(length(results[[k]])<=1||length(results[[k]]$cterm)==0||length(results[[k]]$p.post)!=runemjmcmc.params$interact.param$Nvars.max)
{
nulls=c(nulls,k)
#warning(paste0("Thread ",k,"did not converge or was killed by OS!"))
next
}
else
{
not.null = k
}
}
if(length(nulls) == M)
{
warning("All threads did not converge or gave an error! Returning stats from the threads only!")
return(list(feat.stat = NULL,predictions = NULL,allposteriors = NULL, threads.stats = results))
}
#for all of the successful runs collect the results into the corresponding data structures
for(k in 1:M)
{
if(k %in% nulls)
{
results[[k]]=results[[not.null]]
}
max.popul[k]=results[[k]]$cterm
post.popul[k]=results[[k]]$post.populi
resa[,k*3-2]=c(results[[k]]$fparam,"Post.Gen.Max")
resa[,k*3-1]=c(results[[k]]$p.post,results[[k]]$cterm)
resa[,k*3]=rep(post.popul[k],length(results[[k]]$p.post)+1)
}
#renormalize estimates of the marginal inclusion probabilities
#based on all of the runs
ml.max=max(max.popul)
post.popul=post.popul*exp(-ml.max+max.popul)
p.gen.post=post.popul/sum(post.popul)
#perform BMA of the redictions across the runs
pred = NULL
if(predict){
pred = results[[1]]$preds*p.gen.post[1]
if(M > 1) {
for(i in 2:M)
{
pred=pred+results[[i]]$preds*p.gen.post[i]
}
}
}
hfinal=hash()
for(ii in 1:M)
{
resa[,ii*3]=p.gen.post[ii]*as.numeric(resa[,ii*3-1])
resa[length(resa[,ii*3]),ii*3]=p.gen.post[ii]
if(p.gen.post[ii]>0)
{
for(jj in 1:(length(resa[,ii*3])-1))
{
if(resa[jj,ii*3]>0)
{
if(as.integer(has.key(hash = hfinal,key =resa[jj,ii*3-2]))==0)
hfinal[[resa[jj,ii*3-2]]]=as.numeric(resa[jj,ii*3])
else
hfinal[[resa[jj,ii*3-2]]]=hfinal[[resa[jj,ii*3-2]]]+as.numeric(resa[jj,ii*3])
}
}
}
}
posteriors=values(hfinal)
clear(hfinal)
#delete the unused further variables
rm(hfinal)
rm(resa)
rm(post.popul)
rm(max.popul)
#simplify the found trees and their posteriors
posteriors=as.data.frame(posteriors)
posteriors=data.frame(X=row.names(posteriors),x=posteriors$posteriors)
posteriors$X=as.character(posteriors$X)
res1 = NULL
if(simplify){
res1=simplifyposteriors.infer(X = runemjmcmc.params$data,posteriors = posteriors, thf = report.level,resp = as.character(runemjmcmc.params$formula)[2])
rownames(res1) = NULL
res1$feature = as.character(res1$feature)
}
posteriors=posteriors[order(posteriors$x, decreasing = T),]
colnames(posteriors)=c("feature","posterior")
rm(params)
gc()
return(list(feat.stat = cbind(res1$feature,res1$posterior),predictions = pred,allposteriors = posteriors, threads.stats = results))
}
estimate.logic.lm <- function(formula, data, n, m, r = 1)
{
out <- lm(formula = formula,data = data)
p <- out$rank
fmla.proc<-as.character(formula)[2:3]
fobserved <- fmla.proc[1]
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam <-stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]]
sj<-(stri_count_fixed(str = fparam, pattern = "&"))
sj<-sj+(stri_count_fixed(str = fparam, pattern = "|"))
sj<-sj+1
Jprior <- prod(factorial(sj)/((m^sj)*2^(2*sj-2)))
#tn<-sum(stri_count_fixed(str = fmla.proc[2], pattern = "I("))
mlik = (-BIC(out)+2*log(Jprior) + 2*p*log(r)+n)/2
if(mlik==-Inf)
mlik = -10000
return(list(mlik = mlik,waic = AIC(out)-n , dic = BIC(out)-n,summary.fixed =list(mean = coef(out))))
}
#estimate elastic nets
estimate.elnet <- function(formula,response, data, family,alpha)
{
X <- model.matrix(object = formula,data = data)
if(dim(X)[2]<=2)
return(list(mlik = -10000,waic = 10000 , dic = 10000,summary.fixed =list(mean = array(0,dim=dim(X)[2]))))
out <- glmnet(x=X[,-1], y = data[[response]], family=family, a=alpha)
dout<- as.numeric(-deviance(out)[[out$dim[2]]])
return(list(mlik = dout,waic = -dout , dic = -dout,summary.fixed =list(mean = coef(out)[,out$dim[2]])))
}
# use dic and aic as bic and aic correspondinly
estimate.speedglm <- function(formula, data, family, prior, logn) # weird behaviour, bad control of singularity
{
X <- model.matrix(object = formula,data = data)
out <- speedglm.wfit(y = data[,1], X = X, intercept=FALSE, family=family,eigendec = T, method = "Cholesky")
if(prior == "AIC")
return(list(mlik = -out$aic ,waic = -(out$deviance + 2*out$rank) , dic = -(out$RSS),summary.fixed =list(mean = out$coefficients)))
if(prior=="BIC")
return(list(mlik = -out$RSS-logn*out$rank ,waic = -(out$deviance + 2*out$rank) , dic = -(out$RSS+logn*out$rank),summary.fixed =list(mean = out$coefficients)))
}
estimate.bigm <- function(formula, data, family, prior,n, maxit = 2,chunksize = 1000000) # nice behaviour
{
out <- bigglm(data = data, family=family,formula = formula, sandwich = F,maxit = maxit, chunksize = chunksize)
if(prior == "AIC")
return(list(mlik = -AIC(out,k = 2) ,waic = AIC(out,k = 2) , dic = AIC(out,k = n),summary.fixed =list(mean = coef(out))))
if(prior=="BIC")
return(list(mlik = -AIC(out,k = n) ,waic = AIC(out, k = 2) , dic = AIC(out,k = n),summary.fixed =list(mean = coef(out))))
}
sigmoid<- function(x)
{
return(1/(1+(exp(-x))))
}
erf <- function(x)
{
return(2 * pnorm(x * sqrt(2)) - 1)
}
estimate.bas.lm <- function(formula, data, prior, n, g = 0)
{
out <- lm(formula = formula,data = data)
# 1 for aic, 2 bic prior, else g.prior
p <- out$rank
if(prior == 1)
{
ss<-sum(out$residuals^2)
logmarglik <- -0.5*(log(ss)+2*p)
}
else if(prior ==2)
{
ss<-sum(out$residuals^2)
logmarglik <- -0.5*(log(ss)+log(n)*p)
}
else
{
Rsquare <- summary(out)$r.squared
#logmarglik = .5*(log(1.0 + g) * (n - p -1) - log(1.0 + g * (1.0 - Rsquare)) * (n - 1))*(p!=1)
logmarglik = .5*(log(1.0 + g) * (n - p) - log(1.0 + g * (1.0 - Rsquare)) * (n - 1))*(p!=1)
}
# use dic and aic as bic and aic correspondinly
return(list(mlik = logmarglik,waic = AIC(out) , dic = BIC(out),summary.fixed =list(mean = coef(out))))
}
estimate.inla <- function(formula, args)
{
out<-NULL
tryCatch(capture.output({
out <- do.call(inla, c(args,formula = formula))}))
if(is.null(out))
return(list(mlik = -10000,waic = 10000 , dic = 10000, summary.fixed =list(mean = NULL)))
# use dic and aic as bic and aic correspondinly
coef<-out$summary.fixed$mode
coef[1]<-coef[1]+out$summary.hyperpar$mode[1]
return(list(mlik = out$mlik[1],waic = out$waic[1] , dic = out$dic[1], summary.fixed =list(mean = coef)))
}
estimate.inla.poisson <- function(formula, data,r = 1.0/200.0,logn=log(200.0), relat=c("*","+","cos","sigmoid","tanh","atan","sin","erf"))
{
out<-NULL
capture.output({tryCatch(capture.output({
fmla.proc<-as.character(formula)[2:3]
sj<-sum(stri_count_fixed(str = fmla.proc[2],pattern = relat))
out <-inla(family = "poisson",silent = 2L,data = data,formula = formula,control.compute = list(dic = TRUE, waic = TRUE, mlik = TRUE))
}))})
if(is.null(out))
return(list(mlik = -10000+log(r)*(sj),waic = 10000 , dic = 10000, summary.fixed =list(mean = NULL)))
if(length(out$waic[1]$waic)==0)
return(list(mlik = -10000+log(r)*(sj),waic = 10000 , dic = 10000, summary.fixed =list(mean = NULL)))
# use dic and aic as bic and aic correspondinly
coef<-out$summary.fixed$mode
#coef[1]<-coef[1]+out$summary.hyperpar$mode[1]
return(list(mlik = out$mlik[1]+log(r)*(sj),waic = out$waic[1]$waic , dic = out$dic[1]$dic, summary.fixed =list(mean = coef)))
}
estimate.gamma.cpen <- function(formula, data,r = 1.0/1000.0,logn=log(1000.0),relat=c("cos","sigmoid","tanh","atan","sin","erf"))
{
fparam<-NULL
fmla.proc<-as.character(formula)[2:3]
fobserved <- fmla.proc[1]
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam <-stri_split_fixed(str = fmla.proc[2],pattern = "+I",omit_empty = F)[[1]]
sj<-(stri_count_fixed(str = fparam, pattern = "*"))
sj<-sj+(stri_count_fixed(str = fparam, pattern = "+"))
for(rel in relat)
sj<-sj+(stri_count_fixed(str = fparam, pattern = rel))
#sj<-sj+1
tryCatch(capture.output({
out <- glm(formula = formula,data = data, family = gaussian)
# 1 for aic, 2 bic prior, else g.prior
mlik = (-(BIC(out) -2*log(r)*sum(sj))+1000)/2
waic = (out$deviance + 2*out$rank)+10000
dic = (out$deviance + logn*out$rank)+10000
summary.fixed =list(mean = coefficients(out))
}, error = function(err) {
print(err)
mlik = -10000
waic = 10000
dic = 10000
summary.fixed =list(mean = array(0,dim=length(fparam)))
}))
return(list(mlik = mlik,waic = waic , dic = dic,summary.fixed =summary.fixed))
}
parallelize<-function(X,FUN)
{
max.cpu <- length(X)
cl <-makeCluster(max.cpu ,type = paral.type,outfile = "")#outfile = ""
clusterEvalQ(cl = cl,expr = c(library(INLA),library(bigmemory)))
if(exists("statistics"))
{
clusterExport(cl=cl, "statistics")
clusterEvalQ(cl,{statistics <- attach.resource(statistics);1})
}
res.par <- parLapply(cl = cl, X, FUN)
stopCluster(cl)
return(res.par)
}
estimate.glm <- function(formula, data, family, prior, n=1, g = 0)
{
out <- glm(formula = formula, family = family, data = data)
# 1 for aic, 2 bic prior, else g.prior
p <- out$rank
if(prior == 1)
{
logmarglik <- -AIC(out)
}
else if(prior ==2)
{
logmarglik <- -BIC(out)
}
else
{
Rsquare <- summary(out)$r.squared
#logmarglik = .5*(log(1.0 + g) * (n - p -1) - log(1.0 + g * (1.0 - Rsquare)) * (n - 1))*(p!=1)
logmarglik = .5*(log(1.0 + g) * (n - p) - log(1.0 + g * (1.0 - Rsquare)) * (n - 1))*(p!=1)
}
# use dic and aic as bic and aic correspondinly
return(list(mlik = logmarglik,waic = AIC(out) , dic = BIC(out),summary.fixed =list(mean = coef(out))))
}
simplify.formula<-function(fmla,names)
{
fmla.proc<-as.character(fmla)[2:3]
fobserved <- fmla.proc[1]
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam <- names[which(names %in% stri_split_fixed(str = fmla.proc[2],pattern = "+",omit_empty = F)[[1]] )]
return(list(fparam = fparam,fobserved = fobserved))
}
simplifyposteriors<-function(X,posteriors,th=0.0001,thf=0.2, resp)
{
posteriors<-posteriors[-which(posteriors[,2]<th),]
rhash<-hash()
for(i in 1:length(posteriors[,1]))
{
expr<-posteriors[i,1]
#print(expr)
res<-model.matrix(data=X,object = as.formula(paste0(resp,"~",expr)))
ress<-c(stri_flatten(round(res[,2],digits = 4),collapse = ""),stri_flatten(res[,2],collapse = ""),posteriors[i,2],expr)
if(!((ress[1] %in% values(rhash))))
rhash[[ress[1]]]<-ress
else
{
if(ress[1] %in% keys(rhash))
{
rhash[[ress[1]]][3]<- (as.numeric(rhash[[ress[1]]][3]) + as.numeric(ress[3]))
if(stri_length(rhash[[ress[1]]][4])>stri_length(expr))
rhash[[ress[1]]][4]<-expr
}
}
}
res<-as.data.frame(t(values(rhash)[c(3,4),]))
res$V1<-as.numeric(as.character(res$V1))
res<-res[which(res$V1>thf),]
res<-res[order(res$V1, decreasing = T),]
clear(rhash)
rm(rhash)
res[which(res[,1]>1),1]<-1
colnames(res)<-c("posterior","tree")
return(res)
}
do.call.emjmcmc<-function(vect)
{
set.seed(as.integer(vect$cpu))
do.call(runemjmcmc, vect[1:vect$simlen])
vals<-values(hashStat)
fparam<-mySearch$fparam
cterm<-max(vals[1,],na.rm = T)
ppp<-mySearch$post_proceed_results_hash(hashStat = hashStat)
post.populi<-sum(exp(values(hashStat)[1,][1:vect$NM]-cterm),na.rm = T)
clear(hashStat)
#rm(hashStat)
rm(vals)
gc()
return(list(post.populi = post.populi, p.post = ppp$p.post, cterm = cterm, fparam = fparam))
}
parall.gmj <- function(X,M=16,preschedule = F) mclapply(X = X, FUN = do.call.emjmcmc,mc.preschedule = preschedule, mc.cores = M,mc.cleanup = T)
# a function that creates an EMJMCMC2016 object with specified values of some parameters and default values of other parameters
runemjmcmc<-function(formula, data, secondary = vector(mode="character", length=0), latnames="",
estimator,estimator.args = "list",n.models,p.add.default = 1,p.add = 0.5, unique = F,save.beta=F, locstop.nd = F, latent="",max.cpu=4,max.cpu.glob=2,create.table=T, hash.length = 20, presearch=T, locstop =F ,pseudo.paral = F,interact = F,deep.method =1,relations = c("","sin","cos","sigmoid","tanh","atan","erf"),relations.prob =c(0.4,0.1,0.1,0.1,0.1,0.1,0.1),gen.prob = c(1,10,5,1,0),pool.cross = 0.9,p.epsilon = 0.0001, del.sigma = 0.5,pool.cor.prob = F, interact.param=list(allow_offsprings=2,mutation_rate = 100,last.mutation=2000, max.tree.size = 10000, Nvars.max = 100, p.allow.replace = 0.7,p.allow.tree=0.1,p.nor=0.3,p.and = 0.7), prand = 0.01,keep.origin = T, sup.large.n = 5000, recalc_margin = 2^10, create.hash=F,interact.order=1,burn.in=1, eps = 10^6, max.time = 120,max.it = 25000, print.freq = 100,outgraphs=F,advanced.param=NULL, distrib_of_neighbourhoods=t(array(data = c(7.6651604,16.773326,14.541629,12.839445,2.964227,13.048343,7.165434,
0.9936905,15.942490,11.040131,3.200394,15.349051,5.466632,14.676458,
1.5184551,9.285762,6.125034,3.627547,13.343413,2.923767,15.318774,
14.5295380,1.521960,11.804457,5.070282,6.934380,10.578945,12.455602,
6.0826035,2.453729,14.340435,14.863495,1.028312,12.685017,13.806295),dim = c(7,5))), distrib_of_proposals = c(76.91870,71.25264,87.68184,60.55921,15812.39852))
{
#first create the object
assign("data.example",data, envir=globalenv())
variables <- simplify.formula(formula,names(data.example))
assign("fparam.example",variables$fparam, envir=globalenv())
assign("fobserved.example",variables$fobserved, envir=globalenv())
#for(i in 1:length(fparam.example))
#{
# fparam.example[i]<<-paste("I(",variables$fparam[i],")",sep = "")
#}
fparam.tmp<- as.vector(sapply(FUN = paste,"I(",variables$fparam,")",sep="")[,1])
if(latnames[1]!="")
fparam.example<<-c(fparam.tmp,latnames)
else
fparam.example<<-fparam.tmp
#print(fparam.tmp)
#print(fparam.example)
assign("mySearch",EMJMCMC2016(), envir=globalenv())
if(length(secondary)>0)
mySearch$filtered <<- sapply(FUN = paste,"I(",secondary,")",sep="")
mySearch$estimator <<- estimator
mySearch$latnames <<- latnames
mySearch$estimator.args <<- estimator.args
mySearch$latent.formula <<- latent
mySearch$save.beta <<- save.beta
mySearch$prand<<-prand
mySearch$p.add<<-array(p.add,length(fparam.example))
mySearch$p.add.default<<-p.add.default
mySearch$recalc.margin <<- as.integer(recalc_margin)
mySearch$max.cpu <<- as.integer(max.cpu)
mySearch$locstop.nd <<- locstop.nd
mySearch$pool.cor.prob<<-pool.cor.prob
mySearch$sup.large.n<<-as.integer(sup.large.n)
mySearch$max.cpu.glob <<- as.integer(max.cpu.glob)
mySearch$deep.method <<- as.integer(deep.method)
if(interact)
{
mySearch$allow_offsprings <<- as.integer(interact.param$allow_offsprings)
mySearch$mutation_rate <<- as.integer(interact.param$mutation_rate)
mySearch$Nvars.max <<- as.integer(interact.param$Nvars.max)
mySearch$max.tree.size <<- as.integer(interact.param$max.tree.size)
mySearch$p.allow.replace <<- interact.param$p.allow.replace
mySearch$p.allow.tree <<- interact.param$p.allow.tree
mySearch$p.epsilon <<- p.epsilon
mySearch$keep.origin<<- keep.origin
mySearch$sigmas<<-relations
mySearch$sigmas.prob<<-relations.prob
mySearch$del.sigma<<-del.sigma
mySearch$pool.cross<<-pool.cross
mySearch$gen.prob<<-gen.prob
mySearch$p.nor <<- interact.param$p.nor
mySearch$p.and <<- interact.param$p.and
mySearch$last.mutation <<- as.integer(interact.param$last.mutation)
}
if(!is.null(advanced.param))
{
mySearch$max.N.glob<<-as.integer(advanced.param$max.N.glob)
mySearch$min.N.glob<<-as.integer(advanced.param$min.N.glob)
mySearch$max.N<<-as.integer(advanced.param$max.N)
mySearch$min.N<<-as.integer(advanced.param$min.N)
mySearch$printable.opt<<-advanced.param$printable
}
#distrib_of_proposals = с(0,0,0,0,10)
if(exists("hashStat"))
{
clear(hashStat)
remove(hashStat,envir=globalenv())
}
if(exists("statistics1"))
{
remove(statistics,envir=globalenv() )
remove(statistics1,envir=globalenv())
}
if(exists("hash.keys1"))
{
remove(hash.keys,envir=globalenv())
remove(hash.keys1,envir=globalenv())
}
if(create.table)
{
if(pseudo.paral)
mySearch$parallelize <<- lapply
#carry the search (training out)
assign("statistics1",big.matrix(nrow = 2 ^min((length(fparam.example)),hash.length)+1, ncol = 16+length(fparam.example)*save.beta,init = NA, type = "double"), envir=globalenv())
assign("statistics",describe(statistics1), envir=globalenv())
mySearch$g.results[4,1]<<-0
mySearch$g.results[4,2]<<-0
mySearch$p.add <<- array(data = 0.5,dim = length(fparam.example))
if((length(fparam.example))>20)
{
mySearch$hash.length<<-as.integer(hash.length)
mySearch$double.hashing<<-T
hash.keys1 <<- big.matrix(nrow = 2 ^(hash.length)+1, ncol = length(fparam.example),init = 0, type = "char")
hash.keys <<- describe(hash.keys1)
}
}else if(create.hash)
{
assign("hashStat",hash(), envir=globalenv())
mySearch$parallelize <<- lapply
mySearch$hash.length<<-as.integer(20)
mySearch$double.hashing<<-F
}
# now as the object is created run the algorithm
initsol=rbinom(n = length(fparam.example),size = 1,prob = 0.5)
if(unique)
resm<-mySearch$modejumping_mcmc(list(varcur=initsol,locstop=locstop,presearch=presearch,statid=5, distrib_of_proposals =distrib_of_proposals,distrib_of_neighbourhoods=distrib_of_neighbourhoods, eps = eps, trit = n.models*100, trest = n.models, burnin = burn.in, max.time = max.time, maxit = max.it, print.freq = print.freq))
else
resm<-mySearch$modejumping_mcmc(list(varcur=initsol,locstop=locstop,presearch=presearch,statid=5, distrib_of_proposals =distrib_of_proposals,distrib_of_neighbourhoods=distrib_of_neighbourhoods, eps = eps, trit = n.models, trest = n.models*100, burnin = burn.in, max.time = max.time, maxit = max.it, print.freq = print.freq))
ppp<-1
print("MJMCMC is completed")
if(create.table)
{
print("Post Proceed Results")
ppp<-mySearch$post_proceed_results(statistics1 = statistics1)
truth = ppp$p.post # make sure it is equal to Truth column from the article
truth.m = ppp$m.post
truth.prob = ppp$s.mass
ordering = sort(ppp$p.post,index.return=T)
print("pi truth")
sprintf("%.10f",truth[ordering$ix])
sprintf(fparam.example[ordering$ix])
}
else if(create.hash)
{
print("Post Proceed Results")
ppp<-mySearch$post_proceed_results_hash(hashStat = hashStat)
truth = ppp$p.post # make sure it is equal to Truth column from the article
truth.m = ppp$m.post
truth.prob = ppp$s.mass
ordering = sort(ppp$p.post,index.return=T)
print("pi truth")
sprintf("%.10f",truth[ordering$ix])
sprintf(fparam.example[ordering$ix])
}
if(outgraphs)
{
par(mar = c(10,4,4,2) + 4.1)
barplot(resm$bayes.results$p.post,density = 46,border="black",main = "Marginal Inclusion (RM)",ylab="Probability",names.arg = mySearch$fparam,las=2)
barplot(resm$p.post,density = 46,border="black",main = "Marginal Inclusion (MC)",ylab="Probability",names.arg = mySearch$fparam,las=2)
}
return(ppp)
}
# add plot(ppp), summary(ppp), print(ppp), ppp as a class itself, coef(ppp)
EMJMCMC2016 <- setRefClass(Class = "EMJMCMC2016",
fields = list(estimator.args = "list",
max.cpu = "integer",
objective = "integer",
p.prior = "numeric",
min.N = "integer",
estimator = "function",
parallelize = "function",
parallelize.global = "function",
parallelize.hyper = "function",
min.N.randomize = "integer",
max.N.randomize = "integer",
type.randomize = "integer",
thin_rate = "integer",
aa = "numeric",
cc = "numeric",
printable.opt = "logical",
fobserved = "vector",
switch.type = "integer",
n.size ="integer",
deep.method = "integer",
sup.large.n = "integer",
LocImprove = "array",
max.N = "integer",
save.beta = "logical",
keep.origin = "logical",
recalc.margin = "numeric",
max.N.glob = "integer",
min.N.glob = "integer",
max.cpu.glob = "integer",
max.cpu.hyper = "integer",
p.add.default="numeric",
switch.type.glob = "integer",
isobsbinary = "array",
filtered = "vector",
fparam = "vector",
latnames = "vector",
fparam.pool = "vector",
p.add = "array",
latent.formula = "character",
Nvars = "integer",
seed = "integer",
M.nd = "integer",
locstop.nd = "logical",
pool.cor.prob = "logical",
M.mcmc = "integer",
SA.param = "list",
p.epsilon = "numeric",
p.allow.tree = "numeric",
p.nor = "numeric",
p.and = "numeric",
sigmas.prob ="numeric",
del.sigma = "numeric",
pool.cross = "numeric",
gen.prob = "numeric",
sigmas = "vector",
p.allow.replace = "numeric",
max.tree.size = "integer",
double.hashing = "logical",
prand = "numeric",
hash.length = "integer",
update.marg.mc = "logical",
Nvars.max = "integer",
Nvars.init = "integer",
last.mutation = "integer",
allow_offsprings = "integer",
mutation_rate = "integer",
g.results = "big.matrix"
),
methods = list(
#class constructor
