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JackGlmer3 <-
function(observ,dam,sire,response,fam_link,remain,quasi=F,size=1,first=NULL) {
if (missing(observ)) stop("Need the observed data frame")
if (missing(dam)) stop("Need the dam column name")
if (missing(sire)) stop("Need the sire column name")
if (missing(response)) stop("Need the response column name")
if (missing(fam_link)) stop("Need the family(link) for the glmer")
if (missing(remain)) stop("Need the remaining formula")
if (size %% 1 != 0) stop("Size needs to be a positive integer")
if (size %% 1 == 0 && size < 0) stop("Size needs to be a positive integer")
if (!is.null(first) && first %% 1 != 0) stop("First needs to be a positive integer")
if (!is.null(first) && first %% 1 == 0 && first < 0) stop("First needs to be a positive integer")
print(time1<- Sys.time()) #start time
#error component constants
if(paste(fam_link)[2]== "logit") { m_err<- (pi^2)/3 }
if(paste(fam_link)[2]== "probit") { m_err<- 1 }
if(paste(fam_link)[2]== "sqrt") { m_err<- 0.25 }
##Drop a single-observation
if (size == 1) {
#variable matrices
var_fixed<- matrix(0,ncol=1,nrow=length(observ[,1])) #variance of fixed effects
if (quasi == F) {
rand_l<- nchar(remain)- nchar(gsub(")","",remain)) #number of random effects
var_rand<- matrix(0,ncol=rand_l+3,nrow=length(observ[,1])) } #variance of random effects (no res, total)
if (quasi == T) {
rand_l<- nchar(remain)- nchar(gsub(")","",remain)) + 1 #number of random effects + quasi
var_rand<- matrix(0,ncol=rand_l+3,nrow=length(observ[,1]))
observ$dispersion<- as.factor(1:length(observ[,1])) }
res<- matrix(0,ncol=1,nrow=length(observ[,1])) #for poisson(log)
#
if (is.null(first)) { iter<- nrow(observ) }
if (!is.null(first)) { iter<- first }
for (i in 1:iter) {
print(paste0("Removing observation: ",i," of ",length(observ[,1])))
#Model
if (quasi == F) {
m<- glmer(formula= noquote(paste(response,"~ (1|",dam,") + (1|",sire,") + (1|",dam,":",sire,") +",remain,sep="")),
family=fam_link,data=observ[-i,]) }
if (quasi == T) {
observ$dispersion<- as.factor(1:length(observ[,1]))
m<- glmer(formula= noquote(paste(response,"~ (1|",dam,") + (1|",sire,") + (1|",dam,":",sire,") + (1|dispersion) +",remain,sep="")),
family=fam_link,data=observ[-i,]) }
#
if(paste(fam_link)[2]== "log") {
#Get random effects names to generate null model
rand.formula <- reformulate(sapply(findbars(formula(m)),function(x) paste0("(", deparse(x), ")")),response=".")
#Generate null model (intercept and random effects only, no fixed effects)
null.m <- update(m, rand.formula)
res[i,]<- log(1/exp(fixef(null.m)[1]) + 1) }
var_fixed[i,] <- var(as.vector(fixef(m) %*% t(m@pp$X))) #total variation of fixed effects
var_rand[i,]<- colSums(diag(VarCorr(m)))
col_names<- as.data.frame(VarCorr(m))$grp } #end loop
#combining together
if (sum(var_fixed[,1]) != 0) {
if(paste(fam_link)[2]!= "log") { jack<- as.data.frame(cbind(var_rand,m_err,var_fixed)) }
if(paste(fam_link)[2]== "log") { jack<- as.data.frame(cbind(var_rand,res,var_fixed)) }
colnames(jack)<- c(col_names,"Residual","Fixed") }
if (sum(var_fixed[,1]) == 0) {
if(paste(fam_link)[2]!= "log") { jack<- as.data.frame(cbind(var_rand,m_err)) }
if(paste(fam_link)[2]== "log") { jack<- as.data.frame(cbind(var_rand,res)) }
