Nothing
`fpederr` <-
function(truePedigree,founders=NULL,sex=NULL,samp=NULL,sireE=NULL,damE=NULL,
sireA=NULL,damA=NULL,cohort=NULL,first=NULL,last=NULL,monoecey=0,modifyAssumedPedigree=0){
fpederrR <- function(Ped,found,sex,samp,dade,mume,dadA,mumA,cohort,first,last,mono)
.C("FPEDERR_R",
as.integer(Ped$id),
as.integer(Ped$dam),
as.integer(Ped$sire),
as.integer(found),
as.integer(sex),
as.integer(samp),
as.double(dade),
as.double(mume),
as.double(dadA),
as.double(mumA),
as.integer(cohort),
as.integer(first),
as.integer(last),
as.integer(length(Ped$id)),
as.integer(Ped$dam*0),
as.integer(Ped$sire*0),
as.integer(Ped$dam*0),
as.integer(Ped$sire*0),
as.integer(mono),PACKAGE="pedantics")
warnings<-NULL
if(is.null(founders)) {
founders<-rep(1,length(truePedigree[,1]))
warnings<-rbind(warnings,"All individuals set to founder status")
}
if(is.null(sex)) {
sex<-rep(-1,length(truePedigree[,1]))
warnings<-rbind(warnings,"All individuals sex set to unknown")
}
if(is.null(samp))
samp<-rep(1,length(truePedigree[,1]))
if(is.null(sireE))
sireE<-rep(0,length(truePedigree[,1]))
if(is.null(damE))
damE<-rep(0,length(truePedigree[,1]))
if(is.null(sireA))
sireA<-rep(1,length(truePedigree[,1]))
if(is.null(damA))
damA<-rep(1,length(truePedigree[,1]))
if(is.null(cohort)) {
cohort<-rep(1,length(truePedigree[,1]))
warnings<-rbind(warnings,"No cohort designations - impossible pedigree loops could result")
}
if(is.null(first))
first<-rep(1,length(truePedigree[,1]))
if(is.null(last))
last<-rep(1,length(truePedigree[,1]))
if(length(sireE)==1) sireE<-rep(sireE,length(truePedigree[,1]))
if(length(damE)==1) damE<-rep(damE,length(truePedigree[,1]))
if(length(sireA)==1) sireA<-rep(sireA,length(truePedigree[,1]))
if(length(damA)==1) damA<-rep(damA,length(truePedigree[,1]))
numericPed<-makePedigreeNumeric(as.character(truePedigree$id),as.character(truePedigree$sire),
as.character(truePedigree$dam),missingVal=-1)
fpederrRrun<-fpederrR(Ped=numericPed$numericPedigree,
found=founders,sex=sex,samp=samp,
dade=sireE,mume=damE,dadA=sireA,mumA=damA,
cohort=cohort,first=first,last=last,mono=0)
assumedPed<-makePedigreeFactor(fpederrRrun[[1]],fpederrRrun[[16]],fpederrRrun[[15]],numericPed$idKey)
supplementalPed<-NULL
if(modifyAssumedPedigree==1){
supplementalPed<-assumedPed
for(i in 1:length(assumedPed[,1])){
if(is.na(assumedPed$sire[x])==FALSE) supplementalPed$sire[x] <- truePedigree$sire[x]
if(is.na(assumedPed$dam[x])==FALSE) supplementalPed$dam[x] <- truePedigree$dam[x]
}
}
if(modifyAssumedPedigree==2){
supplementalPed<-makePedigreeFactor(fpederrRrun[[1]],fpederrRrun[[18]],fpederrRrun[[17]],numericPed$idKey)
}
fpederrResults<-list(assumedPedigree=assumedPed,truePedigree=truePedigree)
if(is.null(supplementalPed)==FALSE) fpederrResults<-list(assumedPedigree=assumedPed,truePedigree=truePedigree,
supplementalPedigree=supplementalPed)
if(is.null(warnings)==FALSE) {
for(x in 1:length(warnings)) cat(paste("Warning: ",warnings[x],'\n'));
}
fpederrResults
}
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