initialize = function(estimator.function = inla, estimator.args.list = list(family = "gaussian",data = data.example, control.fixed=list(prec=list(default= 0.00001),prec.intercept = 0.00001,mean=list(default= 0),mean.intercept = 0),
control.family = list(hyper = list(prec = list(prior = "loggamma",param = c(0.00001,0.00001),initial = 0))),
control.compute = list(dic = TRUE, waic = TRUE, mlik = TRUE)), search.args.list = NULL,latent.formula = "")
{
estimator <<- estimator.function
estimator.args <<- estimator.args.list
latent.formula <<- latent.formula
g.results <<- big.matrix(nrow = 4,ncol = 2)
g.results[1,1]<- -Inf
g.results[1,2]<- 1
g.results[2,1]<- Inf
g.results[2,2]<- 1
g.results[3,1]<- Inf
g.results[3,2]<- 1
g.results[4,1]<- 0
g.results[4,2]<- 0
if(is.null(search.args.list))
{
max.cpu <<- as.integer(Nvars*0.05 + 1)
objective <<- as.integer(1)
if(Sys.info()['sysname']=="Windows")
{
parallelize <<- lapply
parallelize.global <<- lapply
parallelize.hyper <<- lapply
}
else
{
parallelize <<- mclapply
parallelize.global <<- mclapply
parallelize.hyper <<- mclapply
}
Nvars <<- as.integer(length(fparam.example))
min.N <<- as.integer(Nvars/6)
min.N.glob <<- as.integer(Nvars/3)
max.N.glob <<- as.integer(Nvars/2)
max.N <<- as.integer(Nvars/5)
switch.type.glob <<- as.integer(2)
min.N.randomize <<- as.integer(1)
max.N.randomize <<- as.integer(1)
deep.method<<- as.integer(1)
type.randomize <<- as.integer(3)
pool.cor.prob<<-F
prand<<-0.01
max.cpu.glob <<- as.integer(Nvars*0.05 + 1)
max.cpu.hyper <<- as.integer(2)
sup.large.n<<-as.integer(1000)
save.beta <<- FALSE
filtered<<-vector(mode="character", length=0)
printable.opt <<- FALSE
keep.origin<<-FALSE
thin_rate<<- as.integer(-1)
p.allow.tree <<- 0.6
p.epsilon<<- 0.0001
latnames<<-""
p.add.default<<-1
p.allow.replace <<- 0.3
sigmas<<-c("","sin","cos","sigmoid","tanh","atan","erf")
sigmas.prob<<-c(0.4,0.1,0.1,0.1,0.1,0.1,0.1)
del.sigma<<-0.5
pool.cross<<-0.9
gen.prob<<-c(1,1,1,1,1)
p.nor <<- 0.3
p.and <<- 0.7
max.tree.size<<- as.integer(15)
Nvars.max <<- as.integer(Nvars)
Nvars.init <<- as.integer(Nvars)
allow_offsprings <<- as.integer(0)
mutation_rate <<- as.integer(100)
locstop.nd <<-FALSE
double.hashing <<- (Nvars > 20)
hash.length <<- as.integer(25)
filtered<<-vector(mode="character", length=0)
aa <<- 0.9
cc <<- 0.0
M.nd <<- as.integer(min(Nvars,100))
M.mcmc <<- as.integer(5)
SA.param <<- list(t.min = 0.0001,t.init = 10, dt = 3, M = as.integer(min(Nvars/5+1,20)))
fobserved <<- fobserved.example
switch.type <<- as.integer(2)
n.size <<- as.integer(10)
LocImprove <<- as.array(c(50,50,50,50,150))
isobsbinary <<- as.array(0:(length(fparam.example)-1))
fparam <<- fparam.example
fparam.pool <<- fparam.example
p.add <<- array(data = 0.5,dim = Nvars)
if(exists("statistics"))
{
recalc.margin <<- 2^Nvars
}else if(exists("statistics1"))
{
recalc.margin <<- 2^Nvars
}else
{
recalc.margin <<- 2^Nvars
}
last.mutation<<-as.integer(2^(Nvars/2)*0.01)
seed <<- as.integer(runif(n = 1,min = 1,max = 10000))
p.prior <<- runif(n = Nvars, min = 0.5,max = 0.5)
}
else
{
max.cpu <<- as.integer(search.args.list$max.cpu)
objective <<- as.integer(search.args.list$objective)
parallelize <<- search.args.list$parallelize
latnames <<- search.args.list$latnames
parallelize.global <<- search.args.list$parallelize.global
parallelize.hyper <<- search.args.list$parallelize.hyper
p.prior <<- search.args.list$p.prior
min.N <<- as.integer(search.args.list$min.N)
printable.opt <<- search.args.list$printable.opt
min.N.glob <<- as.integer(search.args.list$min.N.glob)
max.N.glob <<- as.integer(search.args.list$max.N.glob)
switch.type.glob <<- as.integer(search.args.list$switch.type.glob)
min.N.randomize <<- as.integer(search.args.list$min.N.randomize)
max.N.randomize <<- as.integer(search.args.list$max.N.randomize)
type.randomize <<- as.integer(search.args.list$type.randomize)
max.cpu.glob <<- as.integer(search.args.list$max.cpu.glob)
locstop.nd <<-search.args.list$locstop.nd
max.cpu.hyper <<- as.integer(search.args.list$max.cpu.hyper)
save.beta <<- search.args.list$save.beta
aa <<- search.args.list$lambda.a
prand<<-search.args.list$prand
p.add.default<<-search.args.list$ p.add.default
sup.large.n<<-search.args.list$sup.large.n
thin_rate <-search.args.list$thin_rate
keep.origin<<-search.args.list$keep.origin
cc <<- search.args.list$lambda.c
pool.cor.prob<<-search.args.list$pool.cor.prob
M.nd <<- as.integer(search.args.list$stepsGreedy)
M.mcmc <<- as.integer(search.args.list$stepsLocMCMC)
SA.param <<- search.args.list$SA.params
fobserved <<- search.args.list$fobserved
switch.type <<- as.integer(search.args.list$fswitch.type)
n.size <<- as.integer(search.args.list$n.size)
LocImprove <<-search.args.list$prior.optimizer.freq
max.N <<- as.integer(search.args.list$max.N)
fparam <<- search.args.list$fparam
fparam.pool <<- search.args.list$fparam
isobsbinary <<- as.array(0:(length(fparam)-1))
p.add <<- as.array(search.args.list$p.add)
recalc.margin <<- search.args.list$recalc.margin
Nvars <<- as.integer(length(fparam))
seed <<- search.args.list$seed
max.tree.size<<- as.integer(search.args.list$max.tree.size)
Nvars.max <<- as.integer(search.args.list$Nvars.max)
Nvars.init <<- as.integer(search.args.list$Nvars)
allow_offsprings <<- as.integer(search.args.list$allow_offsprings)
mutation_rate <<- as.integer(search.args.list$mutation_rate)
p.allow.tree <<- search.args.list$p.allow.tree
p.epsilon <<-search.args.list$p.epsilon
p.allow.replace <<- search.args.list$p.allow.replace
last.mutation<<-as.integer(search.args.list$last.mutation)
p.nor <<- search.args.list$p.nor
p.and <<- search.args.list$p.and
deep.method<<-as.integer(search.args.list$deep.method)
sigmas<<-search.args.list$sigmas
sigmas.prob<<-search.args.list$sigmas.prob
del.sigma<<-search.args.list$del.sigma
pool.cross<<-search.args.list$pool.cross
gen.prob<<-search.args.list$gen.prob
double.hashing <<- search.args.list$double.hashing
hash.length <<- as.integer(search.args.list$hash.length)
}
},
#transform binary numbers to decimal
bittodec.alt = function(bit) #transform a binary vector into a natural number to correspond between vector of solutions and storage array
{
n<-length(bit)
dec <- 0
for(i in 1:n)
{
j<-n-i
dec <- dec + ((2)^j)*bit[i]
}
return(dec)
},
bittodec = function(bit) #transform a binary vector into a natural number to correspond between vector of solutions and storage array
{
if(!double.hashing){
n<-length(bit)
dec <- 0
for(i in 1:n)
{
j<-n-i
dec <- dec + ((2)^j)*bit[i]
}
return(dec)
}
else
{
if(exists("statistics1"))
{
hash.level<-0
dec<- hashing(bit)+1
#print(dec)
sum.one<- sum(bit)*which.max(bit) + sum(bit[Nvars -7:Nvars+1])*Nvars
jjj<-1
while(!add.key(dec,bit,sum.one,T))
{
hash.level<-hash.level+1
bit1<- dectobit.alt(2654435761*(dec+97*sum.one+hash.level*36599)+hash.level*59+hash.level)
dec<- hashing(bit1)+1
#jjj<-jjj+1
#print(dec)
}
#print(jjj)
dec <- dec - 1
}
else if(exists("statistics"))
{
hash.level<-0
dec<- hashing(bit)+1
sum.one<- sum(bit)*which.max(bit) + sum(bit[Nvars -7:Nvars +1])*Nvars
while(!add.key(dec,bit,sum.one,F))
{
hash.level<-hash.level+1
bit1<- dectobit.alt(2654435761*(dec+97*sum.one+hash.level*36599)+hash.level*59+hash.level)
dec<- hashing(bit1)+1
#print(dec)
}
dec <- dec - 1
}
return(dec)
}
},
add.key = function(dec,bit,sum.one,levl)
{
lb<-length(bit)
if(dec>2^hash.length)
return(FALSE)
if(levl)
{
if(is.na(statistics1[dec,1]))
{
statistics1[dec,16]<-sum.one
hash.keys1[dec,]<-bit
return(TRUE)
}
if(is.na(statistics1[dec,16]))
{
statistics1[dec,16]<-sum.one
hash.keys1[dec,]<-bit#c(array(0,dim = Nvars-lb),bit)
return(TRUE)
}
if(statistics1[dec,16]!=sum.one)
return(FALSE)
i<-1
#print(lb)
lb <- length(bit)
while(i<=lb&&(hash.keys1[dec,Nvars-i+1])==bit[lb - i +1])
i<-i+1
return((i-1)==lb)
}
else
{
if(is.na(statistics[dec,1]))
{
statistics[dec,16]<-sum.one
hash.keys[dec,]<-bit
return(TRUE)
}
if(is.na(statistics[dec,16]))
{
statistics[dec,16]<-sum.one
hash.keys[dec,]<-bit#c(array(0,dim = Nvars-lb),bit)
return(TRUE)
}
if(statistics[dec,16]!=sum.one)
return(FALSE)
i<-1
lb <- length(bit)
while(i<=lb&&(hash.keys[dec,Nvars-i+1])==bit[lb - i +1])
i<-i+1
return((i-1)==lb)
}
},
hashing = function(bit)# a hash function to find where to place the key in the hash
{
n<-length(bit)
if(n<hash.length)
return(bittodec.alt(bit))
return(bittodec.alt(bit[(n-hash.length+1):n]))
},
binlog = function (x) # bitwise logorithm (base 2) computations based on Al Kashi's algorithm
{
lx <- length(x)
tol = -lx
y <- 0 # initialise output
b <- 0.5 # initialise mantissa
# arrange the input into a known range
if(lx == 1){
if(x[1] == 0)
return(-Inf)
if(x[1] == 1)
return(0)
}
# move one bit to the left end
# elsewhise
if(x[2]==0 && lx==2)
return(1)
powto<-2^(-c(1:(lx-1)))
float.x<-sum(x[2:lx]*powto)
x <- 1 + float.x
y <- lx -1
f<-0
fb<--1
# move one bit to the right end
# now x = 1.5
# loop until desired tolerance met
while(fb > tol)
{
x <- x*x
# update the index
if (x >= 2)
{
x <- x/2
y <- y + b
f <- log(exp(f)+exp(fb))
}
# scale for the next bit
b <- b/2
fb <- (fb-log(2))
}
return(list(y = y,z = lx -1, f = f))
},
#transform decimal numbers to binary
dectobit = function(dec) #transform a natural number into a binary vector to correspond between vector of solutions and storage array
{
if(!double.hashing){
if(dec == 0)
return(0)
q<-dec
bin<-NULL
while(q!=0)
{
r<-q/2
q=floor(r)
bin<-c(as.integer(2*(r-q)),bin)
}
return(bin)
}
return(dehash(dec+1))
},
dectobit.alt = function(dec) #transform a natural number into a binary vector to correspond between vector of solutions and storage array
{
if(dec == 0)
return(0)
q<-dec
bin<-NULL
while(q!=0)
{
r<-q/2
q=floor(r)
bin<-c(as.integer(2*(r-q)),bin)
}
return(bin)
},
dehash=function(dec)
{
if(exists("hash.keys1"))
return(hash.keys1[dec,])
if(exists("hash.keys"))
return(hash.keys[dec,])
return(NULL)
},
#calculate move probabilities
calculate.move.logprobabilities = function(varold, varnew, switch.type,min.N,max.N)
{
if(switch.type == 1) # random size random N(x)
{
#warning("This option should not be chosen for randomization unless p.add == 0.5 ", call. = FALSE)
min.N = max.N
log.mod.switch.prob <- log(1/(max.N - min.N +1)) # probability of having that many differences
KK<-sum(abs(varold-varnew))
log.mod.switch.prob <- 0 #always the same probabilities for moves within thenighbourhood for p=0.5
log.mod.switchback.prob <- 0
} else if(switch.type == 2) #fixed N(x) inverse operator
{
if(min.N!=max.N)
{
#warning("min.N should be equal to max.N in swap type neighbourhoods min.N:=max.N", call. = FALSE)
min.N = max.N
}
log.mod.switch.prob <- log(1/(max.N - min.N +1))
KK<-max.N
log.mod.switch.prob <- log.mod.switch.prob + KK*log(factorial(Nvars - KK + 1)/factorial(Nvars))
log.mod.switchback.prob <- log.mod.switch.prob
}else if(switch.type == 3) # random sized inverse N(x)
{
log.mod.switch.prob <- log(1/(max.N - min.N +1))
KK<-sum(abs(varold-varnew))
log.mod.switch.prob <- log.mod.switch.prob + KK*log(factorial(Nvars - KK + 1)/factorial(Nvars))
log.mod.switchback.prob <- log.mod.switch.prob
}else if(switch.type == 4) # fixed N(x) for reverse from type 2 swaps
{
if(min.N!=max.N)
{
#warning("min.N should be equal to max.N in swap type neighbourhoods min.N:=max.N", call. = FALSE)
min.N = max.N
}
log.mod.switch.prob <- log(1/(max.N - min.N +1))
KK<-max.N
log.mod.switch.prob <- log.mod.switch.prob + KK*log(factorial(Nvars - KK + 1)/factorial(Nvars))
log.mod.switchback.prob <- log.mod.switch.prob
}else if(switch.type > 4)
{
log.mod.switch.prob <- log(x = 1)
log.mod.switchback.prob <-log(x = 1)
}
return(list(log.switch.forw.prob = log.mod.switch.prob, log.switch.back.prob = log.mod.switchback.prob))
},
#build a new model to draw from the old one return selection probabilities
buildmodel= function(varcur.old,statid, shift.cpu,max.cpu,switch.type,min.N,max.N,changeble.coord = NULL)
{
vect<- vector(length = max.cpu,mode = "list")
shift<-0
for(cpu in 1:(max.cpu))
{
set.seed(runif(1,1,10000), kind = NULL, normal.kind = NULL)
if(!is.null(varcur.old)&&length(varcur.old==Nvars))
{
varcur.old[which(is.na(varcur.old))]<-1
varcur<-varcur.old
}else
{
varcur<-rbinom(n = (Nvars),size = 1,0.5)
varcur.old<-varcur
}
changeble <-FALSE
if(!is.null(changeble.coord))
{
changeble <- TRUE
}
if(switch.type == 1) # random size random N(x) # try avoiding when doing mcmc rather than optimization
{
log.mod.switch.prob <- log(1/(max.N - min.N +1))
KK<-floor(runif(n=1, min.N, max.N + 0.999999999))
log.mod.switch.prob <- log.mod.switch.prob + KK*log(factorial(Nvars - KK + 1)/factorial(Nvars))
log.mod.switchback.prob <- log.mod.switch.prob
change.buf <- array(data = 0,dim = Nvars)
if(changeble){
for(ttt in 1:KK)
{
iid<-floor(runif(n = 1,min = 1,max = Nvars+0.999999999))
if(changeble.coord[iid]==1)
next
change.buf[iid] = 1
varcur[iid] <-rbinom(n = 1,size = 1,prob =round(p.add[iid],digits = 8))
log.mod.switch.prob = 0#log.mod.switch.prob + log(dbinom(x = varcur[iid],size = 1,prob = p.add[iid])) # this is one of the pathes to get there in general
log.mod.switchback.prob = 0# log.mod.switchback.prob + log(dbinom(x = 1-varcur[iid],size = 1,prob = p.add[iid])) # but this is one of the ways to get back only
}
}else
{
iid<-floor(runif(n = KK,min = 1,max = Nvars+0.999999999))
change.buf[iid] = 1
varcur[iid] <-rbinom(n = KK,size = 1,prob = round(p.add,digits = 8))
}
}else if(switch.type == 2) # fixed sized inverse N(x)
{
if(min.N!=max.N)
{
#warning("min.N should be equal to max.N in swap type neighbourhoods min.N:=max.N", call. = FALSE)
min.N <- max.N
}
log.mod.switch.prob <- log(1/(max.N - min.N +1))
KK<-max.N
log.mod.switch.prob <- log.mod.switch.prob + KK*log(factorial(Nvars - KK + 1)/factorial(Nvars))
log.mod.switchback.prob <- log.mod.switch.prob
change.buf <- array(data = 0,dim = Nvars)
if(changeble){
for(ttt in 1:KK)
{
iid<-floor(runif(n = 1,min = 1,max = Nvars+0.999999999))
if(change.buf[iid]==1 || changeble.coord[iid]==1)
{
KK<-KK+1
next
}
change.buf[iid] = 1
varcur[iid] = 1-varcur[iid]
}
}else
{
iid<-floor(runif(n = KK,min = 1,max = Nvars+0.999999999))
change.buf[iid] = 1
varcur[iid] = 1-varcur[iid]
}
}else if(switch.type == 3) # random sized inverse N(x)
{
log.mod.switch.prob <- log(1/(max.N - min.N +1))
KK<-floor(runif(n=1, min.N, max.N + 0.999999999))
log.mod.switch.prob <- log.mod.switch.prob + KK*log(factorial(Nvars - KK + 1)/factorial(Nvars))
log.mod.switchback.prob <- log.mod.switch.prob
change.buf <- array(data = 0,dim = Nvars)
if(changeble){
for(ttt in 1:KK)
{
iid<-floor(runif(n = 1,min = 1,max = Nvars+0.999999999))
if(change.buf[iid]==1 || changeble.coord[iid]==1)
{
KK<-KK+1
next
}
change.buf[iid] = 1
varcur[iid] = 1-varcur[iid]
}
}else
{
iid<-floor(runif(n = KK,min = 1,max = Nvars+0.999999999))
change.buf[iid] = 1
varcur[iid] = 1-varcur[iid]
}
}else if(switch.type == 4) # fixed N(x) for reverse from type 2 swaps
{
if(min.N!=max.N)
{
#warning("min.N should be equal to max.N in swap type neighbourhoods min.N:=max.N", call. = FALSE)
min.N <- max.N
}
log.mod.switch.prob <- log(1/(max.N - min.N +1))
KK<-max.N
log.mod.switch.prob <- log.mod.switch.prob + KK*log(factorial(Nvars - KK + 1)/factorial(Nvars))
log.mod.switchback.prob <- log.mod.switch.prob
ids <- which(changeble.coord == 0)
change.buf <- array(data = 0,dim = Nvars)
if(changeble){
for(ttt in KK)
{
iid<-floor(runif(n = 1,min = 1,max = Nvars+0.999999999))
if(change.buf[iid]==1 || changeble.coord[iid]==1)
{
KK<-KK+1
next
}
change.buf[iid] = 1
varcur[iid] = 1-varcur[iid]
}}
else
{
iid<-floor(runif(n = KK,min = 1,max = Nvars+0.999999999))
change.buf[iid] = 1
varcur[iid] = 1-varcur[iid]
}
}else if(switch.type == 5)
{
change.buf <- array(data = 0,dim = (Nvars))
log.mod.switch.prob<-0
log.mod.switchback.prob <-0
add<-0
if(cpu+shift>Nvars)
{
shift<-1 - cpu
varcur.old<-rep(0,times = Nvars)
}
if(varcur.old[cpu+shift]!=1)
{
varcur<-varcur.old
varcur[cpu+shift]<-1
}else
{
if(cpu+shift<Nvars)
shift<-shift+1
while(varcur.old[cpu+shift]==1)
{
shift<-shift+1
if(cpu+shift>=Nvars)
{
shift <- (Nvars - cpu)
break
}
}
varcur<-varcur.old
varcur[cpu+shift]<-1
}
}else if(switch.type == 6)
{
change.buf <- array(data = 0,dim = (Nvars))
log.mod.switch.prob<-0
log.mod.switchback.prob <-0
add<-0
if(cpu+shift>Nvars)
{
shift<-1 - cpu
varcur.old<-rep(1,times = Nvars)
}
if(varcur.old[cpu+shift]!=0)
{
varcur<-varcur.old
varcur[cpu+shift]<-0
}else
{
if(cpu+shift<Nvars)
shift<-shift+1
while(varcur.old[cpu+shift]==0)
{
shift<-shift+1
if(cpu+shift>=Nvars)
{
shift <- (Nvars - cpu)
break
}
}
varcur<-varcur.old
varcur[cpu+shift]<-0
}
}else if(switch.type == 7)
{
change.buf <- array(data = 0,dim = (Nvars))
log.mod.switch.prob<-0
log.mod.switchback.prob <-0
vec<-dectobit(cpu + shift.cpu)
varcur<-c(array(0,dim = (Nvars -length(vec))),vec) #issues here
}else if(switch.type == 8)
{
log.mod.switch.prob <-0
log.mod.switchback.prob <-0
varcur<-varcur.old
change.buf <- array(data = 0,dim = Nvars)
#if(printable.opt)print("type 8 invoked")
#if(printable.opt)print(varcur)
}else if(switch.type==9)
{
log.mod.switch.prob <-0
log.mod.switchback.prob <-0
change.buf <- array(data = 1,dim = Nvars)
changevar<- rbinom(n = Nvars,size = 1,prob=prand)
varcur<-varcur.old
varcur[which(changevar==1)]<-(1-varcur[which(changevar==1)])
log.mod.switch.prob<-prand^length(which(changevar==1))
}else{
log.mod.switch.prob <- 0
log.mod.switchback.prob <-0
change.buf <- array(data = 1,dim = Nvars)
varcur <-rbinom(n = Nvars,size = 1,prob = round(p.add,digits = 8))
#if(printable.opt)print("type 8 invoked")
#if(printable.opt)print(varcur)
}
# for(g in 1:max(isobsbinary))
# {
# if(length(varcur[which(isobsbinary == g && varcur %in% c(1,3))])==length(which(isobsbinary == g)))
# varcur[which(isobsbinary == g && varcur %in% c(1,3))[1]]=0
# if(length(varcur[which(isobsbinary == g && varcur %in% c(2,3))])==length(which(isobsbinary == g)))
# varcur[which(isobsbinary == g && varcur %in% c(2,3))[1]]=0
# }
covobs <- if(fparam[1]=="Const")fparam[which(varcur[-1] == 1)+1]else fparam[which(varcur==1)]
#obsconst<-2*as.integer((varcur[1] %in% c(1,3)) || length(covobs) == 0 || (length(covobs)==length(which(isobsbinary != 0))) ) -1
obsconst<-ifelse(fparam[1]=="Const",2*as.integer((varcur[1])) -1,1)
id<-bittodec(varcur)
id<-id+1
if(ifelse(exists("statistics1"),is.na(statistics1[id,1]),ifelse(exists("statistics"),is.na(statistics[id,1,]),ifelse(exists("hashStat"),!has.key(hash = hashStat,key = paste(varcur,collapse = "")),TRUE))))#||TRUE)
{
# formula <- NULL
# formula <- as.formula(ifelse(length(covobs)>0,(stri_join(stri_flatten(fobserved[1]), " ~ ",obsconst,"+", stri_flatten(covobs, collapse=" + "), latent.formula)),(stri_join(stri_flatten(fobserved[1]), " ~ ",obsconst, latent.formula))))
#
# if(is.null(formula)){
# formula <- as.formula(ifelse(length(covobs)>0,(stri_join(stri_flatten(fobserved[1]), " ~ ",obsconst,"+", stri_flatten(covobs, collapse=" + "))),(stri_join(stri_flatten(fobserved[1]), " ~ ",obsconst))))
#
# }
formula <- NULL
capture.output({withRestarts(tryCatch(capture.output({formula <- as.formula(paste(paste(fobserved[1]), " ~ ",obsconst,ifelse(length(covobs)>0," + ",""), paste(covobs, collapse=" + "), latent.formula)) })), abort = function(){onerr<-TRUE;fm<-NULL})})
if(is.null(formula)){
formula <- as.formula(paste(paste(fobserved[1]), " ~ ",obsconst,ifelse(length(covobs)>0," + ",""), paste(covobs, collapse=" + ")))
}
}else
{
formula <- NULL
}
vect[[cpu]]<-list(formula = formula, varcur = varcur, statid = statid, changed = change.buf, log.mod.switch.prob = log.mod.switch.prob , log.mod.switchback.prob = log.mod.switchback.prob )
}
return(vect)
},
#fit the given model by means of the specified estimator
fitmodel = function(model)
{
if(!is.null(model))
{
fm<-NULL
id<-bittodec(model$varcur)
if(is.null(id))
id = 0
id<-id+1
if(exists("statistics1")){
if(is.na(statistics1[id,1]))
{
#if(printable.opt)print("Invoked from EMJMCMC environment")
onerr<-FALSE
#if(printable.opt)print("INLA internal error")
statistics1[id,c(2,3)]<-100000
