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## BART: Bayesian Additive Regression Trees
## Copyright (C) 2017 Robert McCulloch and Rodney Sparapani
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 2 of the License, or
## (at your option) any later version.
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
## You should have received a copy of the GNU General Public License
## along with this program; if not, a copy is available at
## https://www.R-project.org/Licenses/GPL-2
pbart=function(
x.train, y.train, x.test=matrix(0.0,0,0),
sparse=FALSE, theta=0, omega=1,
a=0.5, b=1, augment=FALSE, rho=NULL,
xinfo=matrix(0.0,0,0), usequants=FALSE,
cont=FALSE, rm.const=TRUE,
k=2.0, power=2.0, base=.95,
binaryOffset=NULL,
ntree=50L, numcut=100L,
ndpost=1000L, nskip=100L, keepevery=1L,
nkeeptrain=ndpost, nkeeptest=ndpost,
##nkeeptestmean=ndpost,
nkeeptreedraws=ndpost,
printevery=100L, transposed=FALSE
##treesaslists=FALSE
)
{
#--------------------------------------------------
#data
n = length(y.train)
if(length(binaryOffset)==0) binaryOffset=qnorm(mean(y.train))
if(!transposed) {
temp = bartModelMatrix(x.train, numcut, usequants=usequants,
cont=cont, xinfo=xinfo, rm.const=rm.const)
x.train = t(temp$X)
numcut = temp$numcut
xinfo = temp$xinfo
## if(length(x.test)>0)
## x.test = t(bartModelMatrix(x.test[ , temp$rm.const]))
if(length(x.test)>0) {
x.test = bartModelMatrix(x.test)
x.test = t(x.test[ , temp$rm.const])
}
rm.const <- temp$rm.const
grp <- temp$grp
rm(temp)
}
else {
rm.const <- NULL
grp <- NULL
}
if(n!=ncol(x.train))
stop('The length of y.train and the number of rows in x.train must be identical')
p = nrow(x.train)
np = ncol(x.test)
if(length(rho)==0) rho <- p
if(length(rm.const)==0) rm.const <- 1:p
if(length(grp)==0) grp <- 1:p
#--------------------------------------------------
#set nkeeps for thinning
if((nkeeptrain!=0) & ((ndpost %% nkeeptrain) != 0)) {
nkeeptrain=ndpost
cat('*****nkeeptrain set to ndpost\n')
}
if((nkeeptest!=0) & ((ndpost %% nkeeptest) != 0)) {
nkeeptest=ndpost
cat('*****nkeeptest set to ndpost\n')
}
## if((nkeeptestmean!=0) & ((ndpost %% nkeeptestmean) != 0)) {
## nkeeptestmean=ndpost
## cat('*****nkeeptestmean set to ndpost\n')
## }
if((nkeeptreedraws!=0) & ((ndpost %% nkeeptreedraws) != 0)) {
nkeeptreedraws=ndpost
cat('*****nkeeptreedraws set to ndpost\n')
}
#--------------------------------------------------
#prior
## nu=sigdf
## if(is.na(lambda)) {
## if(is.na(sigest)) {
## if(p < n) {
## df = data.frame(t(x.train),y.train)
## lmf = lm(y.train~.,df)
## rm(df)
## sigest = summary(lmf)$sigma
## } else {
## sigest = sd(y.train)
## }
## }
## qchi = qchisq(1.0-sigquant,nu)
## lambda = (sigest*sigest*qchi)/nu #lambda parameter for sigma prior
## }
## if(is.na(sigmaf)) {
## tau=(max(y.train)-min(y.train))/(2*k*sqrt(ntree));
## } else {
## tau = sigmaf/sqrt(ntree)
## }
#--------------------------------------------------
ptm <- proc.time()
#call
res = .Call("cpbart",
n, #number of observations in training data
p, #dimension of x
np, #number of observations in test data
x.train, #p*n training data x
y.train, #n*1 training data y
x.test, #p*np test data x
ntree,
numcut,
ndpost*keepevery,
nskip,
power,
base,
binaryOffset,
3/(k*sqrt(ntree)),
sparse,
theta,
omega,
grp,
a,
b,
rho,
augment,
nkeeptrain,
nkeeptest,
##nkeeptestmean,
nkeeptreedraws,
printevery,
##treesaslists,
xinfo
)
res$proc.time <- proc.time()-ptm
if(nkeeptrain>0) {
##res$yhat.train.mean <- NULL
##res$yhat.train.mean = res$yhat.train.mean+binaryOffset
res$yhat.train = res$yhat.train+binaryOffset
res$prob.train = pnorm(res$yhat.train)
res$prob.train.mean <- apply(res$prob.train, 2, mean)
} else {
res$yhat.train <- NULL
##res$yhat.train.mean <- NULL
}
if(np>0) {
##res$yhat.test.mean <- NULL
##res$yhat.test.mean = res$yhat.test.mean+binaryOffset
res$yhat.test = res$yhat.test+binaryOffset
res$prob.test = pnorm(res$yhat.test)
res$prob.test.mean <- apply(res$prob.test, 2, mean)
} else {
res$yhat.test <- NULL
##res$yhat.test.mean <- NULL
}
if(nkeeptreedraws>0) ## & !treesaslists)
names(res$treedraws$cutpoints) = dimnames(x.train)[[1]]
dimnames(res$varcount)[[2]] = as.list(dimnames(x.train)[[1]])
dimnames(res$varprob)[[2]] = as.list(dimnames(x.train)[[1]])
res$varcount.mean <- apply(res$varcount, 2, mean)
res$varprob.mean <- apply(res$varprob, 2, mean)
res$rm.const <- rm.const
res$binaryOffset=binaryOffset
attr(res, 'class') <- 'pbart'
return(res)
}
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