colnames(jack)<- c(col_names,"Residual") }
jack$Total<- rowSums(jack)
} #end single Jack
##Drop a a block
if (size > 1) {
observS1 <- observ[sample(nrow(observ)),];rm(observ) #shuffle once
observS2 <- observS1[sample(nrow(observS1)),];rm(observS1) #shuffle twice
n_mod<- floor(nrow(observS2)/size) #number of models in data frame
#variable matrices
var_fixed<- matrix(0,ncol=1,nrow=n_mod) #variance of fixed effects
if (quasi == F) {
rand_l<- nchar(remain)- nchar(gsub(")","",remain)) #number of random effects
var_rand<- matrix(0,ncol=rand_l+3,nrow=n_mod) } #variance of random effects (no res, total)
if (quasi == T) {
rand_l<- nchar(remain)- nchar(gsub(")","",remain)) + 1 #number of random effects + quasi
var_rand<- matrix(0,ncol=rand_l+3,nrow=n_mod)
observS2$dispersion<- as.factor(1:length(observS2[,1])) }
res<- matrix(0,ncol=1,nrow=n_mod) #for poisson(log)
#
if (is.null(first)) { iter<- n_mod }
if (!is.null(first)) { iter<- first }
#begining values
beg<- matrix(0,ncol=1,nrow=n_mod)
beg[1]<- 1 #always
for (i in 2:n_mod) { beg[i]<- beg[i-1] + size }
#finishing values
finn<- matrix(0,ncol=1,nrow=n_mod)
finn[1]<- size #always
for (i in 2:n_mod) { finn[i]<- finn[i-1] + size }
#jacking
for (i in 1:iter) {
print(paste0("Removing block: ",i," of ",n_mod))
if (quasi == F) {
m<- glmer(formula= noquote(paste(response,"~ (1|",dam,") + (1|",sire,") + (1|",dam,":",sire,") +",remain,sep="")),
family=fam_link,data=observS2[-c(beg[i]:finn[i]),]) }
if (quasi == T) {
observS2$dispersion<- as.factor(1:length(observS2[,1]))
m<- glmer(formula= noquote(paste(response,"~ (1|",dam,") + (1|",sire,") + (1|",dam,":",sire,") + (1|dispersion) +",remain,sep="")),
family=fam_link,data=observS2[-c(beg[i]:finn[i]),]) }
#
if(paste(fam_link)[2]== "log") {
#Get random effects names to generate null model
rand.formula <- reformulate(sapply(findbars(formula(m)),function(x) paste0("(", deparse(x), ")")),response=".")
#Generate null model (intercept and random effects only, no fixed effects)
null.m <- update(m, rand.formula)
res[i,]<- log(1/exp(fixef(null.m)[1]) + 1) }
var_fixed[i,] <- var(as.vector(fixef(m) %*% t(m@pp$X))) #total variation of fixed effects
var_rand[i,]<- colSums(diag(VarCorr(m)))
col_names<- as.data.frame(VarCorr(m))$grp } #end loop
#combining together
if (sum(var_fixed[,1]) != 0) {
if(paste(fam_link)[2]!= "log") { jack<- as.data.frame(cbind(var_rand,m_err,var_fixed)) }
if(paste(fam_link)[2]== "log") { jack<- as.data.frame(cbind(var_rand,res,var_fixed)) }
colnames(jack)<- c(col_names,"Residual","Fixed") }
if (sum(var_fixed[,1]) == 0) {
if(paste(fam_link)[2]!= "log") { jack<- as.data.frame(cbind(var_rand,m_err)) }
if(paste(fam_link)[2]== "log") { jack<- as.data.frame(cbind(var_rand,res)) }
colnames(jack)<- c(col_names,"Residual") }
jack$Total<- rowSums(jack)
} #end block Jack
#Maternal, additive, nonadditive
temp<- jack #to not override column names
colnames(temp)[which(colnames(temp)==dam)]<- "dam"
colnames(temp)[which(colnames(temp)==sire)]<- "sire"
colnames(temp)[which(colnames(temp)==noquote(paste(dam,":",sire,sep="")))]<- "dam:sire"
jack$additive<- 4*temp$sire
jack$nonadd<- 4*temp$'dam:sire'
jack$maternal<- temp$dam- temp$sire
#
print(Sys.time()- time1) #end time
invisible(jack) #after time
}
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