statistics1[id,1]<--100000
statistics1[id,4:14]<-0
#prior = "normal",param = c(model$beta.mu.prior,model$beta.tau.prior))
# capture.output({withRestarts(tryCatch(capture.output({fm<-inla(formula = model$formula,family = "binomial",Ntrials = data$total_bases,data = data,control.fixed = list(mean = list(default = model$beta.mu.prior),mean.intercept = model$beta.mu.prior, prec = list(default = model$beta.tau.prior), prec.intercept = model$beta.tau.prior) ,control.compute = list(dic = model$dic.t, waic = model$waic.t, mlik = model$mlik.t))
# })), abort = function(){onerr<-TRUE;fm<-NULL})}) # fit the modal, get local improvements
#
capture.output({withRestarts(tryCatch(capture.output({fm<-do.call(estimator, c(estimator.args, model$formula))
})), abort = function(){onerr<-TRUE;fm<-NULL})}) # fit the model, get local improvements
if(!is.null(fm))
{
statistics1[id,2]<-fm$waic[[1]]
statistics1[id,1]<-fm$mlik[[1]]
statistics1[id,3]<-fm$dic[[1]]
if(save.beta)
{
if(fparam[1]=="Const")
{
inxx<-which(model$varcur==1)
if(length(inxx)==length(fm$summary.fixed$mean))
statistics1[id,15+inxx]<-fm$summary.fixed$mean
}else
{
inxx<-c(0,which(model$varcur==1))
if(length(inxx)==length(fm$summary.fixed$mean))
statistics1[id,16+inxx]<-fm$summary.fixed$mean
}
}
if(fm$waic[[1]]<g.results[2,1] && !is.na(fm$waic[[1]]))
{
g.results[2,1]<-fm$waic[[1]]
g.results[2,2]<-as.integer(id)
}
if(fm$mlik[[1]]>g.results[1,1] && !is.na(fm$mlik[[1]]))
{
g.results[1,1]<-fm$mlik[[1]]
g.results[1,2]<-as.integer(id)
}
if(fm$dic[[1]]<g.results[3,1]&& !is.na(fm$dic[[1]]))
{
g.results[3,1]<-fm$dic[[1]]
g.results[3,2]<-as.integer(id)
}
g.results[4,2] <- g.results[4,2]+1
if(g.results[4,2]%%recalc.margin == 0)
{
p.add <<- as.array(post_proceed_results(statistics1)$p.post)
}
}
}
if(model$statid!=-1)
statistics1[id,model$statid+1]<-statistics1[id,model$statid+1] + 1
g.results[4,1] <- g.results[4,1]+1
return(list(mlik=statistics1[id,1],waic=statistics1[id,2],dic=statistics1[id,3]))
}else if(exists("statistics")){
if(is.na(statistics[id,1]))
{
#if(printable.opt)print("Invoked from EMJMCMC SUB environment")
onerr<-FALSE
#if(printable.opt)print("INLA internal error")
statistics[id,c(2,3)]<-100000
statistics[id,1]<--100000
statistics[id,4:14]<-0
#prior = "normal",param = c(model$beta.mu.prior,model$beta.tau.prior))
# capture.output({withRestarts(tryCatch(capture.output({fm<-inla(formula = model$formula,family = "binomial",Ntrials = data$total_bases,data = data,control.fixed = list(mean = list(default = model$beta.mu.prior),mean.intercept = model$beta.mu.prior, prec = list(default = model$beta.tau.prior), prec.intercept = model$beta.tau.prior) ,control.compute = list(dic = model$dic.t, waic = model$waic.t, mlik = model$mlik.t))
# })), abort = function(){onerr<-TRUE;fm<-NULL})}) # fit the modal, get local improvements
#
capture.output({withRestarts(tryCatch(capture.output({fm<-do.call(estimator, c(estimator.args, model$formula))
})), abort = function(){onerr<-TRUE;fm<-NULL})}) # fit the modal, get local improvements
if(!is.null(fm))
{
statistics[id,2]<-fm$waic[[1]]
statistics[id,1]<-fm$mlik[[1]]
statistics[id,3]<-fm$dic[[1]]
if(save.beta)
{
if(fparam[1]=="Const")
{
inxx<-which(model$varcur==1)
if(length(inxx)==length(fm$summary.fixed$mean))
statistics[id,15+inxx]<-fm$summary.fixed$mean
}else
{
inxx<-c(0,which(model$varcur==1))
if(length(inxx)==length(fm$summary.fixed$mean))
statistics[id,16+inxx]<-fm$summary.fixed$mean
}
}
if(fm$waic[[1]]<g.results[2,1] && !is.na(fm$waic[[1]]))
{
g.results[2,1]<-fm$waic[[1]]
g.results[2,2]<-as.integer(id)
}
if(fm$mlik[[1]]>g.results[1,1] && !is.na(fm$mlik[[1]]))
{
g.results[1,1]<-fm$mlik[[1]]
g.results[1,2]<-as.integer(id)
}
if(fm$dic[[1]]<g.results[3,1]&& !is.na(fm$dic[[1]]))
{
g.results[3,1]<-fm$dic[[1]]
g.results[3,2]<-as.integer(id)
}
g.results[4,2] <- g.results[4,2]+1
if(g.results[4,2]%%recalc.margin == 0)
{
proceeeded <- post_proceed_results(statistics)
p.add <<- as.array(proceeeded$p.post)
#g.results[4,2] <-
}
}
}
if(model$statid!=-1)
statistics[id,model$statid+1]<-statistics[id,model$statid+1] + 1
g.results[4,1] <- g.results[4,1]+1
return(list(mlik=statistics[id,1],waic=statistics[id,2],dic=statistics[id,3]))
}else if(exists("hashStat")){
if(Nvars.max>Nvars)
idd<- as.character(paste(c(model$varcur,array(0,Nvars.max-Nvars)),collapse = ""))
else
idd<- as.character(paste(c(model$varcur),collapse = ""))
if(!has.key(key = idd,hash = hashStat))
{
#if(printable.opt)print("Invoked from EMJMCMC hash table environment")
onerr<-FALSE
#if(printable.opt)print("INLA internal error")
#prior = "normal",param = c(model$beta.mu.prior,model$beta.tau.prior))
# capture.output({withRestarts(tryCatch(capture.output({fm<-inla(formula = model$formula,family = "binomial",Ntrials = data$total_bases,data = data,control.fixed = list(mean = list(default = model$beta.mu.prior),mean.intercept = model$beta.mu.prior, prec = list(default = model$beta.tau.prior), prec.intercept = model$beta.tau.prior) ,control.compute = list(dic = model$dic.t, waic = model$waic.t, mlik = model$mlik.t))
# })), abort = function(){onerr<-TRUE;fm<-NULL})}) # fit the modal, get local improvements
#
capture.output({withRestarts(tryCatch(capture.output({fm<-do.call(estimator, c(estimator.args, model$formula))
})), abort = function(){onerr<-TRUE;fm<-NULL})}) # fit the modal, get local improvements
if(!save.beta)
{
hashBuf<-array(data = NA,dim = 3)
}else
{
if(allow_offsprings==0||Nvars.max<Nvars)
{
if(fparam[1]=="Const")
{
linx<-Nvars
inxx<-which(model$varcur==1)
}else
{
linx<-Nvars + 1
inxx<-c(0,which(model$varcur==1))
}
}else
{
if(fparam[1]=="Const")
{
linx<-Nvars.max
inxx<-which(model$varcur==1)
}else
{
linx<-Nvars.max + 1
inxx<-c(0,which(model$varcur==1))
}
}
hashBuf<-array(data = NA,dim = 3 + linx)
}
hashBuf[c(2,3)]<-100000
hashBuf[1]<- -100000
if(!is.null(fm))
{
hashBuf[2]<-fm$waic[[1]]
hashBuf[1]<-fm$mlik[[1]]
hashBuf[3]<-fm$dic[[1]]
if(save.beta)
{
if(fparam[1]=="Const")
{
if(length(inxx)==length(fm$summary.fixed$mean))
hashBuf[3+inxx]<-fm$summary.fixed$mean
}else
{
if(length(inxx)==length(fm$summary.fixed$mean))
hashBuf[4+inxx]<-fm$summary.fixed$mean
}
}
hashStat[idd] <- hashBuf
# if(id>1)
# {
# inxx<-which(model$varcur==1)
# if(length(inxx)==length(fm$summary.fixed$mean))
# statistics[id,14+inxx]<-fm$summary.fixed$mean
# }
if(fm$waic[[1]]<g.results[2,1] && !is.na(fm$waic[[1]]))
{
g.results[2,1]<-fm$waic[[1]]
g.results[2,2]<-(id)
}
if(fm$mlik[[1]]>g.results[1,1] && !is.na(fm$mlik[[1]]))
{
g.results[1,1]<-fm$mlik[[1]]
g.results[1,2]<-(id)
}
if(fm$dic[[1]]<g.results[3,1]&& !is.na(fm$dic[[1]]))
{
g.results[3,1]<-fm$dic[[1]]
g.results[3,2]<-(id)
}
g.results[4,2] <- g.results[4,2]+1
}
}
g.results[4,1] <- g.results[4,1]+1
if(has.key(hash = hashStat,key=idd))
hasRes<- values(hashStat[idd])
else
hasRes<-c(-10000,10000,10000)
if(g.results[4,2]%%recalc.margin == 0)
{
proceeeded <- post_proceed_results_hash(hashStat)
p.add <<- as.array(proceeeded$p.post)
#g.results[4,2] <-
}
return(list(mlik=hasRes[1],waic=hasRes[2],dic=hasRes[3]))
}else
{
capture.output({withRestarts(tryCatch(capture.output({fm<-do.call(estimator, c(estimator.args, model$formula))
})), abort = function(){onerr<-TRUE;fm<-NULL})}) # fit the modal, get local improvements
if(!is.null(fm)){
if(fm$waic[[1]]<g.results[2,1] && !is.na(fm$waic[[1]]))
{
g.results[2,1]<-fm$waic[[1]]
g.results[2,2]<-(id)
}
if(fm$mlik[[1]]>g.results[1,1] && !is.na(fm$mlik[[1]]))
{
g.results[1,1]<-fm$mlik[[1]]
g.results[1,2]<-(id)
}
if(fm$dic[[1]]<g.results[3,1]&& !is.na(fm$dic[[1]]))
{
g.results[3,1]<-fm$dic[[1]]
g.results[3,2]<-(id)
}
g.results[4,1] <- g.results[4,1]+1
g.results[4,2] <- g.results[4,2]+1
return(list(mlik=fm$mlik[[1]],waic=fm$waic[[1]],dic=fm$dic[[1]]))
}
else
{
g.results[4,1] <- g.results[4,1]+1
return(list(mlik=-Inf,waic=Inf,dic=Inf))
}
}
}
g.results[4,1] <- g.results[4,1]+1
g.results[4,2] <- g.results[4,2]+1
return(list(mlik=-Inf,waic=Inf,dic=Inf))
},
#lambda function for mtmcmc
lambda = function(c,alpha,g1,g2,g.domain.pos) # simmetric choice driving function
{
if((c!=0))
{
res<-((((1/c)*(1+(g1+g2)*(g.domain.pos))/(1-(g1+g2)*(1-g.domain.pos)))^alpha))
#!#if(printable.opt)print(res)
return(res)
}else
{
#!#if(printable.opt)print(1)
return(1)
}
},
#norm between probabilities vectors
normprob=function(p1,p2)
{
nn<-abs(1-sum((p1+0.1)/(p2+0.1))/length(p1))
if(is.na(nn))
nn<-Inf
return(nn)
},
#local mcmc procedure
learnlocalMCMC=function(model)
{
M<-M.mcmc
mlikcur<- model$mlikcur
waiccur<-model$waiccur
varcand<-model$varcur
varcur<-model$varcur
varcurb<-model$varcur
varglob<-model$varcur
modglob<-NULL
fm<-NULL
fmb<-NULL
# estimate large jump in a reverse move
if(model$reverse || is.infinite(mlikcur))
{
vectbg<-buildmodel(max.cpu = 1,varcur.old = varcur,statid = model$statid,switch.type=8, min.N = min.N,max.N = max.N)
if(!is.null(vectbg[[1]]$formula))
{
bgmod <- lapply(X = vectbg,FUN = .self$fitmodel)
waiccur<-bgmod[[1]]$waic
mlikcur<-bgmod[[1]]$mlik
}
else if(exists("statistics1"))
{
iidd<-bittodec(varcur)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcur,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
}
if(printable.opt)print(paste("Begin with ", mlikcur))
mlikglob<- mlikcur
mlikcand<- mlikcur
waiccand<- waiccur
waicglob<- waiccur
waiccur<- waiccur
for(m in 1:M)
{
withRestarts(tryCatch({
# statistics <- describe(statistics)
vect<-buildmodel(varcur.old = varcur,statid = model$statid,max.cpu = max.cpu,switch.type=switch.type, min.N = min.N, max.N = max.N)
cluster<-TRUE
flag1<-0
for(mod_id in 1:max.cpu)
{
if(is.null(vect[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
#flag1<-sum(is.null(vect[[]]$formula))
if(flag1==max.cpu)
{
cluster<-FALSE
if(printable.opt)print("!!!!MTMCMC models already estimated!!!!")
}else
{
res.par <- parallelize(X = vect,FUN = .self$fitmodel)
}
p.select.y <- array(data = 0, dim = max.cpu)
for(mod_id in 1:max.cpu)
{
if(cluster)
{
fm<-res.par[[mod_id]]
if(is.null(fm)&&(is.na(res.par[[mod_id]]$waic)))
{
varcand<-varcurb
if(printable.opt)print("locMTMCMC Model Fit Error!?")
next
}
}
varcand<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand<-res.par[[mod_id]]$waic
mlikcand<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
if((mlikcand>mlikglob)) #update the parameter of interest
{
if(printable.opt)print(paste("locMTMCMC update waic.glob = ", waiccand))
if(printable.opt)print(paste("locMTMCMC update waic.glob.mlik = ", mlikglob))
mlikglob<-mlikcand
waicglob<-waiccand
varglob<-varcand
if(cluster)
modglob<-fm
}
g1 <- waiccur
if(waiccur == Inf)
{
g1 = 1
}
p.select.y[mod_id]<-(mlikcand + vect[[mod_id]]$log.mod.switchback.prob+log(lambda(c = cc, alpha = aa, g1 = -g1, g2 = -waiccand,g.domain.pos = FALSE))) # correct for different criteria later
if(is.na(p.select.y[mod_id]))
p.select.y[mod_id] <- 0
if(is.infinite(p.select.y[mod_id]) || p.select.y[mod_id]>100000000)
{
#if(printable.opt)print(paste("very large log.w.y detected ",p.select.y[mod_id]))
p.select.y[mod_id] <- 100000000
}
}
max.p.select.y <- max(p.select.y)
p.select.y<-p.select.y-max.p.select.y
if(printable.opt)print(paste("max log.w.y is ",max.p.select.y,"normilized log.w.n.y is ", paste(p.select.y,collapse = ", ")))
ID<-sample.int(n = max.cpu,size = 1,prob = exp(p.select.y))
if(printable.opt)print(paste("cand ",ID," selected"))
varcand<-vect[[ID]]$varcur
if(cluster)
{
waiccand<-res.par[[ID]]$waic
mlikcand<-res.par[[ID]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
#p.Q.cand<- p.select.y[ID]/sum(p.select.y)
if(printable.opt)print("do reverse step")
p.select.z <- array(data = 0.01, dim = max.cpu)
if(max.cpu!=1)
{
vect1<-buildmodel(max.cpu = max.cpu -1,varcur.old = varcand,statid = model$statid,switch.type = switch.type, min.N = min.N, max.N = max.N)
cluster<-TRUE
flag1<-0
for(mod_id in 1:(max.cpu-1))
{
if(is.null(vect1[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==(max.cpu-1))
{
cluster<-FALSE
if(printable.opt)print("!!!!MTMCMC reverse models already estimated!!!!")
}else
{
res.par.back <- parallelize(X = vect1,FUN = .self$fitmodel)
}
for(mod_id in 1:(max.cpu-1))
{
if(cluster)
{
if(is.null(fm)&&(is.na(res.par.back[[mod_id]]$waic)))
{
if(printable.opt)print("locMTMCMC Model Fit Error!?")
next
}
}
varcand.b<-vect1[[mod_id]]$varcur
if(cluster)
{
waiccand.b<-res.par.back[[mod_id]]$waic
mlikcand.b<-res.par.back[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand.b)+1
waiccand.b<-statistics1[iidd,2]
mlikcand.b<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand.b,collapse = "")
waiccand.b<-values(hashStat[iidd])[2]
mlikcand.b<-values(hashStat[iidd])[1]
}
if((mlikcand.b>mlikglob))
{
if(printable.opt)print(paste("locMTMCMC update waic.glob = ", waiccand.b))
if(printable.opt)print(paste("locMTMCMC update waic.glob.mlik = ", mlikcand.b))
mlikglob<-mlikcand.b
waicglob<-waiccand.b
varglob<-varcand.b
if(cluster)
modglob<-fm
}
g1 = waiccand
if(waiccand == Inf)
{
g1 = 1
}
p.select.z[mod_id]<-(mlikcand.b+vect1[[mod_id]]$log.mod.switchback.prob+(lambda(c = cc, alpha = aa, g1 = -g1, g2 = -waiccand.b,g.domain.pos = FALSE))) # correct for different criteria later
if(is.na(p.select.z[mod_id]))
p.select.z[mod_id]=0
if(is.infinite(p.select.z[mod_id]) || p.select.z[mod_id] > 100000000)
{
#if(printable.opt)print(paste("very large log.w.y detected ",p.select.z[mod_id]))
p.select.z[mod_id] <- 100000000
}
}
}
if( waiccur == Inf)
{
g1 = 1
}
p.select.z[max.cpu] <- (mlikcur+vect[[ID]]$log.mod.switch.prob+(lambda(c = cc, alpha = aa, g1 = -g1, g2 = -waiccand,g.domain.pos = FALSE)))
if(is.na(p.select.z[mod_id]))
p.select.z[mod_id]=0
if(is.infinite(p.select.z[mod_id]) || p.select.z[mod_id] > 100000000)
{
#if(printable.opt)print(paste("very large log.w.y detected ",p.select.z[mod_id]))
p.select.z[mod_id] <- 100000000
}
max.p.select.z <- max(p.select.z)
p.select.z<-p.select.z-max.p.select.z
if(printable.opt)print(paste("max log.w.z is ",max.p.select.z,"normilized log.w.n.z is ", paste(p.select.z,collapse = ", ")))
if(log(runif(n = 1,min = 0,max = 1)) < (log(sum(exp(p.select.y)))-log(sum(exp(p.select.z)))) + max.p.select.y - max.p.select.z )
{
mlikcur<-mlikcand
if(printable.opt)print(paste("locMTMCMC update ratcur = ", mlikcand))
if(printable.opt)print(paste("locMTMCMC accept move with ", waiccand))
varcur<-varcand
waiccur<-waiccand
}
}),abort = function(){fm<-fmb;closeAllConnections();options(error=traceback); onerr<-TRUE})
}
#if(printable.opt)print("FINISH LOCAL MTMCMC")
#!#if(printable.opt)print(points)
if(model$reverse == FALSE)
{
if(is.null(varcur))
{
#if(printable.opt)print("No moves acceoted in the procedure")
varcur<-varcand
waiccur<-waiccand
varcur<-varcand
}
vect<-buildmodel(max.cpu = 1,varcur.old = varcur,statid = model$statid,switch.type = type.randomize,min.N = min.N.randomize,max.N = max.N.randomize)
varcur<-vect[[1]]$varcur
#if(printable.opt)print(varcur)
cluster<-TRUE
if(is.null(vect[[1]]$formula))
{
cluster<-FALSE
if(printable.opt)print("!!!!MTMCMC reverse models already estimated!!!!")
}else
{
mod<-fitmodel(vect[[1]])
}
if(cluster)
{
waiccur<-mod$waic
mlikcur<-mod$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcur)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcur,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
# incorporate what happens for the backward optimization
model.prob<-vect[[1]]$log.mod.switch.prob
model.prob.fix<-vect[[1]]$log.mod.switchback.prob
}else # incorporate what happens for the reverse move
{
if(is.null(varcur))
{
#if(printable.opt)print("No moves acceoted in the reverse procedure")
varcur<-varcand
waiccur<-waiccand
}
model.probs<-calculate.move.logprobabilities(varold = varcur, varnew = model$varold,switch.type = type.randomize,min.N = min.N.randomize,max.N = max.N.randomize)
model.prob<-model.probs$log.switch.forw.prob
model.prob.fix<-model.probs$log.switch.back.prob
}
if(is.null(varcur))
{
#if(printable.opt)print("NO VARCUR OBTAINED")
varcur<-i
waiccur<-Inf
varcur<-model$varold
}
return(list(varcur = varcur, waiccur = waiccur, mlikcur = mlikcur, log.prob.cur = model.prob,log.prob.fix = model.prob.fix, varglob = varglob, waicglob = waicglob, mlikglob = mlikglob, modglob = modglob))
},
#local simulated annealing optimization
learnlocalSA=function(model)
{
t.min<-SA.param$t.min
t<-SA.param$t.init
dt<-SA.param$dt
M<-SA.param$M
varcand<-model$varcur
varcurb<-model$varcur
varcur<-model$varcur
varglob<-model$varcur
varglob<-NULL
modglob<-NULL
probcur<-1
probrevcur<-1
first.prob <- 1
fm<-NULL
fmb<-NULL
mlikcur<- model$mlikcur
waiccur<-model$waiccur
# estimate large jump in a reverse move
# estimate large jump in a reverse move
if((model$reverse && !model$sa2) || is.infinite(mlikcur))
{
vectbg<-buildmodel(max.cpu = 1,varcur.old = varcur,statid = model$statid,switch.type=8, min.N = min.N,max.N = max.N)
if(!is.null(vectbg[[1]]$formula))
{
bgmod <- lapply(X = vectbg,FUN = .self$fitmodel)
waiccur<-bgmod[[1]]$waic
mlikcur<-bgmod[[1]]$mlik
}
else if(exists("statistics1"))
{
iidd<-bittodec(varcur)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcur,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
}
if(printable.opt)print(paste("Begin with ", mlikcur))
mlikglob<- mlikcur
mlikcand<- mlikcur
waiccand<- waiccur
waicglob<- waiccur
waiccur<- waiccur
while(t>t.min)
{
if(printable.opt)print(paste("anneal to ",t))
t.new<-t*exp(-dt)
if(model$reverse == TRUE && t.new <= t.min)
{
M<-M -1
}
for(m in 1:M)
{
withRestarts(tryCatch({
mmax.cpu = max.cpu
if(model$switch.type == 5)
{
mmax.cpu = Nvars - sum(varcur)
}else if(model$switch.type == 6)
{
mmax.cpu = sum(varcur)
}
if(mmax.cpu == 0)
mmax.cpu = 1
vect<-buildmodel(max.cpu = mmax.cpu,varcur.old = varcur,statid = model$statid,switch.type=model$switch.type, min.N = min.N,max.N = max.N)
cluster<-TRUE
flag1<-0
for(mod_id in 1:mmax.cpu)
{
if(is.null(vect[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==mmax.cpu)
{
cluster<-FALSE
if(printable.opt)print("!!!!SA Models already estimated!!!!")
}else
{
res.par <- parallelize(X = vect,FUN = .self$fitmodel)
}
for(mod_id in 1:mmax.cpu)
{
if(cluster)
{
fmb<-fm
fm<-res.par[[mod_id]]
waiccand<-Inf
if(is.null(fm)&&(is.na(res.par[[mod_id]]$waic)))
{
varcand<-varcurb
if(printable.opt)print("SA Model Fit Error!?")
next
}
}
varcand<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand<-res.par[[mod_id]]$waic
mlikcand<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-stri_paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
if(objective==0)
{
objcand<-waiccand
objcur<-waiccur
objglob<-waicglob
}else
{
objcand<- -mlikcand
objcur<- -mlikcur
objglob<- -mlikglob
}
if(t == SA.param$t.init && mod_id == 1 && m == 2)
{
delta<-objcand - objcur
first.prob <- vect[[mod_id]]$log.mod.switchback.prob + log(punif(q = exp(x = delta/t),min = 0,max = 1))
}
if(objcand<objcur)
{
if(printable.opt)print(paste("SA accept move with ", objcand))
waiccur<-waiccand
varcur<-varcand
mlikcur<-mlikcand
if(objcand<objglob)
{
waicglob<-waiccand
varglob<-varcand
mlikglob<-mlikcand
if(cluster)
modglob<-fm
if(printable.opt)print(paste("SA update global optima with", objcand))
}
}else
{
delta<-objcand - objcur
if(runif(n = 1,min = 0,max = 1) <= exp(x = -delta/t))
{
model.probs<-calculate.move.logprobabilities(varold = varcur, varnew = varcand,switch.type = model$switch.type,min.N = min.N,max.N = max.N)
probcur<-model.probs$log.switch.forw.prob
probrevcur<-model.probs$log.switch.back.prob
waiccur<-waiccand
varcur<-varcand
mlikcur<-mlikcand
if(printable.opt)print(paste("SA accept move with ", objcand))
}
}
}
}),abort = function(){varcur<-varcurb; fm<-fmb;closeAllConnections();options(error=traceback); onerr<-TRUE})
}
t<-t.new
}
t<-t/exp(-dt)
if(model$reverse == FALSE)
{
model.prob<-log(punif(q = exp(x = -delta/t),min = 0,max = 1)) + probcur # log(P(Mk,Mk-1))
model.prob.fix<-log(punif(q = exp(x = delta/t),min = 0,max = 1)) + probrevcur # log(P(Mk-1,Mk))
if(model$sa2 == TRUE)
{
model.prob.fix<-model.prob.fix + first.prob # correcting for the term for local improvements of type 3.
