Nothing
"NPOdata" <- function(phen, Classes, proportion=TRUE, symmetric=FALSE, quiet=FALSE){
phen <- phen[phen$Class %in% Classes, ]
withoutSexes <- any(is.na(phen$Sex))
if(withoutSexes){ #Not yet implemented. Function returns Zero-Matrix
nPO <- matrix(0, nrow=length(Classes), ncol=length(Classes))
rownames(nPO) <- Classes
colnames(nPO) <- Classes
return(nPO)
}
phen$Sire.Class <- phen[phen$Sire,"Class"]
phen$Dam.Class <- phen[phen$Dam, "Class"]
TabS <- table(phen$Class, phen$Sire.Class)
TabD <- table(phen$Class, phen$Dam.Class)
TabS <- TabS[rownames(TabS) %in% Classes, colnames(TabS) %in% Classes]
TabD <- TabD[rownames(TabD) %in% Classes, colnames(TabD) %in% Classes]
nPO <- matrix(0,nrow=length(Classes), ncol=length(Classes))
rownames(nPO) <- Classes
colnames(nPO) <- Classes
nPO[rownames(TabS), colnames(TabS)] <- TabS
nPO[rownames(TabD), colnames(TabD)] <- TabD
if(proportion){
nvec <- table(phen$Class)[Classes]
nvec[is.na(nvec)] <- 1
nPO <- diag(1/nvec) %*% nPO %*% diag(1/nvec)
rownames(nPO) <- Classes
colnames(nPO) <- Classes
}
if(symmetric){
nPO[is.na(nPO)]<-0
nPO <- nPO + t(nPO)
diag(nPO) <- 0
}
nPO
}
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