R/resampLmer.R

In fullfact: Full Factorial Breeding Analysis

resampLmer <-
function(resamp,dam,sire,response,start,end,ml=F) {
  if (missing(resamp)) stop("Need the resampled 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(start)) stop("Need the starting model number")
  if (missing(end)) stop("Need the ending model number")
  print(time1<- Sys.time()) #start time
#column labels
  response2<- colnames(resamp)[grep(paste(response), colnames(resamp))]
  dam2<- colnames(resamp)[grep(paste(dam), colnames(resamp))]
  sire2<- colnames(resamp)[grep(paste(sire), colnames(resamp))]
#Model
  mod<- matrix(0,ncol=4,nrow=length(response2))   #variance
 for (j in start:end) { 
  print(paste("Working on model: ", j, sep=""))
 if (ml == F) {
  m<- lmer(formula= noquote(paste(response2[j],"~ (1|",dam2[j],") + (1|",sire2[j],") + (1|",dam2[j],":",sire2[j],")",sep="")),
    data=resamp) }
 if (ml == T) {
  m<- lmer(formula= noquote(paste(response2[j],"~ (1|",dam2[j],") + (1|",sire2[j],") + (1|",dam2[j],":",sire2[j],")",sep="")),
    data=resamp, REML=F) } 
  mod[j,]<- c(colSums(diag(VarCorr(m))),attr(VarCorr(m),"sc")^2)
  col_names<- as.data.frame(VarCorr(m))$grp; rm(m)   }
#combining together
   comp<- as.data.frame(mod)
   colnames(comp)<- col_names
   comp$Total<- rowSums(comp)
#remove last number
colnames(comp)<- gsub(end,'', colnames(comp))
#Maternal, additive, nonadditive
  temp<- comp #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"
  comp$additive<- 4*temp$sire
  comp$nonadd<- 4*temp$'dam:sire'
  comp$maternal<- temp$dam- temp$sire
#
   print(Sys.time()- time1) #end time
   invisible(comp)  #after time
}