Nothing
"reordXlist"<-function(X.list, marker.type="MSW"){
nind<-length(X.list$id)
if(TRUE%in%(X.list$X[[1]]$dam.id>nind)){
USdam<-TRUE
}else{
USdam<-FALSE
}
if(TRUE%in%(X.list$X[[1]]$sire.id>nind)){
USsire<-TRUE
}else{
USsire<-FALSE
}
npar<-c(ncol(X.list$X[[1]]$XDus), ncol(X.list$X[[1]]$XDs), ncol(X.list$X[[1]]$XSus), ncol(X.list$X[[1]]$XSs), ncol(X.list$X[[1]]$XDSus), ncol(X.list$X[[1]]$XDSs))
for(off in 1:length(X.list$X)){
if(is.null(X.list$X[[off]]$mmS)){
Sorder<-rep(1, length(X.list$X[[off]]$sire.id))
Dorder<-rep(1, length(X.list$X[[off]]$dam.id))
}else{
if(marker.type!="AFLP"){
Sorder<-X.list$X[[off]]$mmS
Dorder<-X.list$X[[off]]$mmD
}else{
if(is.null(X.list$X[[off]]$G)){
Sorder<-rep(1, length(X.list$X[[off]]$sire.id))
Dorder<-rep(1, length(X.list$X[[off]]$dam.id))
}else{
Sorder<-matrix(-X.list$X[[off]]$G, length(X.list$X[[off]]$sire.id), length(X.list$X[[off]]$dam.id))
Dorder<-colSums(Sorder)
Sorder<-rowSums(Sorder)
}
}
}
if(USdam==TRUE){
Dorder[which(X.list$X[[off]]$dam.id>nind)]<-999
}
if(USsire==TRUE){
Sorder[which(X.list$X[[off]]$sire.id>nind)]<-999
}
if(length(X.list$X[[off]]$restdam.id)!=length(X.list$X[[off]]$dam.id)){
Dorder[which(X.list$X[[off]]$dam.id%in%X.list$X[[off]]$restdam.id==FALSE)]<-9999
}
if(length(X.list$X[[off]]$restsire.id)!=length(X.list$X[[off]]$sire.id)){
Sorder[which(X.list$X[[off]]$sire.id%in%X.list$X[[off]]$restsire.id==FALSE)]<-9999
}
restDorder<-order(Dorder[match(X.list$X[[off]]$restdam.id, X.list$X[[off]]$dam.id)])
restSorder<-order(Sorder[match(X.list$X[[off]]$restsire.id, X.list$X[[off]]$sire.id)])
Dorder<-order(Dorder)
Sorder<-order(Sorder)
X.list$X[[off]]$mmD<-X.list$X[[off]]$mmD[Dorder]
X.list$X[[off]]$mmS<-X.list$X[[off]]$mmS[Sorder]
X.list$X[[off]]$dam.id<-X.list$X[[off]]$dam.id[Dorder]
X.list$X[[off]]$sire.id<-X.list$X[[off]]$sire.id[Sorder]
X.list$X[[off]]$restdam.id<-X.list$X[[off]]$restdam.id[restDorder]
X.list$X[[off]]$restsire.id<-X.list$X[[off]]$restsire.id[restSorder]
if(npar[1]>0){
X.list$X[[off]]$XDus<-matrix(X.list$X[[off]]$XDus[Dorder,], ncol=npar[1], dimnames=dimnames(X.list$X[[off]]$XDus))
}
if(npar[2]>0){
X.list$X[[off]]$XDs<-matrix(X.list$X[[off]]$XDs[Dorder,], ncol=npar[2], dimnames=dimnames(X.list$X[[off]]$XDs))
}
if(npar[3]>0){
X.list$X[[off]]$XSus<-matrix(X.list$X[[off]]$XSus[Sorder,], ncol=npar[3], dimnames=dimnames(X.list$X[[off]]$XSus))
}
if(npar[4]>0){
X.list$X[[off]]$XSs<-matrix(X.list$X[[off]]$XSs[Sorder,], ncol=npar[4], dimnames=dimnames(X.list$X[[off]]$XSs))
}
if(npar[5]>0){
X.list$X[[off]]$XDSus<-matrix(X.list$X[[off]]$XDSus[c(t(outer(length(X.list$X[[off]]$sire.id)*(Dorder-1), Sorder, "+"))),], ncol=npar[5], dimnames=dimnames(X.list$X[[off]]$XDSus))
}
if(npar[6]>0){
X.list$X[[off]]$XDSs<-matrix(X.list$X[[off]]$XDSs[c(t(outer(length(X.list$X[[off]]$sire.id)*(Dorder-1), Sorder, "+"))),], ncol=npar[6], dimnames=dimnames(X.list$X[[off]]$XDSs))
}
if(is.null(X.list$X[[off]]$G)==FALSE){
X.list$X[[off]]$G<-as.matrix(X.list$X[[off]]$G[c(t(outer(length(X.list$X[[off]]$sire.id)*(Dorder-1), Sorder, "+")))])
}
}
X.list
}
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