}
}else # incorporate what happens for the reverse move
{
if(is.null(varcur))
{
if(printable.opt)print("No moves accepted in the reverse procedure")
varcur<-model$varcur
objcur<-model$objcur
}
delta<-objcur-model$objold
model.probs<-calculate.move.logprobabilities(varold = varcur, varnew = model$varold, switch.type = model$switch.type,min.N = min.N,max.N = max.N)
model.prob<-punif(q = exp(x = -delta/t),min = 0,max = 1,log.p = TRUE) + model.probs$log.switch.forw.prob
model.prob.fix<-punif(q = exp(x = delta/t),min = 0,max = 1,log.p = TRUE) + model.probs$log.switch.back.prob
if(model.prob==-Inf)
{
model.prob<- -100000000
}
if(model.prob.fix==-Inf)
{
model.prob.fix<- -100000000
}
}
return(list(varcur = varcur, waiccur = waiccur, mlikcur = mlikcur, log.prob.cur = model.prob,log.prob.fix = model.prob.fix, varglob = varglob, waicglob = waicglob, mlikglob = mlikglob, modglob = modglob))
},
#forward selection procedure
forward_selection=function(model)
{
if(printable.opt)print("begin forward selection procedure")
varcand<-model$varcur
varcurb<-model$varcur
varglob<-varcand
mlikglob<- model$mlikcur
mlikcur<- model$mlikcur
waiccand<- model$waiccur
waicglob<-model$waiccur
waiccur<-model$waiccur
waiccurb<-model$waiccur
varglob<-NULL
modglob<-NULL
fm<-NULL
fmb<-NULL
ub<-bittodec(array(1,length(varcurb)))
layer<-length(which(varcurb == 0))
mlikcur<- model$mlikcur
waiccur<-model$waiccur
# estimate large jump in a reverse move
# estimate large jump in a reverse move
if(is.infinite(mlikcur))
{
vectbg<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = model$statid,switch.type=8, min.N = min.N,max.N = max.N)
if(!is.null(vectbg[[1]]$formula))
{
bgmod <- lapply(X = vectbg,FUN = .self$fitmodel)
waiccur<-bgmod[[1]]$waic
mlikcur<-bgmod[[1]]$mlik
}
else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}
else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
if(!is.na(mlikcur) && !is.na(waiccur) )
{
mlikglob<- mlikcur
mlikcur<- mlikcur
waiccand<- waiccur
waicglob<- waiccur
waiccur<- waiccur
waiccurb<- waiccur
}
}
while(layer>0)
{
withRestarts(tryCatch({
if(printable.opt)print(paste("proceed with layer",layer))
if(printable.opt)print(paste("current solution is",as.character(varcand)))
vect<-buildmodel(max.cpu = layer,varcur.old = varcurb,statid = model$statid, switch.type = 5,min.N = min.N, max.N = max.N)
if(printable.opt)print(paste("finish preparing models at layer",layer))
cluster<-TRUE
flag1<-0
for(mod_id in 1:layer)
{
if(is.null(vect[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==layer)
{
cluster<-FALSE
if(printable.opt)print("!!!!forward Models already estimated!!!!")
}else
{
res.par <- parallelize(X = vect,FUN = .self$fitmodel)
}
if(printable.opt)print(paste("end forward optimizing at layer",layer))
for(mod_id in 1:layer)
{
if(cluster){
fmb<-fm
fm<-res.par[[mod_id]]
waiccand<-Inf
if(is.null(fm)&&(is.na(res.par[[mod_id]]$waic)))
{
varcand<-varcurb
if(printable.opt)print("forward Model Fit Error!?")
next
}
}
varcand<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand<-res.par[[mod_id]]$waic
mlikcand<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
if(objective==0)
{
objcand<-waiccand
objcur<-waiccur
objglob<-waicglob
}else
{
objcand<- -mlikcand
objcur<- -mlikcur
objglob<- -mlikglob
}
if(objcand<=objcur || mod_id ==1)
{
if(printable.opt)print(paste("forward accept with ", objcand))
objcur<-objcand
varcurb<-varcand
waiccur<-waiccand
varcur<-varcand
mlikcur<-mlikcand
if(objcur<objglob)
{
objglob<-objcur
waicglob<-waiccand
varglob<-varcand
mlikglob<-mlikcand
if(!is.null(fm))
modglob<-fm
if(printable.opt)print(paste("forward global optima with ", objcand))
}
}
# else
# {
# if(waiccand<=waiccur)
# {
# waiccur<-waiccand
# varcur<-varcand
# }
#
# }
}
if(objcur!=objglob)
{
if(model$locstop)
{
break
}else
{
varcurb<-varcur
}
}
}),abort = function(){varcur<-varcurb; fm<-fmb;closeAllConnections();options(error=traceback); onerr<-TRUE})
layer<-layer-1
}
model.prob<-1
model.prob.fix<-1
return(list(varcur = varglob, waiccur = waicglob, mlikcur = mlikglob, log.prob.cur = model.prob,log.prob.fix = model.prob.fix, varglob = varglob, waicglob = waicglob, mlikglob = mlikglob, modglob = modglob))
},
#backward selection procedure
backward_selection=function(model)
{
#if(printable.opt)print("begin backward selection procedure")
varcand<-model$varcur
varcurb<-model$varcur
varglob<-varcand
mlikglob<- model$mlikcur
mlikcur<- model$mlikcur
waiccur<- model$waiccur
waicglob<-model$waiccur
varglob<-NULL
modglob<-NULL
waiccurb<- model$waiccur
fm<-NULL
fmb<-NULL
ub<-bittodec(array(1,length(varcurb)))
layer<-length(which(varcurb == 1))
if(is.infinite(mlikcur))
{
vectbg<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = model$statid,switch.type=8, min.N = min.N,max.N = max.N)
if(!is.null(vectbg[[1]]$formula))
{
bgmod <- lapply(X = vectbg,FUN = .self$fitmodel)
waiccur<-bgmod[[1]]$waic
mlikcur<-bgmod[[1]]$mlik
}
else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
if(!is.na(mlikcur) && !is.na(waiccur) )
{
mlikglob<- mlikcur
mlikcur<- mlikcur
waiccand<- waiccur
waicglob<- waiccur
waiccur<- waiccur
waiccurb<- waiccur
}
}
while(layer>0)
{
withRestarts(tryCatch({
if(printable.opt)print(paste("backward proceed with layer",layer))
if(printable.opt)print(paste("current backward solution is",as.character(varcand)))
vect<-buildmodel(max.cpu = layer,varcur.old = varcurb,statid = model$statid, switch.type = 6,min.N = min.N, max.N = max.N)
if(printable.opt)print(paste("finish backward preparing models at layer",layer))
cluster<-TRUE
flag1<-0
for(mod_id in 1:layer)
{
if(is.null(vect[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==layer)
{
cluster<-FALSE
if(printable.opt)print("!!!!backward Models already estimated!!!!")
}else
{
res.par <- parallelize(X = vect,FUN = .self$fitmodel)
}
if(printable.opt)print(paste("end backward optimizing at layer",layer))
for(mod_id in 1:layer)
{
if(cluster){
fmb<-fm
fm<-res.par[[mod_id]]
waiccand<-Inf
if(is.null(fm)&&(is.na(res.par[[mod_id]]$waic)))
{
varcand<-varcurb
if(printable.opt)print("backward Model Fit Error!?")
next
}
}
varcand<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand<-res.par[[mod_id]]$waic
mlikcand<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
if(objective==0)
{
objcand<-waiccand
objcur<-waiccur
objglob<-waicglob
}else
{
objcand<- -mlikcand
objcur<- -mlikcur
objglob<- -mlikglob
}
if(objcand<=objcur|| mod_id ==1)
{
if(printable.opt)print(paste("backward accept with ", objcand))
objcur<-objcand
varcurb<-varcand
waiccur<-waiccand
varcur<-varcand
mlikcur<-mlikcand
if(objcur<objglob)
{
objglob<-objcur
waicglob<-waiccand
varglob<-varcand
mlikglob<-mlikcand
if(!is.null(fm))
modglob<-fm
if(printable.opt)print(paste("backward global optima with ", objcand))
}
}
}
if(objcur!=objglob)
{
if(model$locstop)
{
break
}else
{
varcurb<-varcur
}
}
}),abort = function(){varcur<-varcurb; fm<-fmb;closeAllConnections();options(error=traceback); onerr<-TRUE})
layer<-layer-1
}
model.prob<-1
model.prob.fix<-1
return(list(varcur = varglob, waiccur = waicglob, mlikcur = mlikglob, log.prob.cur = model.prob,log.prob.fix = model.prob.fix, varglob = varglob, waicglob = waicglob, mlikglob = mlikglob, modglob = modglob))
},
#full selection procedure
full_selection=function(model)
{
if(printable.opt)print(paste("begin full selection procedure!","Careful, ",2^Nvars," models have to be estimated"))
if(Nvars>30)
if(printable.opt)print("Finishing the procedure might well take forever!")
varcand<-array(0,Nvars)
varcurb<-varcand
varglob<-varcand
varglob<-NULL
modglob<-NULL
mlikglob<- model$mlikcur
mlikcur<- model$mlikcur
waiccand<- model$waiccur
waicglob<-model$waiccur
waiccur<-model$waiccur
waiccurb<-model$waiccur
fm<-NULL
fmb<-NULL
ubs<-as.integer(bittodec(array(1,Nvars)) + 1)
ub<-model$ub
totit<-as.integer(ubs/ub) + 1
if(model$totalit<totit)
{
totit<-model$totalit
}
if(is.infinite(mlikcur))
{
vectbg<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = model$statid,switch.type=8, min.N = min.N,max.N = max.N)
if(!is.null(vectbg[[1]]$formula))
{
bgmod <- lapply(X = vectbg,FUN = .self$fitmodel)
waiccur<-bgmod[[1]]$waic
mlikcur<-bgmod[[1]]$mlik
}
else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
if(!is.na(waiccur)&&!is.na(mlikcur))
{
mlikglob<- mlikcur
mlikcand<- mlikcur
waiccand<- waiccur
waicglob<- waiccur
waiccur<- waiccur
waiccurb<- waiccur
}
}
for(i in 1:totit)
{
if(ub*i>ubs)
{
ub<-ubs - ub*(i-1)-1
if(printable.opt)print(paste("last ",ub," iterations to complete"))
varcurb<-varcand
}
withRestarts(tryCatch({
vect<-buildmodel(max.cpu = ub,varcur.old = varcurb,statid = model$statid,switch.type = 7, shift.cpu = model$ub*(i-1),min.N = min.N,max.N = max.N)
if(printable.opt)print(paste("proceed with full ecumeration"))
if(printable.opt)print(paste("current solution is",as.character(varcand)))
cluster<-TRUE
flag1<-0
for(mod_id in 1:ub)
{
if(is.null(vect[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==ub)
{
cluster<-FALSE
if(printable.opt)print("!!!!full models already estimated!!!!")
}else
{
res.par <- parallelize(X = vect,FUN = .self$fitmodel)
}
if(printable.opt)print(paste("end optimizing full ecumeration"))
for(mod_id in 1:ub)
{
if(cluster){
fmb<-fm
fm<-res.par[[mod_id]]
waiccand<-Inf
if(is.null(fm)&&(is.na(res.par[[mod_id]]$waic)))
{
varcand<-varcurb
if(printable.opt)print("full Model Fit Error!?")
next
}
}
varcand<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand<-res.par[[mod_id]]$waic
mlikcand<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
if(objective==0)
{
objcand<-waiccand
objcur<-waiccur
objglob<-waicglob
}else
{
objcand<- -mlikcand
objcur<- -mlikcur
objglob<- -mlikglob
}
if(objcand<=objcur)
{
if(printable.opt)print(paste("full accept with ", objcand))
objcur<-objcand
varcurb<-varcand
waiccur<-waiccand
varcur<-varcand
mlikcur<-mlikcand
if(objcur<objglob)
{
objglob<-objcur
waicglob<-waiccand
varglob<-varcand
mlikglob<-mlikcand
if(!is.null(fm))
modglob<-fm
if(printable.opt)print(paste("full global optima with ", objcand))
}
}
varcurb<-varcand
}
#waiccurb<-waiccur
}),abort = function(){varcur<-varcurb; fm<-fmb;closeAllConnections();options(error=traceback); onerr<-TRUE})
}
# if(length(which(varcur == 1))==(Nvars-1))
# {
# vectbg<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = model$statid,switch.type=8, min.N = min.N,max.N = max.N)
# if(!is.null(vectbg[[1]]$formula))
# {
# bgmod <- lapply(X = vectbg,FUN = .self$fitmodel)
# waiccand<-bgmod[[1]]$waic
# mlikcand<-bgmod[[1]]$mlik
# }
# else
# {
# iidd<-bittodec(varcur)+1
# waiccand<-statistics1[iidd,2]
# mlikcand<-statistics1[iidd,1]
# }
# if(objective==0)
# {
# objcand<-waiccand
# objcur<-waiccur
# objglob<-waicglob
# }else
# {
# objcand<- -mlikcand
# objcur<- -mlikcur
# objglob<- -mlikglob
# }
#
#
# if(objcand<=objcur)
# {
# if(printable.opt)print(paste("full accept with ", objcand))
# objcur<-objcand
# varcurb<-varcand
# waiccur<-waiccand
# varcur<-varcand
# mlikcur<-mlikcand
#
# if(objcur<objglob)
# {
# objglob<-objcur
# waicglob<-waiccand
# varglob<-varcand
# mlikglob<-mlikcand
# if(!is.null(fm))
# modglob<-fm
#
# if(printable.opt)print(paste("full global optima with ", objcand))
# }
# }
# }
#
model.prob<-1
model.prob.fix<-1
return(list(varcur = varglob, waiccur = waicglob, mlikcur = mlikglob, log.prob.cur = model.prob,log.prob.fix = model.prob.fix, varglob = varglob, waicglob = waicglob, mlikglob = mlikglob, modglob = modglob))
},
#forward backward random dance
forw_backw_walk = function(model)
{
varcur<-rbinom(n = Nvars,size = 1,prob = runif(n = 1,min = 0,max = model$p1))
mlikcur<- -Inf
waiccur<- Inf
for(i in 1:model$steps)
{
fff<-forward_selection(list(varcur=rbinom(n = Nvars,size = 1,prob = runif(n = 1,min = 0,max = model$p1)),mlikcur=-Inf,waiccur =Inf,locstop = FALSE,statid=-1))
if(objective ==1)
{
if(fff$mlikglob>mlikcur)
{
mlikcur<-fff$mlikglob
varcur<-fff$varglob
waiccur<-fff$waicglob
}
}
else
{
if(fff$waicglob<waiccur)
{
mlikcur<-fff$mlikglob
varcur<-fff$varglob
waiccur<-fff$waicglob
}
}
set.seed(i*model$steps)
bbb<-backward_selection(list(varcur=rbinom(n = Nvars,size = 1,prob = runif(n = 1,min = model$p1,max = 1)),mlikcur=-Inf,waiccur =Inf,locstop = FALSE,statid=-1))
if(objective ==1)
{
if(bbb$mlikglob>mlikcur)
{
mlikcur<-bbb$mlikglob
varcur<-bbb$varglob
waiccur<-bbb$waicglob
}
}
else
{
if(bbb$waicglob<waiccur)
{
mlikcur<-bbb$mlikglob
varcur<-bbb$varglob
waiccur<-bbb$waicglob
}
}
}
if(model$reverse == FALSE)
{
vect<-buildmodel(max.cpu = 1,varcur.old = varcur,statid = -1,switch.type = type.randomize,min.N = min.N.randomize,max.N = max.N.randomize)
varcur<-vect[[1]]$varcur
#if(printable.opt)print(varcur)
cluster<-TRUE
if(is.null(vect[[1]]$formula))
{
cluster<-FALSE
if(printable.opt)print("!!!!Back Forw reverse model already estimated!!!!")
}else
{
mod <- lapply(X = vect, FUN = fitmodel)
}
if(cluster)
{
waiccur<-mod[[1]]$waic
mlikcur<-mod[[1]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcur)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcur,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
# incorporate what happens for the backward optimization
model.prob<-vect[[1]]$log.mod.switch.prob
model.prob.fix<-vect[[1]]$log.mod.switchback.prob
}else # incorporate what happens for the reverse move
{
model.probs<-calculate.move.logprobabilities(switch.type = type.randomize,varold = varcur, varnew = model$varold,min.N = min.N.randomize,max.N = max.N.randomize)
model.prob<-model.probs$log.switch.forw.prob
model.prob.fix<-model.probs$log.switch.back.prob
}
return(list(varcur = varcur, waiccur = waiccur, mlikcur = mlikcur, log.prob.cur = model.prob,log.prob.fix = model.prob.fix, varglob = varcur, waicglob = waiccur, mlikglob = mlikcur))
},
#local greedy optimization
learnlocalND=function(model)
{
# Step.nd
varcand<-model$varcur
varglob<-model$varcur
varcurb<-model$varcur
mlikcand<- model$mlikcur
waiccand<-model$waiccur
modglob<-NULL
fm<-NULL
fmb<-NULL
opt.achieved<-FALSE
# estimate large jump in a reverse move
if(model$reverse || is.infinite(mlikcand))
{
vectbg<-buildmodel(max.cpu = 1,varcur.old = varcand,statid = model$statid,switch.type=8, min.N = min.N,max.N = max.N)
if(!is.null(vectbg[[1]]$formula))
{
bgmod <- lapply(X = vectbg,FUN = .self$fitmodel)
waiccand<-bgmod[[1]]$waic
mlikcand<-bgmod[[1]]$mlik
}
else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
}
if(printable.opt)print(paste("Begin with ",mlikcand))
mlikglob<- mlikcand
mlikcand<- mlikcand
waiccand<- waiccand
waicglob<- waiccand
waiccur<- waiccand
buf.M.nd <- M.nd
if(model$switch.type == 5)
{
buf.M.nd = Nvars - sum(varcurb)
}else if(model$switch.type == 6)
{
buf.M.nd = sum(varcurb)
}
if(buf.M.nd == 0)
buf.M.nd = 1
if(M.nd<buf.M.nd)
buf.M.nd<-M.nd
for(iterat in 1:buf.M.nd)
{
withRestarts(tryCatch({
# statistics <- describe(statistics)
mmax.cpu = max.cpu
if(model$switch.type == 5)
{
mmax.cpu = Nvars - sum(varcurb)
}else if(model$switch.type == 6)
{
mmax.cpu = sum(varcurb)
}
if(mmax.cpu == 0)
mmax.cpu = 1
vect<-buildmodel(max.cpu = mmax.cpu,varcur.old = varcurb,statid = model$statid, switch.type = model$switch.type,min.N = min.N,max.N = max.N)
cluster<-TRUE
flag1<-0
for(mod_id in 1:mmax.cpu)
{
if(is.null(vect[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==mmax.cpu)
{
cluster<-FALSE
if(printable.opt)print("!!!!Greedy Models already estimated!!!!")
}else
{
res.par <- parallelize(X = vect,FUN = .self$fitmodel)
}
for(mod_id in 1:mmax.cpu)
{
varcand1<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand1<-res.par[[mod_id]]$waic
mlikcand1<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand1)+1
waiccand1<-statistics1[iidd,2]
mlikcand1<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand1,collapse = "")
waiccand1<-values(hashStat[iidd])[2]
mlikcand1<-values(hashStat[iidd])[1]
}
if(objective==0)
{
objcand<-waiccand1
objcur<-waiccand
objglob<-waicglob
}
else
{
objcand<- -mlikcand1
objcur<- -mlikcand
objglob<- -mlikglob
}
if(objcand<objcur || mod_id ==1)
{
varcand<-varcand1
waiccand<-waiccand1
mlikcand<-mlikcand1
if(printable.opt)print(paste("GREEDY update local optima with ", objcand))
if(cluster)
fm<-res.par[[mod_id]]
}
}
#if(printable.opt)print(waiccand)
if(objective==0)
{
objcand<-waiccand1
objcur<-waiccand
objglob<-waicglob
}
else
{
objcand<- -mlikcand1
objcur<- -mlikcand
objglob<- -mlikglob
}
if(objcur<objglob)
{
waicglob<-waiccand
varglob<-varcand
varcurb<-varcand
mlikglob<-mlikcand
if(cluster)
modglob<-fm
if(printable.opt)print(paste("GREEDY update global optima with ", objcur))
}
}),abort = function(){opt.achieved <- TRUE; fm<-fmb;closeAllConnections();options(error=traceback); onerr<-TRUE})
if(objcur!=objglob)
{
if(locstop.nd)
{
break
}else
{
varcurb<-varcand
}
}
}
#!#if(printable.opt)print(points)
if(model$reverse == FALSE)
{
vect<-buildmodel(max.cpu = 1,varcur.old = varcand,statid = model$statid,switch.type = type.randomize,min.N = min.N.randomize,max.N = max.N.randomize)
varcur<-vect[[1]]$varcur
#if(printable.opt)print(varcur)
cluster<-TRUE
if(is.null(vect[[1]]$formula))
{
cluster<-FALSE
if(printable.opt)print("!!!!Greedy reverse model already estimated!!!!")
}else
{
mod <- lapply(X = vect, FUN = fitmodel)
}
if(cluster)
{
waiccur<-mod[[1]]$waic
mlikcur<-mod[[1]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcur)+1
waiccur<-statistics1[iidd,2]
mlikcur<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcur,collapse = "")
waiccur<-values(hashStat[iidd])[2]
mlikcur<-values(hashStat[iidd])[1]
}
# incorporate what happens for the backward optimization
model.prob<-vect[[1]]$log.mod.switch.prob
model.prob.fix<-vect[[1]]$log.mod.switchback.prob
}else # incorporate what happens for the reverse move
{
model.probs<-calculate.move.logprobabilities(switch.type = type.randomize,varold = varcand, varnew = model$varold,min.N = min.N.randomize,max.N = max.N.randomize)
model.prob<-model.probs$log.switch.forw.prob
model.prob.fix<-model.probs$log.switch.back.prob
varcur <- varcand
waiccur <- waiccand
mlikcur <- mlikcand
}
return(list(varcur = varcur, waiccur = waiccur, mlikcur = mlikcur, log.prob.cur = model.prob,log.prob.fix = model.prob.fix, varglob = varglob, waicglob = waicglob, mlikglob = mlikglob, modglob = modglob))
},
#global emjmcmc procedure for model selection (hyper heuristic logic in terms of COP)
modejumping_mcmc=function(glob.model)
{
stm <- proc.time()
if(printable.opt)print("Begin model selection EMJMCMC2016 procedure")
set.seed(runif(n = 1, min = 1, max = seed), kind = NULL, normal.kind = NULL)
acc_moves<-1
accept_old<-1
distrib_of_proposals <- glob.model$distrib_of_proposals
distrib_of_neighbourhoods <- glob.model$distrib_of_neighbourhoods
# do the search and simulations accross the modes
g.results[4,1]<- 0
g.results[4,2]<- 0
if(glob.model$presearch)
{
forward_selection(list(varcur=rep(0,length(fparam.example)),mlikcur=-Inf,waiccur =Inf,locstop = glob.model$locstop,statid=-1))
backward_selection(list(varcur=rep(1,length(fparam.example)),mlikcur=-Inf,waiccur =Inf,locstop = glob.model$locstop,statid=-1))
if(exists("statistics1")&&recalc.margin < 2^Nvars)
{
p.add <<- as.array(post_proceed_results(statistics1)$p.post)
}
else if(exists("hashStat")&&recalc.margin < 2^Nvars)
{
p.add <<- as.array(post_proceed_results_hash(hashStat)$p.post)
}
}else
{
p.add<<-array(data = 0.1,Nvars)
p.post<-array(data = 0.1,Nvars)
vec<-rbinom(n = Nvars,size = 1,prob = 0.0000001) # generate an initial solution
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
}
waiccur<-Inf
waicglob<-Inf
mlikcur<- -Inf
mlikglob<- -Inf
ratcur<- -Inf
#set up initial parameters
if(is.null(glob.model$varcur))
{
if((!is.na(g.results[1,2]))&&g.results[1,2]>0)
{
vec<-dectobit(g.results[1,2]-1)
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
waiccur<-g.results[2,1]
waicglob<- g.results[2,1]
mlikcur<- g.results[1,1]
mlikglob<- g.results[1,1]
ratcur<- g.results[1,1]
print(paste("initial solution is set with mlik of ",mlikcur))
}else{
vec<-rbinom(n = Nvars,size = 1,prob = 0.5) # generate an initial solution
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
}
}else if(length(glob.model$varcur[which(glob.model$varcur %in% c(0,1))])==Nvars)
{
varcur<-glob.model$varcur
}
else
{
if(printable.opt)print("Incorrect initial solution set be the user, a random one is generated")
vec<-rbinom(n = Nvars,size = 1,prob = 0.5) # generate an initial solution
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
}
varcurb<-varcur
varglob<-varcur
modglob<-NULL
p1 = array(data = 0.0001,dim = Nvars)
p2 = array(data = 0.9999,dim = Nvars)
j<-0
j.a<-0
p.post<-array(data = 1,dim = Nvars)
waiccur<-Inf
waicglob<-Inf
mlikcur<- -Inf
mlikglob<- -Inf
ratcur<- -Inf
fm<-NULL
eps.emp<-normprob(p1,p2)
max.cpu.buf<-max.cpu
delta.time <- 0
LocImprove<-0
LocNeighbor<-0
max.cpu.buf<-max.cpu.glob
while((eps.emp>=glob.model$eps || j<= glob.model$maxit || j <= glob.model$burnin) && delta.time < glob.model$max.time && g.results[4,1]<= glob.model$trit && g.results[4,2]<= glob.model$trest)
{
p1<-p.post/acc_moves
set.seed(runif(n = 1, min = 1, max = seed*100), kind = NULL, normal.kind = NULL)
LocImprove <- (sample.int(n = 5,size = 1,prob = distrib_of_proposals) - 1)
LocNeighbor<-(sample.int(n = 7,size = 1,prob = distrib_of_neighbourhoods[LocImprove+1,]))
switch.type.glob.buf = LocNeighbor
switch.type.buf = LocNeighbor
if(LocNeighbor == 7)
{
switch.type.glob.buf = 9
switch.type.buf = 9
}
#if(printable.opt)print(LocImprove)
j<-j+1
j.a<-j.a+1
if(j%%glob.model$print.freq == 0)
{
print(paste(j," iterations completed up to now after ",delta.time," cpu minutes"," best MLIK found ",g.results[1,1] ," current mlik found ",mlikcur, "current acceptance ratio ",acc_moves/j.a))
}
if(j%%100==0)
seed = runif(n = 1,min = 0,max = 100000)
# the small part of the code to be upgraded at least slightly
if(allow_offsprings %in% c(1,2) && j%%mutation_rate == 0 && (j<=last.mutation || Nvars!=Nvars.max))
{
if(Nvars>Nvars.max || j==mutation_rate)
{
#do the stuff here
if(j==mutation_rate)
fparam.pool<<-c(fparam.pool,filtered)
to.del <- which(p.add < p.allow.tree)
if(length(to.del)==Nvars)
to.del<-to.del[-sample.int(n = Nvars,size = sample.int(n=Nvars-1,size = 1),prob = p.add+p.epsilon)]
if(length(to.del)<Nvars-Nvars.max)
{
tdl.id<-order(p.add,decreasing = T)
to.del<-to.del[-tdl.id[1:Nvars.max]]
}
print("Data filtered! Insignificant variables deleted!")
