Nothing
"summary.Pedig"<-function(object, keep.only=NULL, maxd=50, d=4, ...){
PedigAsDataTable <- "data.table" %in% class(object)
object <- as.data.frame(object)
if(is.logical(keep.only)){keep.only <- object[keep.only,1]}
ids <- as.character(object[[1]])
if(!is.null(keep.only)){
keep.only <- as.character(keep.only)
keep.only <- setdiff(keep.only, c(NA))
}
Pedig <- prePed(object, keep=keep.only, addNum=TRUE)
ids <- ids[ids %in% Pedig$Indiv]
Pedig$Inbreeding <- pedInbreeding(Pedig)$Inbr
compl <- completeness(Pedig, maxd=maxd, by="Indiv")
setDT(compl)
setDT(Pedig)
Completeness <- NULL
equiGen <- NULL
fullGen <- NULL
Indiv <- NULL
maxGen <- NULL
meanCom <- NULL
numSire <- NULL
numDam <- NULL
Inbreeding <- NULL
Res <- compl[, list(maxGen=length(Completeness)-1, equiGen=sum(Completeness)-1), by="Indiv"]
sRes <- compl[compl$Completeness==1, list(fullGen=length(Completeness)-1), by="Indiv"]
Res <- sRes[Res, list(Indiv, equiGen, fullGen, maxGen), on="Indiv"]
sRes <- compl[compl$Generation %in% (0:(d-1)), list(meanCom=sum(Completeness)/(1*d)), by="Indiv"]
Res <- sRes[Res, list(Indiv, equiGen, fullGen, maxGen, meanCom), on="Indiv"]
Res$meanCom[is.na(Res$meanCom)]<-0
Pedig <- Res[Pedig,list(Indiv, numSire, numDam, equiGen, fullGen, maxGen, meanCom, Inbreeding), on="Indiv"]
Pedig <- as.data.frame(Pedig)
setDF(Pedig)
Pedig$patIndex <- 0
Pedig[Pedig$numSire!=0,"patIndex"]<-Pedig[Pedig$numSire[Pedig$numSire!=0],"meanCom"]
Pedig$matIndex <- 0
Pedig[Pedig$numDam!=0,"matIndex"]<-Pedig[Pedig$numDam[Pedig$numDam!=0],"meanCom"]
Pedig$PCI <- 2*Pedig$matIndex*Pedig$patIndex/(Pedig$matIndex+Pedig$patIndex)
Pedig[is.na(Pedig$PCI),"PCI"]<-0
Pedig <- Pedig[,c("Indiv","equiGen", "fullGen", "maxGen", "PCI","Inbreeding")]
if(!is.null(keep.only)){
ids<-ids[ids %in% keep.only]
}
rownames(Pedig)<-Pedig$Indiv
Pedig <- Pedig[ids,]
if(PedigAsDataTable){setDT(Pedig)}
Pedig
}
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