# keysarr <- as.array(keys(hashStat))
# keysarr.new<-NULL
# values.new<-values(hashStat)
# for(id.replace in to.del){
# for(jjj in 1:length(keysarr))
# {
# if(!stri_sub(keysarr[jjj],from = id.replace, to = id.replace)=="1")
# {
# keysarr.new<-c(keysarr.new,stri_sub(keysarr[jjj],from = 1, to = Nvars.max))
# }
# else
# {
#
# }
# }
# }
# keysarr.new<-unique(keysarr.new)
if(length(to.del)>0)
{
clear(hashStat)
#rm(hashStat)
gc()
#hashStat<<-hash(keys=keysarr.new,values=as.list(data.frame((values.new))))
hashStat<<-hash()
fparam<<-fparam[-to.del]
Nvars<<-length(fparam)
Nvars.init<<-Nvars
p.add<<-p.add[-to.del]
p.post<-array(data = 1,dim = Nvars)
#print(paste("mutation happended ",proposal," tree added"))
varcurb<-varcurb[1:Nvars]
varcand<-varcurb[1:Nvars]
varglob<-varcurb[1:Nvars]
p1 <- array(0,dim = (Nvars))
p2 <- array(1,dim = (Nvars))
acc_moves<-1
j.a<-1
}
}
else
{
if(Nvars>=Nvars.max)
{
idmut<-(which(p.add[(Nvars.init+1):Nvars] <= p.allow.replace) + Nvars.init)
lidmut<-length(idmut) #maximal number of covariates that can die out
if(lidmut>0)
{
p.del<-(lidmut - sum(p.add[idmut]))/lidmut
lidmut<-rbinom(n = 1,size = lidmut,prob = p.del)
}
}else
{
idmut<-(Nvars+1):Nvars.max
lidmut<-Nvars.max-Nvars
}
for(idel in 1:lidmut){
p.del<-1-(sum(p.add))/Nvars
mother<-ifelse(runif(n = 1,min = 0,max = 1)<=p.del,fparam[which(rmultinom(n = 1,size = 1,prob = p.add/2)==1)],fparam[runif(n = 1,min = 1,max=Nvars.init)])
ltreem<-stri_length(mother)
mother<-stri_sub(mother,from=2, to = ltreem)
if(allow_offsprings==1)
sjm<-sum(stri_count_fixed(str = mother, pattern = c("&","|")))
else
sjm<-sum(stri_count_fixed(str = mother, pattern = c("+","*")))
if(sjm<=max.tree.size)
{
#p.del<-1-(sum(p.add))/Nvars
father<-ifelse(runif(n = 1,min = 0,max = 1)<=p.del,fparam.pool[runif(n = 1,min = 1,max=length(fparam.pool))],fparam[which(rmultinom(n = 1,size = 1,prob = p.add/2)==1)])
ltreef<-stri_length(father)
father<-stri_sub(father,from=2, to = ltreef)
if(allow_offsprings==1)
sjf<-sum(stri_count_fixed(str = father, pattern = c("&","|")))
else
sjf<-sum(stri_count_fixed(str = father, pattern = c("+","*")))
if(sjm+sjf+1<=max.tree.size)
{
if(allow_offsprings==1)
{
if(!grepl(father, mother,fixed = T)&&!grepl(mother, father,fixed = T))
{
proposal<-stri_paste(paste(ifelse(runif(n = 1,min = 0,max = 1)<p.nor,"I((1-","I(("),mother,sep = ""),paste(ifelse(runif(n = 1,min = 0,max = 1)<p.nor,"(1-","("),father,"))",sep = ""),sep = ifelse(runif(n = 1,min = 0,max = 1)<p.and,")&",")|"))
}
else
{
if(max(sjm,sjf)>1)
{
t.d<-sample.int(size = 1,n = (max(sjm,sjf)+1))
if(sjm>=sjf)
{
loc<-c(1,stri_locate_all(str = mother,regex = "\\&|\\||\\*|\\+")[[1]][,1],stri_length(mother))
proposal<-stri_paste(stri_sub(mother,from = 1,to = loc[t.d]-1),stri_sub(mother,from = (loc[t.d+1]+(t.d==1)),to = stri_length(mother)))
}else
{
loc<-c(1,stri_locate_all(str = father,regex = "\\&|\\||\\*|\\+")[[1]][,1],stri_length(father))
proposal<-stri_paste(stri_sub(father,from = 1,to = loc[t.d]-1),stri_sub(father,from = (loc[t.d+1]+(t.d==1)),to = stri_length(father)))
}
diffs<-(stri_count_fixed(str = proposal, pattern = "(")-stri_count_fixed(str = proposal, pattern = ")"))
if(diffs>0)
proposal<-stri_paste(proposal,stri_paste(rep(")",diffs),collapse = ""),collapse = "")
if(diffs<0)
proposal<-stri_paste(stri_paste(rep("(",-diffs),collapse = ""),proposal,collapse = "")
proposal<-stri_paste("I",proposal)
#print(paste("&&&&&&",mother,"ssss",father))
}
else
proposal<-stri_paste("I",mother)
}
#proposal<-stri_paste("I",mother)
}
else
{
proposal<-stri_paste(paste(ifelse(runif(n = 1,min = 0,max = 1)<p.nor,"I(","I(-"),mother,sep = ""),paste("(",father,"))",sep = ""),sep = ifelse(runif(n = 1,min = 0,max = 1)<p.and,"*","+"))
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
while((proposal %in% fparam))
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
}
}
else
{
t.d<-sample.int(size = 1,n = (max(sjm,sjf)+1))
if(sjm>=sjf)
{
loc<-c(1,stri_locate_all(str = mother,regex = "\\&|\\||\\*|\\+")[[1]][,1],stri_length(mother))
proposal<-stri_paste(stri_sub(mother,from = 1,to = loc[t.d]-1),stri_sub(mother,from = (loc[t.d+1]+(t.d==1)),to = stri_length(mother)))
}else
{
loc<-c(1,stri_locate_all(str = father,regex = "\\&|\\||\\*|\\+")[[1]][,1],stri_length(father))
proposal<-stri_paste(stri_sub(father,from = 1,to = loc[t.d]-1),stri_sub(father,from = (loc[t.d+1]+(t.d==1)),to = stri_length(father)))
}
diffs<-(stri_count_fixed(str = proposal, pattern = "(")-stri_count_fixed(str = proposal, pattern = ")"))
if(diffs>0)
proposal<-stri_paste(proposal,stri_paste(rep(")",diffs),collapse = ""),collapse = "")
if(diffs<0)
proposal<-stri_paste(stri_paste(rep("(",-diffs),collapse = ""),proposal,collapse = "")
proposal<-stri_paste("I",proposal)
#print(paste("!!!!!",mother,"ssss",father))
}
#maybe check correlations here
if( (!(proposal %in% fparam)) && Nvars<Nvars.max)
{
#if(cor())
fparam<<-c(fparam,proposal)
Nvars<<-as.integer(Nvars+1)
p.add<<-as.array(c(p.add,p.allow.replace))
p.post<-as.array(c(p.post,1))
if(printable.opt)
print(paste("mutation happended ",proposal," tree added"))
}
else if(!(proposal %in% fparam))
{
to.del<-(which(p.add[(Nvars.init+1):Nvars]< p.allow.replace)+ Nvars.init)
lto.del<-length(x = to.del)
if(lto.del>0)
{
id.replace <- to.del[round(runif(n = 1,min = 1,max = lto.del))]
if(printable.opt)
print(paste("mutation happended ",proposal," tree replaced ", fparam[id.replace]))
fparam[id.replace]<<-proposal
keysarr <- as.array(keys(hashStat))
p.add[id.replace]<<-p.allow.replace
for(jjj in 1:length(keysarr))
{
if(stri_sub(keysarr[jjj],from = id.replace, to = id.replace)=="1")
{
del(x = keysarr[jjj],hash = hashStat)
}
}
}
}
}
}
varcurb<-c(varcurb,array(1,dim = (Nvars -length(varcurb))))
varcand<-c(varcand,array(1,dim = (Nvars -length(varcand))))
varglob<-c(varglob,array(1,dim = (Nvars -length(varglob))))
p.post<- array(1,dim = (Nvars))
p1 = c(p1,array(0,dim = (Nvars -length(p1))))
p2 = c(p1,array(1,dim = (Nvars -length(p1))))
acc_moves<-1
j.a<-1
}
} else if(allow_offsprings == 3 && j%%mutation_rate == 0 && (j<=last.mutation || Nvars!=Nvars.max))
{
#if(latnames[1]!="")
# perform preliminary filtration here
if(Nvars>Nvars.max || j==mutation_rate)
{
#pool.cor.prob = T
#do the stuff here
if(j==mutation_rate)
{
fparam.pool<<-unique(c(fparam.pool,filtered))
if(!pool.cor.prob)
pool.probs<-array(data = 1/length(fparam.pool),dim = length(fparam.pool))
else{
fobserved.cleaned<-fobserved
fobserved.cleaned<-stri_replace(str = fobserved.cleaned,fixed = "I(",replacement = "")
fobserved.cleaned<-stri_replace(str = fobserved.cleaned,fixed = ")",replacement = "")
fparam.pool.cleaned<-fparam.pool
fparam.pool.cleaned<-stri_replace(str = fparam.pool.cleaned,fixed = "I(",replacement = "")
fparam.pool.cleaned<-stri_replace(str = fparam.pool.cleaned,fixed = ")",replacement = "")
pool.probs<-abs(cor(estimator.args$data[[fobserved.cleaned]],estimator.args$data[,which(fparam.pool.cleaned %in% names(estimator.args$data))]))+p.epsilon
rm(fobserved.cleaned)
rm(fparam.pool.cleaned)
#print(pool.probs[1:100])
}
}
to.del <- which(p.add < p.allow.tree)
if(length(to.del)==Nvars)
to.del<-to.del[-sample.int(n = Nvars,size = sample.int(n=Nvars-1,size = 1),prob = p.add+p.epsilon)]
if(length(to.del)<Nvars-Nvars.max)
{
tdl.id<-order(p.add,decreasing = T)
to.del<-to.del[-tdl.id[1:Nvars.max]]
}
print("Data filtered! Insignificant variables deleted!")
if(length(to.del)>0)
{
clear(hashStat)
#rm(hashStat)
#gc()
#hashStat<<-hash(keys=keysarr.new,values=as.list(data.frame((values.new))))
#rm(hashStat)
hashStat<<-hash()
#clear(hashStat)
#hashStat<<-hash()
fparam<<-fparam[-to.del]
#if(!keep.origin)
# pool.probs[which(fparam.pool %in% fparam)]<-1
Nvars<<-length(fparam)
Nvars.init<<-Nvars
p.add<<-p.add[-to.del]
p.post<-array(data = 1,dim = Nvars)
#print(paste("mutation happended ",proposal," tree added"))
varcurb<-varcurb[-to.del]
varcand<-varcurb[-to.del]
varglob<-varcurb[-to.del]
p1 <- array(0,dim = (Nvars))
p2 <- array(1,dim = (Nvars))
acc_moves<-1
j.a<-1
}
}
else
{
if(Nvars>=Nvars.max)
{
if(keep.origin)
{
idmut<-(which(p.add[(Nvars.init+1):Nvars] <= p.allow.replace) + Nvars.init)
lidmut<-length(idmut) #maximal number of covariates that can die out
if(lidmut>0)
{
p.del<-(lidmut - sum(p.add[idmut]))/lidmut
lidmut<-rbinom(n = 1,size = lidmut,prob = p.del)
}
}else{
idmut<-which(p.add <= p.allow.replace)
lidmut<-length(idmut) #maximal number of covariates that can die out
if(lidmut>0)
{
p.del<-(lidmut - sum(p.add[idmut]))/lidmut
lidmut<-rbinom(n = 1,size = lidmut,prob = p.del)
}
}
#if(lidmut>0)
#{
# p.del<-(lidmut - sum(p.add[idmut]))/lidmut
# lidmut<-rbinom(n = 1,size = lidmut,prob = p.del)
#}
}else
{
idmut<-(Nvars+1):Nvars.max
lidmut<-Nvars.max-Nvars
}
# now having chosen the candidates to be deleted we can propose new variables
idel<-1
repsd = 1
while(idel <= lidmut && repsd <=lidmut*100){
repsd = repsd +1
#gen.prob<-c(1,1,1,1,1)#just uniform for now
action.type <- sample.int(n = 5,size = 1,prob = gen.prob)
if(action.type==1)
{
# mutation (add a leave not in the search space)
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1,prob = pool.probs)]
}else if(action.type==2){
# crossover type of a proposal
# generate a mother
#actvars<-which(varcurb==1)
mother<-ifelse(runif(n = 1,min = 0,max = 1)<=pool.cross,fparam[sample.int(n =Nvars, size =1,prob = p.add+p.epsilon)],fparam.pool[sample.int(n = length(fparam.pool),size =1,prob = pool.probs)])
ltreem<-stri_length(mother)
mother<-stri_sub(mother,from=1, to = ltreem)
#sjm<-sum(stri_count_fixed(str = mother, pattern = c("+","*")))
# generate a father
father<-ifelse(runif(n = 1,min = 0,max = 1)<=pool.cross,fparam[sample.int(n = Nvars, size =1,prob = p.add+p.epsilon)],fparam.pool[sample.int(n = length(fparam.pool),size =1,prob = pool.probs)])
ltreef<-stri_length(father)
father<-stri_sub(father,from=1, to = ltreef)
#sjf<-sum(stri_count_fixed(str = father, pattern = c("+","*")))
proposal<-stri_paste("I(",stri_paste(mother,father,sep="*"),")",sep = "")
}else if(action.type==3){
proposal<-ifelse(runif(n = 1,min = 0,max = 1)<=pool.cross,fparam[sample.int(n = Nvars,size =1, prob = p.add+p.epsilon)],fparam.pool[sample.int(n = length(fparam.pool),size =1,prob = pool.probs)])
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
}else if(action.type==4){
# select a subset for the projection
spad = sum(p.add)
actvars <- which(rbinom(n = length(fparam),size = 1,prob = p.add/spad+p.epsilon)==1)
if(length(actvars)<=1)
{
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
}else{
capture.output(withRestarts(tryCatch({
#print(as.formula(stri_paste(fobserved,"~ 1 +",paste0(fparam[actvars],collapse = "+"))))
# get the projection coefficients as the posterior mode of the fixed effects
if(deep.method == 1){
bet.act <- do.call(.self$estimator, c(estimator.args,as.formula(stri_paste(fobserved,"~ 1 +",paste0(fparam[actvars],collapse = "+")))))$summary.fixed$mean
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
bet.act<-round(bet.act, digits = 8)
bet.act<-stri_paste("m(",bet.act,",",sep = "")
# make a projection
bet.act<-stri_paste(bet.act,c("1",fparam[actvars]),")",sep = "")
bet.act<-stri_paste("I(",bet.act,")",sep = "")
proposal<-stri_paste("I(",stri_paste(bet.act,collapse = "+"),")",collapse = "")
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
#print(proposal)
}else if(deep.method == 2){
cursigma = sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)]
bet.act = gnlr(y=data.example[[fobserved]],
distribution = estimator.args$distribution,
mu = as.formula(stri_paste("~",estimator.args$link,"(",cursigma,"(","b0 +",paste0("b",1:length(actvars),"*",fparam[actvars],collapse = "+"),"))")),
pmu = rep(0,length(actvars)+1))$coefficients
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
#bet.act<-round(bet.act, digits = 2)
bet.act<-round(bet.act, digits = 8)
bet.act<-stri_paste("m(",bet.act,",",sep = "")
# make a projection
bet.act<-stri_paste(bet.act,c("1",fparam[actvars]),")",sep = "")
bet.act<-stri_paste("I(",bet.act,")",sep = "")
proposal<-stri_paste("I(",stri_paste(bet.act,collapse = "+"),")",collapse = "")
proposal<-stri_paste("I(",cursigma,"(",proposal,"))",sep = "")
}else if(deep.method == 3){
cursigma = sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)]
forstr = stri_paste("~",estimator.args$link,"(",cursigma,"(","m(0,1) +",paste0("m(",rnorm(length(actvars),0,1),",",fparam[actvars],")",collapse = "+"),"))")
forstr = stri_replace_all_fixed(str = forstr,pattern = c("m(-"),replacement = "m(")
forstr = stri_replace_all_fixed(str = forstr,pattern = c("m("),replacement = "m(b_")
#print(as.formula(forstr))
nlrr = gnlr(y=data.example[[fobserved]],
distribution = estimator.args$distribution,
mu = as.formula(forstr),
pmu = rnorm(stri_count_fixed(str = forstr,pattern = "m("),0,0.0001))#$coefficients
beg.rep = stri_locate_all(str = forstr,fixed = "m(b")[[1]][,2]
end.rep = stri_locate_all(str = forstr,fixed = "," )[[1]][,2]
bet.act = nlrr$coefficients
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
bet.act<-round(bet.act, digits = 8)
torepl = stri_sub(str = forstr,from = beg.rep,to = end.rep)
for(i in 1:length(bet.act))
forstr = stri_replace_all_fixed(str = forstr,pattern =torepl[i],replacement = stri_paste(bet.act[i],","))
forstr = stri_replace_all_fixed(str = forstr,pattern =paste0("~",estimator.args$link),replacement = "I")
proposal<-forstr
}
else{
bet.act <- rnorm(n = (length(actvars)+1),mean = 0,sd = 1)
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
bet.act<-round(bet.act, digits = 8)
bet.act<-stri_paste("m(",bet.act,",",sep = "")
# make a projection
bet.act<-stri_paste(bet.act,c("1",fparam[actvars]),")",sep = "")
bet.act<-stri_paste("I(",bet.act,")",sep = "")
proposal<-stri_paste("I(",stri_paste(bet.act,collapse = "+"),")",collapse = "")
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
}
}, error = function(err) {
#print(err)
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
},finally = {
proposal = proposal
})))
#print(proposal)
if(is.na(proposal))
{
print(fparam[actvars])
print(actvars)
print(bet.act)
}
}
}else if(action.type==5)
{
#reduce an operator fparam[idel]
#print("reduction")
#print(idel)
if(idel>length(fparam))
{
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
}else{
cpm<-sum(stri_count_fixed(str = fparam[idel], pattern = c("*")))
if(length(cpm)==0)
cpm<-0
if(cpm>0)
{
t.d<-sample.int(size = 1,n = (cpm))
#print(fparam[idel])
loc<-c(1,stri_locate_all(str = fparam[idel],regex = "\\*")[[1]][,1],stri_length(fparam[idel]))
proposal<-stri_paste(stri_sub(fparam[idel],from = 1,to = loc[t.d]-1+2*(t.d==1)),stri_sub(fparam[idel],from = (loc[t.d+1]+(t.d==1)),to = stri_length(fparam[idel])))
if(runif(n = 1,min = 0,max = 1)<del.sigma){
dsigmas<-sample.int(size = 1,n = length(sigmas))
if(sigmas[dsigmas]!="")
proposal<-stri_replace_all_fixed(replacement = "",str = proposal,pattern = sigmas[dsigmas])
}
so<-stri_count_fixed(str = proposal, pattern="(")
sc<-stri_count_fixed(str = proposal, pattern=")")
#print(proposal)
if(sc>so){
proposal<-stri_paste(stri_paste("I",rep("(",sc-so), collapse = ''),proposal)
}else if(sc<so)
proposal<-stri_paste(proposal,stri_paste(rep(")",so-sc),collapse = ''))
#print(proposal)
}else{
proposal<-fparam[idel]
}
}
}
sj<-(stri_count_fixed(str = proposal, pattern = "*"))
sj<-sj+(stri_count_fixed(str = proposal, pattern = "+"))
sj<-sj+sum(stri_count_fixed(str = proposal, pattern = sigmas))
sj<-sj+1
if(length(sj)==0)
{
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
sj <- 0
}else if(is.na(proposal)||is.na(sj))
{
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
sj <- 0
}
else if(sj>max.tree.size)
{
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
}
add<-T
ids.lat<-integer(0)
if(latnames[1]!="")
{
ids.lat<-which(fparam %in% latnames)
if(sum(stri_count_fixed(str = proposal,pattern = latnames))>0)
add<-F
}
if(length(ids.lat)==0)
ids.lat<-Nvars.max +1
#print(add)
#print(proposal)
if(proposal %in% latnames)
{
if((proposal %in% fparam[ids.lat]))
add<-F
}else{
if(add){
withRestarts(tryCatch(capture.output({
bet.act <- do.call(.self$estimator, c(estimator.args,as.formula(stri_paste(fobserved,"~ 1 +",paste0(c(fparam[-ids.lat],proposal),collapse = "+")))))$summary.fixed$mean
if(is.na(bet.act[length(fparam[-ids.lat])+2])&& (action.type!=4&&gen.prob[2]==0||gen.prob[2]!=0))
{
add<-F
}else
{
idel<-idel+1
}
}, error = function(err) {
add<-F
},finally = {}
)))
}
}
#print(add)
#print("next")
if(add & Nvars<Nvars.max)# alternative restricted to correlation: if((max(cor(eval(parse(text = proposal),envir = data.example),sapply(fparam, function(x) eval(parse(text=x),envir = data.example))))<0.9999) && Nvars<Nvars.max)
{
fparam<<-c(fparam,proposal)
Nvars<<-as.integer(Nvars+1)
p.add<<-as.array(c(p.add,p.allow.replace))
p.post<-as.array(c(p.post,1))
if(printable.opt)
print(paste("mutation happended ",proposal," tree added"))
}
else if(add)#alternative restricted to correlation: if(max(abs(cor(eval(parse(text = proposal),envir = data.example),sapply(fparam, function(x) eval(parse(text=x),envir = data.example)))))<0.9999)
{
#if(action.type==4)
# print(proposal)
if(keep.origin){
to.del<-(which(p.add[(Nvars.init+1):Nvars]< p.allow.replace)+ Nvars.init)
lto.del<-length(x = to.del)
}else{
to.del<-which(p.add < p.allow.replace)
lto.del<-length(x = to.del)
}
#to.del<-(which(p.add[(Nvars.init+1):Nvars]< p.allow.replace)+ Nvars.init)
#lto.del<-length(x = to.del)
if(lto.del>0)
{
id.replace <- to.del[round(runif(n = 1,min = 1,max = lto.del))]
if(printable.opt)
print(paste("mutation happended ",proposal," tree replaced ", fparam[id.replace]))
fparam[id.replace]<<-proposal
keysarr <- as.array(keys(hashStat))
p.add[id.replace]<<-p.allow.replace
for(jjj in 1:length(keysarr))
{
if(stri_sub(keysarr[jjj],from = id.replace, to = id.replace)=="1")
{
del(x = keysarr[jjj],hash = hashStat)
}
}
}
}
}
}
if(p.add.default<1)
p.add<<-array(p.add.default,Nvars)
varcurb<-c(varcurb,array(1,dim = (Nvars -length(varcurb))))
varcand<-c(varcand,array(1,dim = (Nvars -length(varcand))))
varglob<-c(varglob,array(1,dim = (Nvars -length(varglob))))
p.post<- array(1,dim = (Nvars))
p1 = c(p1,array(0,dim = (Nvars -length(p1))))
p2 = c(p1,array(1,dim = (Nvars -length(p1))))
acc_moves<-1
j.a<-1
}else if(allow_offsprings == 4 && j%%mutation_rate == 0 && (j<=last.mutation || Nvars!=Nvars.max))
{
add.buf<-F
# perform preliminary filtration here
if(Nvars>Nvars.max || j==mutation_rate)
{
on.suggested <- 1
preaccepted<-F
#do the stuff here
if(j==mutation_rate)
{
fparam.pool<<-unique(c(fparam.pool,filtered))
if(!pool.cor.prob)
pool.probs<-array(data = 1/length(fparam.pool),dim = length(fparam.pool))
else{
fobserved.cleaned<-fobserved
fobserved.cleaned<-stri_replace(str = fobserved.cleaned,fixed = "I(",replacement = "")
fobserved.cleaned<-stri_replace(str = fobserved.cleaned,fixed = ")",replacement = "")
fparam.pool.cleaned<-fparam.pool
fparam.pool.cleaned<-stri_replace(str = fparam.pool.cleaned,fixed = "I(",replacement = "")
fparam.pool.cleaned<-stri_replace(str = fparam.pool.cleaned,fixed = ")",replacement = "")
pool.probs<-abs(cor(estimator.args$data[[fobserved.cleaned]],estimator.args$data[,which(fparam.pool.cleaned %in% names(estimator.args$data))]))+p.epsilon
rm(fobserved.cleaned)
rm(fparam.pool.cleaned)
#print(pool.probs[1:100])
}
}
to.del <- which(p.add < p.allow.tree)
if(length(to.del)==Nvars)
to.del<-to.del[-sample.int(n = Nvars,size = sample.int(n=Nvars-1,size = 1),prob = p.add+p.epsilon)]
if(length(to.del)<Nvars-Nvars.max)
{
tdl.id<-order(p.add,decreasing = T)
to.del<-to.del[-tdl.id[1:Nvars.max]]
}
print("Data filtered! Insignificant variables deleted!")
if(length(to.del)>0)
{
clear(hashStat)
#rm(hashStat)
#gc()
#hashStat<<-hash(keys=keysarr.new,values=as.list(data.frame((values.new))))
clear(hashStat)
#hashStat<<-hash()
fparam<<-fparam[-to.del]
if(!keep.origin)
pool.probs[which(fparam.pool %in% fparam)]<-1
Nvars<<-length(fparam)
Nvars.init<<-Nvars
p.add<<-p.add[-to.del]
p.post<-array(data = 1,dim = Nvars)
#print(paste("mutation happended ",proposal," tree added"))
varcurb<-varcurb[-to.del]
varcand<-varcurb[-to.del]
varglob<-varcurb[-to.del]
p1 <- array(0,dim = (Nvars))
p2 <- array(1,dim = (Nvars))
acc_moves<-1
j.a<-1
super.backward = F
}
}
else
{
if(Nvars>=Nvars.max)
{
# delete those that are not in the active model with probability 0.5 each
if(keep.origin)
{
idmut<-(which(p.add[(Nvars.init+1):Nvars] <= p.allow.replace) + Nvars.init)
lidmut<-length(idmut) #maximal number of covariates that can die out
if(lidmut>0)
{
p.del<-(lidmut - sum(p.add[idmut]))/lidmut
lidmut<-rbinom(n = 1,size = lidmut,prob = p.del)
}
}else{
idmut<-which(p.add <= p.allow.replace)
lidmut<-length(idmut) #maximal number of covariates that can die out
if(lidmut>0)
{
p.del<-(lidmut - sum(p.add[idmut]))/lidmut
lidmut<-rbinom(n = 1,size = lidmut,prob = p.del)
}
}
#mod.id.old<-runif(n = 1000,min = 1,max = 2^Nvars)
if(on.suggested%%2==1){
if(preaccepted)
{
log.mod.switch.prob.back<-sum(abs(varcurb.buf-varcurb))
eqal.things<-which(varcurb.buf==varcurb)
log.mod.switch.prob.back<-log.mod.switch.prob.back+length(which(fparam[eqal.things]!=tmp.buf.1[eqal.things]))
log.mod.switch.prob.back<-log.mod.switch.prob.back^prand
if(printable.opt) print(paste0("afteracceptance ratio ",log.mod.switch.prob.back/log.mod.switch.prob))
if(runif(1,0,1)<=log.mod.switch.prob.back/log.mod.switch.prob)
{
if(printable.opt) print("preaccepted mutation is accepted")
mlikcur<-mlikcur.buf.2
varcurb<-varcurb.buf.2
fparam<<-tmp.buf.2
p.add<<-p.add.buf.2
}else
{
if(printable.opt) print("preaccepted mutation rejected")
fparam<<-tmp.buf.1
p.add<<-p.add.buf.1
mlikcur<-mlikcur.buf
varcurb<-varcurb.buf
}
preaccepted<-F
}
tmp.buf<-fparam[which(varcurb==1)]
tmp.buf.1<-fparam
p.add.buf.1<-p.add
# hashStat.buf.1<-copy(hashStat)
vect<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = -1,min.N = Nvars,max.N = Nvars,switch.type = 9)
res.par <- lapply(X = vect,FUN = .self$fitmodel)
mlikcur<-res.par[[1]]$mlik
varcurb<-vect[[1]]$varcur
mlikcur.buf<-mlikcur
varcurb.buf<-varcurb
if(printable.opt) print("OLDMOD")
mso=(mlikcur)#(sum(unlist(lapply(res.par, function(x) exp(x$mlik)))))
if(printable.opt) print(mso)
}else if(on.suggested%%2==0){
#tmp.buf2<-fparam[which(varcurb==1)]
tmp.buf.2<-fparam
p.add.buf.2<-p.add
vect<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = -1,min.N = Nvars,max.N = Nvars,switch.type = 9)
log.mod.switch.prob<-vect[[1]]$log.mod.switch.prob
res.par <- lapply(X = vect,FUN = .self$fitmodel)
#print(mlikcur)
mlikcur<-res.par[[1]]$mlik
varcurb<-vect[[1]]$varcur
vect<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = -1,min.N = Nvars,max.N = Nvars,switch.type = 9)
log.mod.switch.prob<-vect[[1]]$log.mod.switch.prob
res.par <- lapply(X = vect,FUN = .self$fitmodel)
#print(mlikcur)
mlikcur<-res.par[[1]]$mlik
varcurb<-vect[[1]]$varcur
mlikcur.buf.2<-mlikcur
varcurb.buf.2<-varcurb
msn=(mlikcur)#(sum(unlist(lapply(res.par, function(x) exp(x$mlik)))))
if(printable.opt) print("NEWMOD")
if(printable.opt) print(msn)
if(msn == Inf && mso == Inf ||msn == 0 && mso == 0)
{
msn<-1
mso<-1
}#*log((sum(tmp.buf%in%fparam)==length(tmp.buf)))
if(log(runif(1,0,1))>=((msn)-(mso)))
{
if(printable.opt)print("proposal is rejected")
fparam<<-tmp.buf.1
p.add<<-p.add.buf.1
mlikcur<-mlikcur.buf
varcurb<-varcurb.buf
preaccepted<-F
#on.suggested<-on.suggested+1
}else{
if(printable.opt)print("mutation is preaccepted")
#fparam<<-tmp.buf.1
#p.add<<-p.add.buf.1
#lidmut<-0
preaccepted<-T
}
}
on.suggested<-on.suggested+1
}else
{
idmut<-(Nvars+1):Nvars.max
lidmut<-Nvars.max-Nvars
}
# now having chosen the candidates to be deleted we can propose new variables
idel<-1
while(idel <= lidmut){
#gen.prob<-c(1,1,1,1,1)#just uniform for now
action.type <- sample.int(n = 5,size = 1,prob = gen.prob)
if(action.type==1)
{
# mutation (add a leave not in the search space)
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1,prob = pool.probs)]
}else if(action.type==2){
# crossover type of a proposal
# generate a mother
#actvars<-which(varcurb==1)
mother<-ifelse(runif(n = 1,min = 0,max = 1)<=pool.cross,fparam[sample.int(n =Nvars, size =1,prob = p.add+p.epsilon)],fparam.pool[sample.int(n = length(fparam.pool),size =1,prob = pool.probs)])
ltreem<-stri_length(mother)
mother<-stri_sub(mother,from=1, to = ltreem)
#sjm<-sum(stri_count_fixed(str = mother, pattern = c("+","*")))
# generate a father
father<-ifelse(runif(n = 1,min = 0,max = 1)<=pool.cross,fparam[sample.int(n = Nvars, size =1,prob = p.add+p.epsilon)],fparam.pool[sample.int(n = length(fparam.pool),size =1,prob = pool.probs)])
ltreef<-stri_length(father)
father<-stri_sub(father,from=1, to = ltreef)
#sjf<-sum(stri_count_fixed(str = father, pattern = c("+","*")))
proposal<-stri_paste("I(",stri_paste(mother,father,sep="*"),")",sep = "")
}else if(action.type==3){
proposal<-ifelse(runif(n = 1,min = 0,max = 1)<=pool.cross,fparam[sample.int(n = Nvars,size =1, prob = p.add+p.epsilon)],fparam.pool[sample.int(n = length(fparam.pool),size =1,prob = pool.probs)])
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
}else if(action.type==4){
# select a sparse subset for the projection
spad = sum(p.add)
actvars <- which(rbinom(n = length(fparam),size = 1,prob = p.add/spad+p.epsilon)==1)
#actvars <- which(rbinom(n = Nvars,size = 1,prob = p.add+p.epsilon)==1)
if(length(actvars)<=1)
{
proposal <- fparam[1]
}else{
capture.output(withRestarts(tryCatch({
#print(as.formula(stri_paste(fobserved,"~ 1 +",paste0(fparam[actvars],collapse = "+"))))
# get the projection coefficients as the posterior mode of the fixed effects
if(deep.method == 1){
bet.act <- do.call(.self$estimator, c(estimator.args,as.formula(stri_paste(fobserved,"~ 1 +",paste0(fparam[actvars],collapse = "+")))))$summary.fixed$mean
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
bet.act<-round(bet.act, digits = 8)
bet.act<-stri_paste("m(",bet.act,",",sep = "")
# make a projection
bet.act<-stri_paste(bet.act,c("1",fparam[actvars]),")",sep = "")
bet.act<-stri_paste("I(",bet.act,")",sep = "")
proposal<-stri_paste("I(",stri_paste(bet.act,collapse = "+"),")",collapse = "")
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
#print(proposal)
}else if(deep.method == 2){
cursigma = sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)]
bet.act = gnlr(y=data.example[[fobserved]],
distribution = estimator.args$distribution,
mu = as.formula(stri_paste("~",estimator.args$link,"(",cursigma,"(","b0 +",paste0("b",1:length(actvars),"*",fparam[actvars],collapse = "+"),"))")),
pmu = rep(0,length(actvars)+1))$coefficients
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
#bet.act<-round(bet.act, digits = 2)
bet.act<-round(bet.act, digits = 8)
bet.act<-stri_paste("m(",bet.act,",",sep = "")
# make a projection
bet.act<-stri_paste(bet.act,c("1",fparam[actvars]),")",sep = "")
bet.act<-stri_paste("I(",bet.act,")",sep = "")
proposal<-stri_paste("I(",stri_paste(bet.act,collapse = "+"),")",collapse = "")
proposal<-stri_paste("I(",cursigma,"(",proposal,"))",sep = "")
}else if(deep.method == 3){
cursigma = sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)]
forstr = stri_paste("~",estimator.args$link,"(",cursigma,"(","m(0,1) +",paste0("m(",rnorm(length(actvars),0,1),",",fparam[actvars],")",collapse = "+"),"))")
forstr = stri_replace_all_fixed(str = forstr,pattern = c("m(-"),replacement = "m(")
forstr = stri_replace_all_fixed(str = forstr,pattern = c("m("),replacement = "m(b_")
#print(as.formula(forstr))
nlrr = gnlr(y=data.example[[fobserved]],
distribution = estimator.args$distribution,
mu = as.formula(forstr),
pmu = rnorm(stri_count_fixed(str = forstr,pattern = "m("),0,0.0001))#$coefficients
beg.rep = stri_locate_all(str = forstr,fixed = "m(b")[[1]][,2]
end.rep = stri_locate_all(str = forstr,fixed = "," )[[1]][,2]
bet.act = nlrr$coefficients
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
bet.act<-round(bet.act, digits = 8)
torepl = stri_sub(str = forstr,from = beg.rep,to = end.rep)
for(i in 1:length(bet.act))
forstr = stri_replace_all_fixed(str = forstr,pattern =torepl[i],replacement = stri_paste(bet.act[i],","))
forstr = stri_replace_all_fixed(str = forstr,pattern =paste0("~",estimator.args$link),replacement = "I")
proposal<-forstr
}
else{
bet.act <- rnorm(n = (length(actvars)+1),mean = 0,sd = 1)
nab<-which(is.na(bet.act))
if(length(nab)>0)
bet.act[nab]<-0
bet.act<-round(bet.act, digits = 8)
bet.act<-stri_paste("m(",bet.act,",",sep = "")
# make a projection
bet.act<-stri_paste(bet.act,c("1",fparam[actvars]),")",sep = "")
bet.act<-stri_paste("I(",bet.act,")",sep = "")
proposal<-stri_paste("I(",stri_paste(bet.act,collapse = "+"),")",collapse = "")
proposal<-stri_paste("I(",sigmas[sample.int(n = length(sigmas),size=1,replace = F,prob = sigmas.prob)],"(",proposal,"))",sep = "")
}
}, error = function(err) {
#print(err)
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
},finally = {
proposal = proposal
})))
#print(proposal)
if(is.na(proposal))
{
print(fparam[actvars])
print(actvars)
print(bet.act)
}
}
}else if(action.type==5)
{
#reduce an operator fparam[idel]
#print("reduction")
#print(idel)
if(idel>length(fparam))
{
proposal<-fparam[1]
}else{
cpm<-sum(stri_count_fixed(str = fparam[idel], pattern = c("*")))
if(length(cpm)==0)
cpm<-0
if(cpm>0)
{
t.d<-sample.int(size = 1,n = (cpm))
#print(fparam[idel])
loc<-c(1,stri_locate_all(str = fparam[idel],regex = "\\*")[[1]][,1],stri_length(fparam[idel]))
proposal<-stri_paste(stri_sub(fparam[idel],from = 1,to = loc[t.d]-1+2*(t.d==1)),stri_sub(fparam[idel],from = (loc[t.d+1]+(t.d==1)),to = stri_length(fparam[idel])))
if(runif(n = 1,min = 0,max = 1)<del.sigma){
dsigmas<-sample.int(size = 1,n = length(sigmas))
if(sigmas[dsigmas]!="")
proposal<-stri_replace_all_fixed(replacement = "",str = proposal,pattern = sigmas[dsigmas])
}
so<-stri_count_fixed(str = proposal, pattern="(")
sc<-stri_count_fixed(str = proposal, pattern=")")
#print(proposal)
if(sc>so){
proposal<-stri_paste(stri_paste("I",rep("(",sc-so), collapse = ''),proposal)
}else if(sc<so)
proposal<-stri_paste(proposal,stri_paste(rep(")",so-sc),collapse = ''))
#print(proposal)
}else{
proposal<-fparam[idel]
}
}
}
sj<-(stri_count_fixed(str = proposal, pattern = "*"))
sj<-sj+(stri_count_fixed(str = proposal, pattern = "+"))
sj<-sj+sum(stri_count_fixed(str = proposal, pattern = sigmas))
sj<-sj+1
if(sj>max.tree.size || length(sj)==0)
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
if(is.na(proposal))
proposal<-fparam.pool[sample.int(n=length(fparam.pool),size = 1)]
add<-T
tryCatch(capture.output({
bet.act <- do.call(.self$estimator, c(estimator.args,as.formula(stri_paste(fobserved,"~ 1 +",paste0(c(fparam,proposal),collapse = "+")))))$summary.fixed$mean
if(is.na(bet.act[length(fparam)+2]))
{
add<-F
}else
{
idel<-idel+1
}
}, error = function(err) {
add<-F
}))
if(add & Nvars<Nvars.max)# alternative restricted to correlation: if((max(cor(eval(parse(text = proposal),envir = data.example),sapply(fparam, function(x) eval(parse(text=x),envir = data.example))))<0.9999) && Nvars<Nvars.max)
{
fparam<<-c(fparam,proposal)
Nvars<<-as.integer(Nvars+1)
p.add<<-as.array(c(p.add,p.allow.replace))
p.post<-as.array(c(p.post,1))
#if(printable.opt)
if(printable.opt) print(paste("mutation happended ",proposal," tree added"))
}
else if(add)#alternative restricted to correlation: if(max(abs(cor(eval(parse(text = proposal),envir = data.example),sapply(fparam, function(x) eval(parse(text=x),envir = data.example)))))<0.9999)
{
if(keep.origin){
to.del<-(which(p.add[(Nvars.init+1):Nvars]< p.allow.replace)+ Nvars.init)
lto.del<-length(x = to.del)
}else{
to.del<-which(p.add < p.allow.replace)
lto.del<-length(x = to.del)
}
if(lto.del>0)
{
id.replace <- to.del[round(runif(n = 1,min = 1,max = lto.del))]
#if(printable.opt)
#print(paste("mutation suggested ",proposal," tree replaced ", fparam[id.replace]))
fparam[id.replace]<<-proposal
keysarr <- as.array(keys(hashStat))
p.add[id.replace]<<-p.allow.replace
for(jjj in 1:length(keysarr))
{
if(stri_sub(keysarr[jjj],from = id.replace, to = id.replace)=="1")
{
del(x = keysarr[jjj],hash = hashStat)
}
}
}
}
}
}
varcurb<-c(varcurb,array(1,dim = (Nvars -length(varcurb))))
varcand<-c(varcand,array(1,dim = (Nvars -length(varcand))))
varglob<-c(varglob,array(1,dim = (Nvars -length(varglob))))
p.post<- array(1,dim = (Nvars))
p1 = c(p1,array(0,dim = (Nvars -length(p1))))
p2 = c(p1,array(1,dim = (Nvars -length(p1))))
acc_moves<-1
j.a<-1
}else if(allow_offsprings > 0 && j%%mutation_rate == 0 && j>last.mutation)
{
recalc.margin = 2^Nvars
}
#withRestarts(tryCatch({
varcur<-varcurb
if(LocImprove<=3)
{
vect<-buildmodel(max.cpu = 1,varcur.old = varcurb,statid = 4 + LocImprove,min.N = min.N.glob,max.N = max.N.glob,switch.type = switch.type.glob.buf)
max.cpu.buf = 1
}else
{
vect<-buildmodel(max.cpu = max.cpu.glob,varcur.old = varcurb,statid = 4 + LocImprove,min.N = min.N,max.N = max.N,switch.type = switch.type.glob.buf)
max.cpu.buf = max.cpu.glob
}
cluster<-TRUE
flag1<-0
for(mod_id in 1:max.cpu.buf)
{
if(is.null(vect[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==max.cpu.glob)
{
cluster<-FALSE
if(printable.opt)print("!!!!Models already estimated!!!!")
}else
{
if(max.cpu.glob > 1)
res.par <- parallelize(X = vect,FUN = .self$fitmodel)
else
res.par <- lapply(X = vect,FUN = .self$fitmodel)
}
if(LocImprove>3)
{
if(printable.opt)print("!!!!Proceed with no local improvements!!!!")
p.select.y <- array(data = 0, dim = max.cpu.glob)
for(mod_id in 1:max.cpu.glob)
{
if(cluster)
{
fm<-res.par[[mod_id]]
if(is.null(fm)&&(is.na(res.par[[mod_id]]$waic)))
{
varcand<-varcurb
if(printable.opt)print("GlobMTMCMC Model Fit Error!?")
next
}
}
varcand<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand<-res.par[[mod_id]]$waic
mlikcand<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
if((mlikcand>mlikglob)) #update the parameter of interest
{
if(printable.opt)print(paste("GlobMTMCMC update waic.glob = ", waiccand))
if(printable.opt)print(paste("GlobMTMCMC update mlik.glob = ", mlikglob))
mlikglob<-mlikcand
waicglob<-waiccand
varglob<-varcand
if(cluster)
modglob<-fm
}
g1 <- waiccur
if(waiccur == Inf)
{
g1 = 1
}
p.select.y[mod_id]<-(mlikcand + vect[[mod_id]]$log.mod.switchback.prob+log(lambda(c = cc, alpha = aa, g1 = -g1, g2 = -waiccand,g.domain.pos = FALSE))) # correct for different criteria later
if(is.na(p.select.y[mod_id]))
p.select.y[mod_id] <- 0
if(is.infinite(p.select.y[mod_id]) || p.select.y[mod_id]>100000000)
{
#if(printable.opt)print(paste("very large log.w.y detected ",p.select.y[mod_id]))
p.select.y[mod_id] <- 100000000
}
}
max.p.select.y <- max(p.select.y)
p.select.y<-p.select.y-max.p.select.y
if(printable.opt)print(paste("max log.w.y is ",max.p.select.y,"normilized log.w.n.y is ", paste(p.select.y,collapse = ", ")))
ID<-sample.int(n = max.cpu.glob,size = 1,prob = exp(p.select.y))
if(printable.opt)print(paste("cand ",ID," selected"))
varcand<-vect[[ID]]$varcur
if(cluster)
{
waiccand<-res.par[[ID]]$waic
mlikcand<-res.par[[ID]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
#p.Q.cand<- p.select.y[ID]/sum(p.select.y)
if(printable.opt)print("do reverse step")
p.select.z <- array(data = 0.01, dim = max.cpu.glob)
if(max.cpu.glob!=1)
{
if(switch.type.glob.buf==5)
cstm<-6
else if(switch.type.glob.buf==6)
{
cstm<-5
}
else
{
cstm <- switch.type.glob.buf
}
vect1<-buildmodel(max.cpu = max.cpu.glob -1,varcur.old = varcand,statid = 4 + LocImprove,switch.type = cstm, min.N = min.N, max.N = max.N)
cluster<-TRUE
flag1<-0
for(mod_id in 1:(max.cpu.glob-1))
{
if(is.null(vect1[[mod_id]]$formula))
{
flag1<-flag1+1
}
}
if(flag1==(max.cpu.glob-1))
{
cluster<-FALSE
if(printable.opt)print("!!!!MTMCMC reverse models already estimated!!!!")
}else
{
res.par.back <- parallelize(X = vect1,FUN = .self$fitmodel)
}
for(mod_id in 1:(max.cpu.glob-1))
{
if(cluster)
{
if(is.null(fm)&&(is.na(res.par.back[[mod_id]]$waic)))
{
if(printable.opt)print("locMTMCMC Model Fit Error!?")
next
}
}
varcand.b<-vect1[[mod_id]]$varcur
if(cluster)
{
waiccand.b<-res.par.back[[mod_id]]$waic
mlikcand.b<-res.par.back[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand.b)+1
waiccand.b<-statistics1[iidd,2]
mlikcand.b<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand.b,collapse = "")
waiccand.b<-values(hashStat[iidd])[2]
mlikcand.b<-values(hashStat[iidd])[1]
}
if((mlikcand.b>mlikglob))
{
if(printable.opt)print(paste("GlobMTMCMC update waic.glob = ", waiccand.b))
if(printable.opt)print(paste("GlobMTMCMC update mlik.glob = ", mlikcand.b))
mlikglob<-mlikcand.b
waicglob<-waiccand.b
varglob<-varcand.b
if(cluster)
modglob<-fm
}
g1 = waiccand
if(waiccand == Inf)
{
g1 = 1
}
p.select.z[mod_id]<-(mlikcand.b+vect1[[mod_id]]$log.mod.switchback.prob+(lambda(c = cc, alpha = aa, g1 = -g1, g2 = -waiccand.b,g.domain.pos = FALSE))) # correct for different criteria later
if(is.na(p.select.z[mod_id]))
p.select.z[mod_id]=0
if(is.infinite(p.select.z[mod_id]) || p.select.z[mod_id] > 100000000)
{
#if(printable.opt)print(paste("very large log.w.y detected ",p.select.z[mod_id]))
p.select.z[mod_id] <- 100000000
}
}
}
if( waiccur == Inf)
{
g1 = 1
}
p.select.z[max.cpu.glob] <- (mlikcur+vect[[ID]]$log.mod.switch.prob+(lambda(c = cc, alpha = aa, g1 = -g1, g2 = -waiccand,g.domain.pos = FALSE)))
if(is.na(p.select.z[mod_id]))
p.select.z[mod_id]=0
if(is.infinite(p.select.z[mod_id]) || p.select.z[mod_id] > 100000000)
{
#if(printable.opt)print(paste("very large log.w.y detected ",p.select.z[mod_id]))
p.select.z[mod_id] <- 100000000
}
max.p.select.z <- max(p.select.z)
p.select.z<-p.select.z-max.p.select.z
if(printable.opt)print(paste("max log.w.z is ",max.p.select.z,"normilized log.w.n.z is ", paste(p.select.z,collapse = ", ")))
if(log(runif(n = 1,min = 0,max = 1)) < (log(sum(exp(p.select.y)))-log(sum(exp(p.select.z)))) + max.p.select.y - max.p.select.z )
{
mlikcur<-mlikcand
ratcur<-mlikcand
if(printable.opt)print(paste("global MTMCMC update ratcur = ", mlikcand))
if(printable.opt)print(paste("global MTMCMC accept move with ", waiccand))
varcurb<-varcand
waiccur<-waiccand
id<-bittodec(varcurb)+1
acc_moves<-acc_moves+1
if(j<glob.model$burnin)
{
distrib_of_proposals[5]<-distrib_of_proposals[5]+1
}else
{
if(exists("statistics1"))
{
statistics1[id,14]<-statistics1[id,14] + 1
statistics1[id,4]<-statistics1[id,4] + 1
}
p.post<- (p.post + varcurb)
}
}else if(j<glob.model$burnin && distrib_of_proposals[5]>0)
{
distrib_of_proposals[5]<-distrib_of_proposals[5] - 1
}
}else
{
if(cluster)
{
fm<-res.par[[mod_id]]
if(is.null(fm)&&(is.na(res.par[[mod_id]]$waic)))
{
varcand<-varcurb
if(printable.opt)print("EMJMCMC Model Fit Error!?")
next
}
}
varcand<-vect[[mod_id]]$varcur
if(cluster)
{
waiccand<-res.par[[mod_id]]$waic
mlikcand<-res.par[[mod_id]]$mlik
}else if(exists("statistics1"))
{
iidd<-bittodec(varcand)+1
waiccand<-statistics1[iidd,2]
mlikcand<-statistics1[iidd,1]
}else if(exists("hashStat"))
{
iidd<-paste(varcand,collapse = "")
waiccand<-values(hashStat[iidd])[2]
mlikcand<-values(hashStat[iidd])[1]
}
varcur<-varcand
}
# try local improvements
if(LocImprove<=3)
{
# sa improvements
if(LocImprove == 0 || LocImprove == 3)
{
if(printable.opt)print("Try SA imptovements")
buf.change <- array(data = 1,dim = Nvars)
buf.change[which(varcur - varcurb!=0)]=0
#buf.opt[floor(runif(n = n.size,min = 1,max = Nvars+0.999999))] = 1
if(objective ==0)
{
objold<-waiccur
objcur<-waiccand
}else
{
objold<- -mlikcur
objcur<- -mlikcand
}
model = list(statid = 4 + LocImprove, switch.type = switch.type.buf, change = buf.change,mlikcur = mlikcur,
varcur = varcur,varold = varcurb, objcur = objcur,objold = objold, sa2 = ifelse(LocImprove == 3,TRUE,FALSE) ,reverse=FALSE)
SA.forw<-learnlocalSA(model)
ratcand<-SA.forw$mlikcur
if(LocImprove == 0)
{
ids = which(buf.change == 1)
model$varcur <- SA.forw$varcur
model$waiccur<-SA.forw$waiccur
model$varcur[ids] = 1 - model$varcur[ids]
model$mlikcur<- -Inf
model$waiccur<- Inf
#estimate the jump!!!
if(objective ==0)
{
model$objold<-waiccur
}else
{
model$objold<- -ratcand
}
model$reverse = TRUE
if(switch.type.buf==5)
{
model$switch.type <- 6
}
else if(switch.type.buf==6)
{
model$switch.type <- 5
}
SA.back<-learnlocalSA(model)
}
if(LocImprove == 0)
{
thact<-sum(ratcand, - ratcur, - SA.forw$log.prob.cur,SA.forw$log.prob.fix,SA.back$log.prob.cur, - SA.back$log.prob.fix,na.rm=T)
if(log(runif(n = 1,min = 0,max = 1))<=thact)
{
ratcur<-ratcand
mlikcur<-ratcand
if(printable.opt)print(paste("update ratcur through SA = ", ratcur))
varcurb<-SA.forw$varcur
acc_moves<-acc_moves+1
id<-bittodec(varcurb)+1
if(j<glob.model$burnin)
{
distrib_of_proposals[1]<-distrib_of_proposals[1]+1
}else
{
if(exists("statistics1")){
statistics1[id,10]<-statistics1[id,10] + 1
statistics1[id,4]<-statistics1[id,4] + 1
}
p.post<- (p.post + varcurb)
}
}else if(j<glob.model$burnin && distrib_of_proposals[1]>0)
{
distrib_of_proposals[1]<-distrib_of_proposals[1] - 1
}
if((SA.back$mlikglob<mlikglob))
{
if(printable.opt)print(paste("update waic.glob sa.back = ", SA.back$waicglob))
if(printable.opt)print(paste("update waic.glob.mlik sa.back= ", SA.back$mlikglob))
waicglob<-SA.back$waicglob
varglob<-SA.back$varglob
modglob<-SA.back$modglob
}
}else
{
thact<-sum(ratcand, - ratcur, - SA.forw$log.prob.cur,SA.forw$log.prob.fix,vect[[mod_id]]$log.mod.switchback.prob, - vect[[mod_id]]$log.mod.switch.prob,na.rm=T)
if(log(runif(n = 1,min = 0,max = 1))<=thact)
{
ratcur<-ratcand
mlikcur<-ratcand
if(printable.opt)print(paste("update ratcur through SA = ", ratcur))
varcurb<-SA.forw$varcur
id<-bittodec(varcurb)+1
acc_moves<-acc_moves+1
if(j<glob.model$burnin)
{
distrib_of_proposals[4]<-distrib_of_proposals[4]+1
}else
{
if(exists("statistics1")){
statistics1[id,13]<-statistics1[id,13] + 1
statistics1[id,4]<-statistics1[id,4] + 1
}
p.post<- (p.post + varcurb)
}
}else if(j<glob.model$burnin && distrib_of_proposals[4]>0)
{
distrib_of_proposals[4]<-distrib_of_proposals[4] - 1
}
}
if((SA.forw$mlikglob<mlikglob))
{
if(printable.opt)print(paste("update waic.glob sa.forw = ", SA.forw$waicglob))
if(printable.opt)print(paste("update waic.glob.mlik sa.forw = ", SA.forw$mlikglob))
waicglob<-SA.forw$waicglob
varglob<-SA.forw$varglob
modglob<-SA.forw$modglob
}
}else if(LocImprove == 1)
{
if(printable.opt)print("Try MTMCMC imptovements")
buf.change <- array(data = 1,dim = Nvars)
buf.change[which(varcur - varcurb!=0)]=0
#buf.opt[floor(runif(n = n.size,min = 1,max = Nvars+0.999999))] = 1
model = list(statid = 4 + LocImprove,reverse = FALSE, change = buf.change,mlikcur = mlikcur,waiccur = waiccur,
varcur = varcur,varold = varcurb)
MTMCMC.forw<-learnlocalMCMC(model)
ids = which(buf.change == 1)
model$varcur <- MTMCMC.forw$varcur
model$varcur[ids] = 1 - model$varcur[ids]
model$mlikcur<- -Inf
model$waiccur<- Inf
model$reverse = TRUE
#if(printable.opt)print("learn reverse local MTMCMC")
MTMCMC.back<-learnlocalMCMC(model)
#if(printable.opt)print("finish reverse local MTMCMC")
MTMCMC.p.forw<-MTMCMC.forw$log.prob.cur
MTMCMC.p.back<-MTMCMC.back$log.prob.fix
ratcand<-MTMCMC.forw$mlikcur
#if(log(runif(n = 1,min = 0,max = 1))<=(ratcand - ratcur - MTMCMC.forw$log.prob.cur + MTMCMC.forw$log.prob.fix + MTMCMC.back$log.prob.cur - MTMCMC.back$log.prob.fix))
thact<-sum(ratcand, - ratcur, - MTMCMC.forw$log.prob.cur,MTMCMC.forw$log.prob.fix,MTMCMC.back$log.prob.cur,- MTMCMC.back$log.prob.fix,na.rm=T)
if(log(runif(n = 1,min = 0,max = 1))<=thact)
{
ratcur<-ratcand
mlikcur<-ratcand
#if(printable.opt)print(paste("update ratcur through MTMCMC = ", ratcur))
varcurb<-MTMCMC.forw$varcur
acc_moves<-acc_moves+1
id<-bittodec(varcurb)+1
if(j<glob.model$burnin)
{
distrib_of_proposals[2]<-distrib_of_proposals[2]+1
}else
{
if(exists("statistics1")){
statistics1[id,11]<-statistics1[id,11] + 1
statistics1[id,4]<-statistics1[id,4] + 1
}
p.post<- (p.post + varcurb)
}
}else if(j<glob.model$burnin && distrib_of_proposals[2]>1)
{
distrib_of_proposals[2]<-distrib_of_proposals[2] - 1
}
if((MTMCMC.forw$mlikglob<mlikglob))
{
#if(printable.opt)print(paste("update waic.glob MTMCMC.forw = ", MTMCMC.forw$waicglob))
#if(printable.opt)print(paste("update waic.glob.mlik MTMCMC.forw = ", MTMCMC.forw$mlikglob))
waicglob<-MTMCMC.forw$waicglob
varglob<-MTMCMC.forw$varglob
modglob<-MTMCMC.forw$modglob
}
if((MTMCMC.back$mlikglob<mlikglob))
{
#if(printable.opt)print(paste("update waic.glob MTMCMC.back = ", MTMCMC.back$waicglob))
#if(printable.opt)print(paste("update waic.glob.mlik MTMCMC.back= ", MTMCMC.back$mlikglob))
waicglob<-MTMCMC.back$waicglob
varglob<-MTMCMC.back$varglob
modglob<-MTMCMC.back$modglob
}
}else if(LocImprove == 2)
{
if(printable.opt)print("Try greedy heuristic imptovements")
buf.change <- array(data = 1,dim = Nvars)
buf.change[which(varcur - varcurb!=0)]=0
#buf.opt <- buf.change
#buf.opt[floor(runif(n = n.size,min = 1,max = Nvars+0.999999))] = 1
if(objective ==0)
{
objold<-waiccur
objcur<-waiccand
}else
{
objold<- -mlikcur
objcur<- -mlikcand
}
model = list(statid = 4 + LocImprove, change = buf.change,
varcur = varcur,varold = varcurb, switch.type = switch.type.buf,mlikcur = mlikcur,objcur = objcur, objold = objold, reverse=FALSE)
GREEDY.forw<-learnlocalND(model)
ids = which(buf.change == 1)
model$varcur <- GREEDY.forw$varcur
model$varcur[ids] = 1 - model$varcur[ids]
model$mlikcur<- -Inf
model$waiccur<- Inf
model$reverse = TRUE
ratcand<-GREEDY.forw$mlikcur
if(objective ==0)
{
model$objold<-waiccur
}else
{
model$objold<- -ratcand
}
if(switch.type.buf==5)
{
model$switch.type <- 6
}
else if(switch.type.buf==6)
{
model$switch.type <- 5
}
GREEDY.back<-learnlocalND(model)
GREEDY.p.forw<-GREEDY.forw$log.prob.cur
GREEDY.p.back<-GREEDY.back$log.prob.fix
#if(log(runif(n = 1,min = 0,max = 1))<=(ratcand - ratcur - GREEDY.forw$log.prob.cur + GREEDY.forw$log.prob.fix + GREEDY.back$log.prob.cur - GREEDY.back$log.prob.fix))
thact<-sum(ratcand, - ratcur, - GREEDY.forw$log.prob.cur,GREEDY.forw$log.prob.fix,GREEDY.back$log.prob.cur,-GREEDY.back$log.prob.fix,na.rm=T)
if(log(runif(n = 1,min = 0,max = 1))<=thact)
{
ratcur<-ratcand
mlikcur<-ratcand
if(printable.opt)print(paste("update ratcur through ND = ", ratcur))
varcurb<-GREEDY.forw$varcur
acc_moves<-acc_moves+1
id<-bittodec(varcurb)+1
if(j<glob.model$burnin)
{
distrib_of_proposals[3]<-distrib_of_proposals[3]+1
}else
{
if(exists("statistics1")){
statistics1[id,12]<-statistics1[id,12] + 1
statistics1[id,4]<-statistics1[id,4] + 1
}
p.post<- (p.post + varcurb)
}
}else if(j<glob.model$burnin && distrib_of_proposals[3]>1)
{
distrib_of_proposals[3]<-distrib_of_proposals[3] - 1
}
if((GREEDY.forw$mlikglob<mlikglob))
{
if(printable.opt)print(paste("update waic.glob ND.forw = ", GREEDY.forw$waicglob))
if(printable.opt)print(paste("update waic.glob.mlik ND.forw = ", GREEDY.forw$mlikglob))
waicglob<-GREEDY.forw$waicglob
varglob<-GREEDY.forw$varglob
modglob<-GREEDY.forw$modglob
}
if((GREEDY.back$mlikglob<mlikglob))
{
if(printable.opt)print(paste("update waic.glob ND.back = ", GREEDY.back$waicglob))
if(printable.opt)print(paste("update waic.glob.mlik ND.back= ", GREEDY.back$mlikglob))
waicglob<-GREEDY.back$waicglob
varglob<-GREEDY.back$varglob
modglob<-GREEDY.back$modglob
}
}
}
#}),abort = function(){if(printable.opt)print("error");varcur<-varcurb;closeAllConnections();options(error=traceback); onerr<-TRUE})
if(thin_rate!=-1)
{
if(acc_moves == accept_old && j>glob.model$burnin && j%%as.integer(thin_rate)==0) #carry out smart thinning
{
if(!is.null(varcurb))
{
p.post<- (p.post + varcurb)
thin_count <- thin_count +1
id<-bittodec(varcurb)+1
if(exists("statistics1"))
{
statistics1[id,4]<-statistics1[id,4] + 1
}
}
}
}
accept_old <- acc_moves
p2<-p.post/acc_moves
if(j>glob.model$burnin && (recalc.margin >= 2^Nvars) && sum(p2)!=0)
{
p.add <<- as.array(p2)
}
eps.emp<-normprob(p1,p2)
etm <- proc.time()
delta.time <- (etm[3] - stm[3])/60.0
}
if(is.null(modglob))
{
vect<-buildmodel(max.cpu = 1,varcur.old = varglob,statid = 3, switch.type = 8)
res.par <- lapply(X = vect, FUN = fitmodel)
modglob<-res.par[[1]]$fm
}
#!#print the results
if(printable.opt)print(paste(j," iterations completed in total"))
#if(printable.opt)print(paste("WAIC.glob = ", waicglob))
etm <- proc.time()
tt<-(etm[3]-stm[3])/60.0
acc_ratio <- acc_moves/j.a
if(printable.opt)print(paste(j," moves proposed in total, ", acc_moves," of them accepted, acceptance ratio is ",acc_ratio))
if(printable.opt)print(paste("posterior distribution ofproposals is", distrib_of_proposals))
if(exists("statistics1"))
{
bayes.res<-post_proceed_results(statistics1)
m.post<-statistics1[,4]/j.a
}else if(exists("hashStat"))
{
bayes.res<-post_proceed_results_hash(hashStat)
m.post<-NULL
}
else
{
bayes.res<-NULL
m.post<-NULL
}
return(list(model=modglob, vars=varglob, waic = waicglob, mlik = mlikglob, time=(tt), freqs = distrib_of_proposals, acc_ratio = acc_ratio, p.post = p.post/acc_moves, m.post = m.post, p.post.freq = p.post, eps=eps.emp, bayes.results = bayes.res))
},
#save big.data results, if the latter are available
save_results_csv = function(statistics1, filename)
{
write.big.matrix(x = statistics1,filename = filename)
},
#vizualize the results graphically if the latter are available
visualize_results = function(statistics1, template, mds_size, crit,draw_dist = FALSE)
{
ids = NULL
if(crit$mlik){
ids<-c(ids,which(statistics1[,1]==-100000))
ids<-c(ids,which(statistics1[,1]==-Inf))}
#ids<-c(ids,which(statistics1[,1]>0))
if(crit$waic){
ids<-c(ids,which(statistics1[,2]==Inf))
ids<-c(ids,which(statistics1[,3]==Inf))}
if(crit$dic){
ids<-c(ids,which(is.na(statistics1[,3])))}
if(length(ids)!=0)
{
if(crit$mlik)
mlik.lim<-c(min(statistics1[-ids,1],na.rm = TRUE),max(statistics1[-ids,1],na.rm = TRUE))
if(crit$waic)
waic.lim<-c(min(statistics1[-ids,2],na.rm = TRUE),max(statistics1[-ids,2],na.rm = TRUE))
if(crit$dic)
dic.lim<-c(min(statistics1[-ids,3],na.rm = TRUE),max(statistics1[-ids,3],na.rm = TRUE))
}else
{
if(crit$mlik)
mlik.lim<-c(min(statistics1[,1],na.rm = TRUE),max(statistics1[,1],na.rm = TRUE))
if(crit$waic)
waic.lim<-c(min(statistics1[,2],na.rm = TRUE),max(statistics1[,2],na.rm = TRUE))
if(crit$dic)
dic.lim<-c(min(statistics1[,3],na.rm = TRUE),max(statistics1[,3],na.rm = TRUE))
}
norm<-0.5*sqrt(sum(statistics1[,4],na.rm = TRUE))
if(crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_legend.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_legend.jpg",sep = ""))
plot(xlab = "posterior probability of a visit found", ylab="visit type",c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(7,7,7,-1,-1,-1,-1),ylim = c(0,9), xlim=c(0,1),pch=19, col = 7,cex= c(2,2,2,0,0,0,0))
points(c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(6,6,6,-1,-1,-1,-1),pch=8, col = 5,cex= c(1,2,3,0,0,0,0))
points(c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(1,1,1,-1,-1,-1,-1),pch=2, col = 2,cex= c(1,2,3,0,0,0,0))
points(c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(2,2,2,-1,-1,-1,-1),pch=3, col = 3,cex= c(1,2,3,0,0,0,0))
points(c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(3,3,3,-1,-1,-1,-1),pch=4, col = 4,cex= c(1,2,3,0,0,0,0))
points(c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(4,4,4,-1,-1,-1,-1),pch=6, col = 6,cex=c(1,2,3,0,0,0,0))
points(c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(5,5,5,-1,-1,-1,-1),pch=1, col = 1,cex= c(1,2,3,0,0,0,0))
points(c(0.1,0.2,0.3,0.4,0.5,0.6,0.7),c(8,8,8,-1,-1,-1,-1),pch=19, col = 2,cex= c(2,2,2,0,0,0,0))
legend(x = 0.35,y = 1.5,legend = "- SA 1 local optimization accepted",bty="n" )
legend(x = 0.35,y = 2.5,legend = "- MTMCMC local optimization accepted",bty="n" )
legend(x = 0.35,y = 3.5,legend = "- GREEDY local optimization accepted",bty="n" )
legend(x = 0.35,y = 4.5,legend = "- SA 2 local optimization accepted",bty="n" )
legend(x = 0.35,y = 5.5,legend = "- NO local optimization accepted",bty="n" )
legend(x = 0.35,y = 6.5,legend = "- Totally accepted",bty="n" )
legend(x = 0.35,y = 7.5,legend = "- Totally explored",bty="n" )
legend(x = 0.35,y = 8.5,legend = "- Bayes formula based posterior",bty="n" )
dev.off()
if(printable.opt)print(paste("drawing ",workdir,template,"_mlik.jpg",sep = ""))
jpeg(file=paste(workdir,template,"_mlik.jpg",sep = ""))
plot(ylim = mlik.lim, xlab = "model_id", ylab="MLIK" , statistics1[,1],pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,1],pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,1],pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,1],pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,1],pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,1],pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,1],pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$waic)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_waic.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_waic.jpg",sep = ""))
plot(ylim = waic.lim, xlab = "model_id", ylab="WAIC" ,statistics1[,2],pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,2],pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,2],pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,2],pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,2],pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,2],pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,2],pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$dic)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_dic.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_dic.jpg",sep = ""))
plot(ylim = dic.lim, xlab = "model_id", ylab="DIC" ,statistics1[,3],pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,3],pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,3],pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,3],pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,3],pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,3],pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,3],pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$waic && crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_mlik-waic.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_mlik-waic.jpg",sep = ""))
plot(ylim = mlik.lim, xlim = waic.lim,xlab = "WAIC", ylab="MLIK" ,statistics1[,2],statistics1[,1], pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,2],statistics1[,1],pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,2],statistics1[,1],pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,2],statistics1[,1],pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,2],statistics1[,1],pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,2],statistics1[,1],pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,2],statistics1[,1],pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$dic && crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_mlik-dic.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_mlik-dic.jpg",sep = ""))
plot(ylim = mlik.lim, xlim = dic.lim,xlab = "DIC", ylab="MLIK" ,statistics1[,3],statistics1[,1], pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,3],statistics1[,1],pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,3],statistics1[,1],pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,3],statistics1[,1],pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,3],statistics1[,1],pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,3],statistics1[,1],pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,3],statistics1[,1],pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$dic && crit$waic)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_waic-dic.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_waic-dic.jpg",sep = ""))
plot(ylim = waic.lim, xlim = dic.lim,xlab = "WAIC", ylab="DIC" ,statistics1[,3],statistics1[,2], pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,3],statistics1[,2],pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,3],statistics1[,2],pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,3],statistics1[,2],pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,3],statistics1[,2],pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,3],statistics1[,2],pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,3],statistics1[,2],pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
norm1<-(sum(statistics1[,4],na.rm = TRUE))
xyz<-which(!is.na(statistics1[,1]))
xyz<-intersect(xyz,which(statistics1[,1]!=-10000))
moddee<-which(statistics1[,1]==max(statistics1[,1],na.rm = TRUE))[1]
zyx<-array(data = NA,dim = 2 ^(Nvars)+1)
nconsum<-sum(exp(-statistics1[moddee,1]+statistics1[xyz,1]),na.rm = TRUE)
if( nconsum > 0)
{
zyx[xyz]<-exp(statistics1[xyz,1]-statistics1[moddee,1])/nconsum
y.post.lim<-c(0,max(zyx[xyz]))
}else{
zyx[xyz]<-statistics1[xyz,3]/norm1
y.post.lim<-c(0,NaN)
}
if(is.nan(y.post.lim[2]))
y.post.lim[2]<-max(statistics1[,3]/norm1,na.rm = TRUE)
if(is.nan(y.post.lim[2]))
y.post.lim[2]<-1
if(crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_Pr(MID).jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_Pr(MID).jpg",sep = ""))
plot(xlab = "model_id", ylab="Pr(M(model_id)ID)",ylim = y.post.lim, statistics1[,4]/norm1,pch=19, col = 7,cex= 3*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,4]/norm1,pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,4]/norm1,pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,4]/norm1,pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,4]/norm1,pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,4]/norm1,pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,4]/norm1,pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
points(zyx,pch=20, col = 2,cex= 2)
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$waic && crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_waic-Pr(MID).jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_waic-Pr(MID).jpg",sep = ""))
plot(xlim = waic.lim, ylim = y.post.lim,xlab = "WAIC(M)", ylab="Pr(MID)",statistics1[,2],statistics1[,4]/norm1, pch=19, col = 7,cex= 3*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,2],statistics1[,4]/norm1,pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,2],statistics1[,4]/norm1,pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,2],statistics1[,4]/norm1,pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,2],statistics1[,4]/norm1,pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,2],statistics1[,4]/norm1,pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,2],statistics1[,4]/norm1,pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
points(statistics1[,2],zyx,pch=20, col = 2,cex= 2)
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$dic && crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_dic-Pr(MID).jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_dic-Pr(MID).jpg",sep = ""))
plot(xlim = dic.lim, ylim = y.post.lim,xlab = "dic(M)", ylab="Pr(MID)",statistics1[,3],statistics1[,4]/norm1, pch=19, col = 7,cex= 3*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,3],statistics1[,4]/norm1,pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/norm+1,0))
points(statistics1[,3],statistics1[,4]/norm1,pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/norm+1,0))
points(statistics1[,3],statistics1[,4]/norm1,pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/norm+1,0))
points(statistics1[,3],statistics1[,4]/norm1,pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/norm+1,0))
points(statistics1[,3],statistics1[,4]/norm1,pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/norm+1,0))
points(statistics1[,3],statistics1[,4]/norm1,pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/norm+1,0))
points(statistics1[,3],zyx,pch=20, col = 2,cex= 2)
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$mlik)
{
jpeg(file=paste(workdir,template,"_mlik-Pr(MID).jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
plot(xlim = mlik.lim,ylim = y.post.lim, xlab = "MLIK", ylab="Pr(MID)",statistics1[,1],statistics1[,4]/norm1, pch=19, col = 7,cex= 3*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(statistics1[,1],statistics1[,4]/norm1,pch=8, col = ifelse(statistics1[,4]>0,5,0),cex= ifelse(statistics1[,4]>0,statistics1[,4]/statistics1[,3]*3 +1,0))
points(statistics1[,1],statistics1[,4]/norm1,pch=2, col = ifelse(statistics1[,10]>0,2,0),cex= ifelse(statistics1[,10]>0,statistics1[,10]/statistics1[,4]*3 +1,0))
points(statistics1[,1],statistics1[,4]/norm1,pch=3, col = ifelse(statistics1[,11]>0,3,0),cex= ifelse(statistics1[,11]>0,statistics1[,11]/statistics1[,4]*3 +1,0))
points(statistics1[,1],statistics1[,4]/norm1,pch=4, col = ifelse(statistics1[,12]>0,4,0),cex= ifelse(statistics1[,12]>0,statistics1[,12]/statistics1[,4]*3 +1,0))
points(statistics1[,1],statistics1[,4]/norm1,pch=6, col = ifelse(statistics1[,13]>0,6,0),cex= ifelse(statistics1[,13]>0,statistics1[,13]/statistics1[,4]*3 +1,0))
points(statistics1[,1],statistics1[,4]/norm1,pch=1, col = ifelse(statistics1[,14]>0,1,0),cex= ifelse(statistics1[,14]>0,statistics1[,14]/statistics1[,4]*3 +1,0))
points(statistics1[,1],zyx,pch=20, col = 2,cex= 2)
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(draw_dist)
{
if(printable.opt)print("Calculating distance matrix, may take a significant amount of time, may also produce errors if your machine does not have enough memory")
capture.output({withRestarts(tryCatch(capture.output({
lldd<-2^(Nvars)+1
moddee<-which(zyx==max(zyx,na.rm = TRUE))
iidr<-which(statistics1[moddee,1]==max(statistics1[moddee,1],na.rm = TRUE))
iidr<-which(statistics1[moddee[iidr],3]==max(statistics1[moddee[iidr],3],na.rm = TRUE))
moddee<-moddee[iidr]
if(length(moddee)>1)
moddee<-moddee[1]
vec<-dectobit.alt(moddee-1)
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
df = data.frame(varcur)
for(i in 1:(lldd-1))
{
if(i==moddee)
{
next
}else
{
vec<-dectobit.alt(i-1)
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
df<-cbind(df,varcur)
#colnames(x = df)[i] <- paste("solution ",i)
}
}
df<-t(df)
x<-dist(x = df,method = "binary")
dists<-c(0,x[1:lldd-1])
#length(dists)
#which(dists==0)
})), abort = function(){onerr<-TRUE})})
if(crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_distance-mlik.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_distance-MLIK.jpg",sep = ""))
plot(xlab = "x = |M* - M| = distance from the main mode", ylab="MLIK(M)",ylim = mlik.lim,y=c(statistics1[moddee,1],statistics1[-moddee,1]),x=dists,pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(y=c(statistics1[moddee,1],statistics1[-moddee,1]),x=dists,pch=8, col = ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,5,0),cex= ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,c(statistics1[moddee,4],statistics1[-moddee,4])/norm+1,0))
points(y=c(statistics1[moddee,1],statistics1[-moddee,1]),x=dists,pch=2, col = ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,2,0),cex= ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,c(statistics1[moddee,10],statistics1[-moddee,10])/norm+1,0))
points(y=c(statistics1[moddee,1],statistics1[-moddee,1]),x=dists,pch=3, col = ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,3,0),cex= ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,c(statistics1[moddee,11],statistics1[-moddee,11])/norm+1,0))
points(y=c(statistics1[moddee,1],statistics1[-moddee,1]),x=dists,pch=4, col = ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,4,0),cex= ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,c(statistics1[moddee,12],statistics1[-moddee,12])/norm+1,0))
points(y=c(statistics1[moddee,1],statistics1[-moddee,1]),x=dists,pch=6, col = ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,6,0),cex= ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,c(statistics1[moddee,13],statistics1[-moddee,13])/norm+1,0))
points(y=c(statistics1[moddee,1],statistics1[-moddee,1]),x=dists,pch=1, col = ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,1,0),cex= ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,c(statistics1[moddee,14],statistics1[-moddee,14])/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$waic)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_distance-waic.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_distance-waic.jpg",sep = ""))
plot(xlab = "x = |M* - M| = distance from the main mode", ylab="WAIC(M)",ylim = waic.lim,y=c(statistics1[moddee,2],statistics1[-moddee,2]),x=dists,pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(y=c(statistics1[moddee,2],statistics1[-moddee,2]),x=dists,pch=8, col = ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,5,0),cex= ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,c(statistics1[moddee,4],statistics1[-moddee,4])/norm+1,0))
points(y=c(statistics1[moddee,2],statistics1[-moddee,2]),x=dists,pch=2, col = ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,2,0),cex= ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,c(statistics1[moddee,10],statistics1[-moddee,10])/norm+1,0))
points(y=c(statistics1[moddee,2],statistics1[-moddee,2]),x=dists,pch=3, col = ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,3,0),cex= ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,c(statistics1[moddee,11],statistics1[-moddee,11])/norm+1,0))
points(y=c(statistics1[moddee,2],statistics1[-moddee,2]),x=dists,pch=4, col = ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,4,0),cex= ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,c(statistics1[moddee,12],statistics1[-moddee,12])/norm+1,0))
points(y=c(statistics1[moddee,2],statistics1[-moddee,2]),x=dists,pch=6, col = ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,6,0),cex= ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,c(statistics1[moddee,13],statistics1[-moddee,13])/norm+1,0))
points(y=c(statistics1[moddee,2],statistics1[-moddee,2]),x=dists,pch=1, col = ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,1,0),cex= ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,c(statistics1[moddee,14],statistics1[-moddee,14])/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$dic)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_distance-dic.jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_distance-dic.jpg",sep = ""))
plot(xlab = "x = |M* - M| = distance from the main mode", ylab="DIC(M)",ylim = dic.lim,y=c(statistics1[moddee,3],statistics1[-moddee,3]),x=dists,pch=19, col = 7,cex= 1*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(y=c(statistics1[moddee,3],statistics1[-moddee,3]),x=dists,pch=8, col = ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,5,0),cex= ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,c(statistics1[moddee,4],statistics1[-moddee,4])/norm+1,0))
points(y=c(statistics1[moddee,3],statistics1[-moddee,3]),x=dists,pch=2, col = ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,2,0),cex= ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,c(statistics1[moddee,10],statistics1[-moddee,10])/norm+1,0))
points(y=c(statistics1[moddee,3],statistics1[-moddee,3]),x=dists,pch=3, col = ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,3,0),cex= ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,c(statistics1[moddee,11],statistics1[-moddee,11])/norm+1,0))
points(y=c(statistics1[moddee,3],statistics1[-moddee,3]),x=dists,pch=4, col = ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,4,0),cex= ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,c(statistics1[moddee,12],statistics1[-moddee,12])/norm+1,0))
points(y=c(statistics1[moddee,3],statistics1[-moddee,3]),x=dists,pch=6, col = ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,6,0),cex= ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,c(statistics1[moddee,13],statistics1[-moddee,13])/norm+1,0))
points(y=c(statistics1[moddee,3],statistics1[-moddee,3]),x=dists,pch=1, col = ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,1,0),cex= ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,c(statistics1[moddee,14],statistics1[-moddee,14])/norm+1,0))
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_distance-Pr(MID).jpg",sep = ""))
capture.output({withRestarts(tryCatch(capture.output({
jpeg(file=paste(workdir,template,"_distance-Pr(MID).jpg",sep = ""))
plot(xlab = "x = |M* - M| = distance from the main mode",ylim = y.post.lim, ylab="Pr(MID)",y=c(statistics1[moddee,4],statistics1[-moddee,4])/norm1,x=dists,pch=19, col = 7,cex= 3*((statistics1[,9]+statistics1[,5]+statistics1[,6]+statistics1[,7]+statistics1[,8])>0))
points(y=c(statistics1[moddee,4],statistics1[-moddee,4])/norm1,x=dists,pch=8, col = ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,5,0),cex= ifelse(c(statistics1[moddee,4],statistics1[-moddee,4])>0,c(statistics1[moddee,4],statistics1[-moddee,4])/norm+1,0))
points(y=c(statistics1[moddee,4],statistics1[-moddee,4])/norm1,x=dists,pch=2, col = ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,2,0),cex= ifelse(c(statistics1[moddee,10],statistics1[-moddee,10])>0,c(statistics1[moddee,10],statistics1[-moddee,10])/norm+1,0))
points(y=c(statistics1[moddee,4],statistics1[-moddee,4])/norm1,x=dists,pch=3, col = ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,3,0),cex= ifelse(c(statistics1[moddee,11],statistics1[-moddee,11])>0,c(statistics1[moddee,11],statistics1[-moddee,11])/norm+1,0))
points(y=c(statistics1[moddee,4],statistics1[-moddee,4])/norm1,x=dists,pch=4, col = ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,4,0),cex= ifelse(c(statistics1[moddee,12],statistics1[-moddee,12])>0,c(statistics1[moddee,12],statistics1[-moddee,12])/norm+1,0))
points(y=c(statistics1[moddee,4],statistics1[-moddee,4])/norm1,x=dists,pch=6, col = ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,6,0),cex= ifelse(c(statistics1[moddee,13],statistics1[-moddee,13])>0,c(statistics1[moddee,13],statistics1[-moddee,13])/norm+1,0))
points(y=c(statistics1[moddee,4],statistics1[-moddee,4])/norm1,x=dists,pch=1, col = ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,1,0),cex= ifelse(c(statistics1[moddee,14],statistics1[-moddee,14])>0,c(statistics1[moddee,14],statistics1[-moddee,14])/norm+1,0))
points(y= c(zyx[moddee],zyx[-moddee]),x=dists,pch=20, col = 2,cex= 2)
dev.off()
})), abort = function(){onerr<-TRUE})})
}
if(crit$mlik)
{
if(printable.opt)print(paste("drawing ",workdir,template,"_mds-Pr(MID).jpg",sep = ""))
if(printable.opt)print("Calculating distance matrix, may take a significant amount of time, may also produce errors if your machine does not have enough memory")
capture.output({withRestarts(tryCatch(capture.output({
# further address subset of the set of the best solution of cardinality 1024
if(lldd>mds_size)
{
lldd<-mds_size
quant<-(sort(statistics1[,1],decreasing = TRUE)[lldd+1])
indmds<-which(statistics1[,1]>quant)
length(indmds)
}else{
quant<- -Inf
indmds<-1:(lldd)
}
vec<-dectobit.alt(moddee-1)
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
df = data.frame(varcur)
for(i in 1:(lldd-1))
{
if(i==moddee)
{
next
}else
{
vec<-dectobit.alt(indmds[i]-1)
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
df<-cbind(df,varcur)
#colnames(x = df)[i] <- paste("solution ",i)
}
}
df<-t(df)
x<-dist(x = df,method = "binary")
dists<-c(0,x[1:lldd-1])
fit.mds <- cmdscale(d = x,eig=FALSE, k=2) # k is the number of dim
#fit.mds # view results
x.mds <- fit.mds[,1]
y.mds <- fit.mds[,2]
jpeg(file=paste(workdir,template,"_mds_map_posteriors.jpg",sep = ""))
plot(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=2,pch = 10,cex= c(zyx[moddee],zyx[setdiff(indmds, moddee)])*50,0)
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=2,pch = 10,cex= c(zyx[moddee],zyx[setdiff(indmds, moddee)])*50,0)
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=5,pch = 8,cex= ifelse(c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])>0,c(statistics1[moddee,4],statistics1[setdiff(indmds, moddee),4])/norm1*50,0))
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=7,pch = 19,cex= 0.4)
points(x.mds[], y.mds[], xlab="Coordinate 1", ylab="Coordinate 2", main="Metric MDS", type="p",col=1,pch = 19,cex= 0.01)
dev.off()
})), abort = function(){onerr<-TRUE})})
}
}
},
#calculates posterior probabilities based on a current search
post_proceed_results = function(statistics1)
{
xyz<-which(!is.na(statistics1[,1]))
g.results[4,2] <- length(xyz)
xyz<-intersect(xyz,which(statistics1[,1]!=-10000))
moddee<-which(statistics1[,1]==max(statistics1[,1],na.rm = TRUE))[1]
zyx<-array(data = NA,dim = length(statistics1[,1]))
nconsum<-sum(exp(-statistics1[moddee,1]+statistics1[xyz,1]),na.rm = TRUE)
if( nconsum > 0)
{
zyx[xyz]<-exp(statistics1[xyz,1]-statistics1[moddee,1])/nconsum
}else{
nnnorm<-sum(statistics1[xyz,4],na.rm = T)
if(nnnorm==0)
nnnorm <- 1
zyx[xyz]<-statistics1[xyz,4]/nnnorm
}
statistics1[,15]<-zyx
lldd<-2^(Nvars)+1
p.post<-array(data = 0,dim = Nvars)
for(i in xyz)
{
vec<-dectobit(i-1)
varcur<-c(array(0,dim = (Nvars -length(vec))),vec)
p.post <- (p.post + varcur*statistics1[i,15])
}
if(!exists("p.post")||is.null(p.post)||sum(p.post,na.rm = T)==0 || sum(p.post,na.rm = T)>Nvars)
{
p.post <- array(data = 0.5,dim = Nvars)
}
return(list(p.post = p.post, m.post = zyx, s.mass = sum(exp(statistics1[xyz,1]),na.rm = TRUE)))
},
post_proceed_results_hash = function(hashStat)
{
if(save.beta)
{
if(allow_offsprings==0||Nvars>Nvars.max)
{
if(fparam[1]=="Const")
{
linx<-Nvars + 3
}else
{
linx<-Nvars + 1 + 3
}
}else
{
if(fparam[1]=="Const")
{
linx<-Nvars.max + 3
}else
{
linx<-Nvars.max + 1 + 3
}
}
}else
{
linx <- 3
}
lHash<-length(hashStat)
mliks <- values(hashStat)[which((1:(lHash * linx)) %% linx == 1)]
xyz<-which(mliks!=-10000)
g.results[4,2] <- lHash
moddee<-which( mliks ==max( mliks ,na.rm = TRUE))[1]
zyx<-array(data = NA,dim = lHash)
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
if( nconsum > 0)
{
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}else{
diff<-0-mliks[moddee]
mliks<-mliks+diff
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}
keysarr <- as.array(keys(hashStat))
p.post<-array(data = 0,dim = Nvars)
for(i in 1:lHash)
{
if(is.na(zyx[i]))
{
del(x = keysarr[i],hash = hashStat)
next
}
#vec<-dectobit(strtoi(keysarr[i], base = 0L)-1) # we will have to write some function that would handle laaaaargeee integers!
varcur<- as.integer(strsplit(keysarr[i],split = "")[[1]])
if(length(which(is.na(varcur)))>0)
{
del(x = keysarr[i],hash = hashStat)
next
}
if(length(varcur)>Nvars)
varcur<-varcur[1:Nvars]
p.post <- (p.post + varcur*zyx[i])
}
if(!exists("p.post") || is.null(p.post) || sum(p.post,na.rm = T)==0 || sum(p.post,na.rm = T)>Nvars)
{
p.post <- array(data = 0.5,dim = Nvars)
}
#values(hashStat)[which((1:(lHash * linx)) %%linx == 4)]<-zyx
return(list(p.post = p.post, m.post = zyx, s.mass = sum(exp(mliks),na.rm = TRUE)))
},
calculate_quality_measures = function(vect,n,truth)
{
rmse.pi <- array(data = 0,Nvars)
bias.pi <- array(data = 0,Nvars)
for(i in 1:n)
{
bias.pi <- (bias.pi + (vect[,i]-truth))
rmse.pi <- (rmse.pi + (vect[,i]^2+truth^2 - 2*vect[,i]*truth))
}
bias.pi <- bias.pi/n
rmse.pi <- rmse.pi/n
return(list(bias.pi = bias.pi, rmse.pi = rmse.pi))
},
forecast=function(covariates,nvars,link.g)
{
ids<-which(!is.na(statistics1[,15]))
res<-0
for(i in ids)
{
res<-res + statistics1[i,15]*link.g(sum(statistics1[i,16:nvars]*covariates,na.rm = T))
}
return(list(forecast=res))
},
forecast.matrix=function(covariates,link.g)
{
res<-NULL
ncases <- dim(covariates)[1]
formula.cur<-as.formula(paste(fparam[1],"/2 ~",paste0(fparam,collapse = "+")))
nvars <- Nvars
if(save.beta)
{
if(exists("statistics1"))
{
ids<-which(!is.na(statistics1[,15]))
lids<-length(ids)
statistics1[ids,(17:(nvars+16))][which(is.na(statistics1[ids,(17:(nvars+16))]))]<-0
res<-t(statistics1[ids,15])%*%g(statistics1[ids,(16:(nvars+16))]%*%t(model.matrix(object = formula.cur,data = covariates)))
}else if(exists("hashStat"))
{
if(allow_offsprings==0)
{
if(fparam[1]=="Const")
{
linx<-Nvars + 3
}else
{
linx<-Nvars + 1 + 3
}
}else
{
if(fparam[1]=="Const")
{
linx<-Nvars.max + 3
}else
{
linx<-Nvars.max + 1 + 3
}
}
lHash<-length(hashStat)
mliks <- values(hashStat)[which((1:(lHash * linx)) %% linx == 1)]
betas <- values(hashStat)[which((1:(lHash * linx)) %% linx == 4)]
for(i in 1:(Nvars-1))
{
betas<-cbind(betas,values(hashStat)[which((1:(lHash * linx)) %% linx == (4+i))])
}
betas<-cbind(betas,values(hashStat)[which((1:(lHash * linx)) %% linx == (0))])
betas[which(is.na(betas))]<-0
xyz<-which(mliks!=-10000)
g.results[4,2] <- lHash
moddee<-which( mliks ==max( mliks ,na.rm = TRUE))[1]
zyx<-array(data = NA,dim = lHash)
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
if( nconsum > 0)
{
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}else{
diff<-0-mliks[moddee]
mliks<-mliks+diff
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}
res<-t(zyx)%*%g(betas%*%t(model.matrix(object = formula.cur,data = covariates)))
}
}else
{
warning("No betas were saved. Prediction is impossible. Please change the search parameters and run the search again.")
}
return(list(forecast=res))
},
forecast.matrix.na=function(covariates,link.g,betas,mliks.in)
{
formula2<-as.formula(paste(fparam[1],"/2 ~ -1+",paste0(fparam,collapse = "+")))
current.na.action <- options('na.action')
options(na.action='na.pass')
covariates<- as.data.frame(model.matrix(object = formula2,data = covariates,na.action=na.include))
options('na.action'= current.na.action$na.action)
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "I",replacement = "Z")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "(",replacement = "o")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = ")",replacement = "c")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "+",replacement = "p")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "-",replacement = "m")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "*",replacement = "M")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "|",replacement = "a")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "&",replacement = "A")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = ",",replacement = "k")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = " ",replacement = "")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "\n",replacement = "")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "cFALSE",replacement = "c")
names(covariates)<-stri_replace_all(str = names(covariates),fixed = "cTRUE",replacement = "c")
fparam.tmp<-stri_replace_all(str = fparam,fixed = "I",replacement = "Z")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = "(",replacement = "o")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = ")",replacement = "c")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = "+",replacement = "p")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = "-",replacement = "m")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = ",",replacement = "k")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = "*",replacement = "M")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = "|",replacement = "a")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = "&",replacement = "A")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = " ",replacement = "")
fparam.tmp<-stri_replace_all(str = fparam.tmp,fixed = "\n",replacement = "")
formula.cur<-as.formula(paste(fparam.tmp[1],"/2 ~",paste0(fparam.tmp,collapse = "+")))
na.ids<-matrix(data = 0,nrow = dim(covariates)[1],ncol = dim(covariates)[2])
na.ids[which(is.na(covariates))]<-1
na.bc<-colSums(na.ids)
ids.betas<-NULL
res.na<-array(NA, dim(covariates)[1])
for(i in which(na.bc>0))
{
if(((names(covariates)[i] %in% fparam.tmp)||(paste0("Zo",names(covariates)[i],"c",collapse = "")%in%fparam.tmp)))
{
ids.betas<-c(ids.betas,which(fparam.tmp==names(covariates)[i] | fparam.tmp == paste0("Zo",names(covariates)[i],"c",collapse = "")))
next
}
else
{
na.ids[which(is.na(covariates[,i])),i]<-0
na.bc[i]<-0
}
}
na.br<-rowSums(na.ids)
lv.br<-sort(unique(na.br))
if(lv.br[1]==0)
{
ids<-which(na.br==0)
mliks<-mliks.in
xyz<-which(mliks!=-10000)
moddee<-which( mliks ==max( mliks ,na.rm = TRUE))[1]
zyx<-array(data = NA,dim = length(mliks))
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
betas1<-betas
betas1[which(is.na(betas1))]<-0
if( nconsum > 0)
{
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}else{
diff<-0-mliks[moddee]
mliks<-mliks+diff
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}
covariates1<- covariates[ids,]
res<-t(zyx)%*%g(betas1%*%t(model.matrix(object = as.formula(formula.cur),data = covariates1)))
res.na[ids]<-res
rm(mliks)
rm(res)
rm(zyx)
rm(xyz)
rm(covariates1)
rm(betas1)
}
k.b<-0
for(i in which(na.bc>0))
{
k.b<-k.b+1
w.ids<-which(!is.na(betas[,(ids.betas[k.b]+1)]))
for(j in lv.br)
{
if(j==0)
next
ids<-((which(na.ids[,i]==1 & na.br==j & is.na(res.na))))
if(length(ids)==0)
next
var.del <- NULL
for(iii in which(na.bc>0))
{
if(iii==i)
next
if(sum(na.ids[ids,iii])>0)
{
var.del<-(which(fparam.tmp==names(covariates)[iii] | fparam.tmp == paste0("I(",names(covariates)[iii],")",collapse = "")))
if(length(var.del>0))
{
w.ids<-union(w.ids,which(!is.na(betas[,(var.del+1)])))
}
}
}
mliks<-mliks.in[-w.ids]
if(length(mliks)==0)
{
warning("not enough models for bagging in prediction. please train the model longer!")
return(-1)
}
xyz<-which(mliks!=-10000)
moddee<-which( mliks ==max( mliks ,na.rm = TRUE))[1]
zyx<-array(data = NA,dim = length(mliks))
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
betas1<-betas[-w.ids,]
betas1[which(is.na(betas1))]<-0
if( nconsum > 0)
{
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}else{
diff<-0-mliks[moddee]
mliks<-mliks+diff
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}
covariates1<- as.matrix(covariates[ids,])
covariates1[which(is.na(covariates1))]<-0
covariates1<-as.data.frame(covariates1)
res<-t(zyx)%*%g(betas1%*%t(model.matrix(object = formula.cur,data = covariates1)))
res.na[ids]<-res
rm(mliks)
rm(zyx)
rm(xyz)
rm(res)
rm(covariates1)
}
}
return(list(forecast = res.na))
},
forecast.matrix.na.fast=function(covariates,link.g,betas,mliks.in)
{
formula.cur<-as.formula(paste(fparam[1],"/2 ~",paste0(fparam,collapse = "+")))
na.ids<-matrix(data = 0,nrow = dim(covariates)[1],ncol = dim(covariates)[2])
na.ids[which(is.na(covariates))]<-1
na.bc<-colSums(na.ids)
ids.betas<-NULL
res.na<-array(NA, dim(covariates)[1])
for(i in which(na.bc>0))
{
if(((names(covariates)[i] %in% fparam)||(paste0("I(",names(covariates)[i],")",collapse = "")%in%fparam)))
{
ids.betas<-c(ids.betas,which(fparam==names(covariates)[i] | fparam == paste0("I(",names(covariates)[i],")",collapse = "")))
next
}
else
{
na.ids[which(is.na(covariates[,i])),i]<-0
na.bc[i]<-0
}
}
na.br<-rowSums(na.ids)
lv.br<-sort(unique(na.br))
if(lv.br[1]==0)
{
ids<-which(na.br==0)
mliks<-mliks.in
xyz<-which(mliks!=-10000)
moddee<-which( mliks ==max( mliks ,na.rm = TRUE))[1]
zyx<-array(data = NA,dim = lHash)
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
betas1<-betas
betas1[which(is.na(betas1))]<-0
if( nconsum > 0)
{
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}else{
diff<-0-mliks[moddee]
mliks<-mliks+diff
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}
covariates1<- covariates[ids,]
res<-t(zyx)%*%g(betas1%*%t(model.matrix(object = formula.cur,data = covariates1)))
res.na[ids]<-res
rm(mliks)
rm(res)
rm(zyx)
rm(xyz)
rm(covariates1)
rm(betas1)
}
ids<-(which(is.na(res.na)))
for(iii in which(na.bc>0))
{
if(sum(na.ids[ids,iii])>0)
{
var.del<-(which(fparam==names(covariates)[iii] | fparam == paste0("I(",names(covariates)[iii],")",collapse = "")))
if(length(var.del>0))
{
w.ids<-union(w.ids,which(!is.na(betas[,(var.del+1)])))
}
}
}
mliks<-mliks.in[-w.ids]
if(length(mliks)==0)
{
warning("not enough models for bagging in prediction. please train the model longer!")
return(-1)
}
xyz<-which(mliks!=-10000)
moddee<-which( mliks ==max( mliks ,na.rm = TRUE))[1]
zyx<-array(data = NA,dim = length(mliks))
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
betas1<-betas[-w.ids,]
betas1[which(is.na(betas1))]<-0
if( nconsum > 0)
{
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}else{
diff<-0-mliks[moddee]
mliks<-mliks+diff
nconsum<-sum(exp(- mliks[moddee]+ mliks[xyz]),na.rm = TRUE)
zyx[xyz]<-exp(mliks[xyz]- mliks[moddee])/nconsum
}
covariates1<- as.matrix(covariates[ids,])
covariates1[which(is.na(covariates1))]<-0
covariates1<-as.data.frame(covariates1)
res<-t(zyx)%*%g(betas1%*%t(model.matrix(object = formula.cur,data = covariates1)))
res.na[ids]<-res
rm(mliks)
rm(zyx)
rm(xyz)
rm(res)
rm(covariates1)
return(list(forecast = res.na))
}
)
)
options(bigmemory.typecast.warning=FALSE)
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