R/get.parentage.R

In jonesor/rcolony: Tools for implementation and visualisation of Colony2 and its outputs

#' A function to extract the paternity and maternity information from the
#' colony object created with get.colony.data.
#'
#' This function extracts the paternity and maternity information from a colony
#' object that was created using \code{\link{get.colony.data}}. The output is a
#' dataframe with 3 columns. (1) mums, (2) dads, (3) frequency. The output can
#' either be derived from pairwise-likelihood or the full-likelihood method (if
#' available).
#'
#'
#' @param colony.object A list created by \code{\link{get.colony.data}}
#' @param pairwise Should the parentage information be derived from the
#' pairwise likelihood estimates (TRUE), of from the full likelihood methods
#' (FALSE). See Wang et al. for details.
#' @return A data frame with 3 columns. (1) mums, (2) dads, (3) frequency.
#' @author Owen R. Jones
#' @seealso \code{\link{get.colony.data}}
#' @references Wang, J. (2004) Sibship reconstruction from genetic data with
#' typing errors.  Genetics 166: 1963-1979.
#' @keywords manip
#' @examples
#'
#'
#' data(testdata)
#' parents<-get.parentage(testdata)
#' head(parents)
#'
#'
#' @export
`get.parentage` <-
function(colony.object,pairwise=FALSE){



if(pairwise==FALSE){
Offspring<-colony.object$offspring
Offspring<-merge(Offspring,colony.object$maternity,by.x="offspringID",by.y="OffspringID",sort=FALSE,all.x=TRUE)
Offspring<-merge(Offspring,colony.object$paternity,by.x="offspringID",by.y="OffspringID",sort=FALSE,all.x=TRUE)



Offspring$InferredMum1<-as.character(Offspring$InferredMum1)
Offspring$InferredMum1[is.na(Offspring$InferredMum1)]<-"Unknown"
Offspring$InferredMum1<-as.factor(Offspring$InferredMum1)


Offspring$InferredDad1<-as.character(Offspring$InferredDad1)
Offspring$InferredDad1[is.na(Offspring$InferredDad1)]<-"Unknown"
Offspring$InferredDad1<-as.factor(Offspring$InferredDad1)


Offspring<-merge(Offspring,colony.object$mothers,by.x="InferredMum1",by.y="motherID")
Offspring<-merge(Offspring,colony.object$fathers,by.x="InferredDad1",by.y="fatherID")

			xx<-as.data.frame(table(Offspring$InferredMum1,Offspring$InferredDad1))
			names(xx)<-c("mums","dads","Freq")

			xx2<-expand.grid(mums=colony.object$mothers$motherID,dads=colony.object$fathers$fatherID)
			xx2$Freq<-rep(0,dim(xx2)[1])

			omit.these<-paste(xx$mums,xx$dads)

			temp<-paste(xx2$mums,xx2$dads)

			xx2<-xx2[!(temp%in%omit.these),]

			xx<-rbind(xx2,xx)

			return(xx)

}else{

Offspring<-colony.object$offspring
Offspring<-merge(Offspring,colony.object$pairwise.maternity,by.x="offspringID",by.y="OffspringID",sort=FALSE,all.x=TRUE)
names(Offspring)[names(Offspring)=="CandidateID"]<-"CandidateMum1"
names(Offspring)[names(Offspring)=="Confidence"]<-"CandidateMum1.Confidence"

Offspring<-merge(Offspring,colony.object$pairwise.paternity,by.x="offspringID",by.y="OffspringID",sort=FALSE,all.x=TRUE)
names(Offspring)[names(Offspring)=="CandidateID"]<-"CandidateDad1"
names(Offspring)[names(Offspring)=="Confidence"]<-"CandidateDad1.Confidence"


Offspring$CandidateMum1<-as.character(Offspring$CandidateMum1)
Offspring$CandidateMum1[is.na(Offspring$CandidateMum1)]<-"Unknown"
Offspring$CandidateMum1<-as.factor(Offspring$CandidateMum1)

Offspring$CandidateDad1<-as.character(Offspring$CandidateDad1)
Offspring$CandidateDad1[is.na(Offspring$CandidateDad1)]<-"Unknown"
Offspring$CandidateDad1<-as.factor(Offspring$CandidateDad1)

Offspring<-merge(Offspring,colony.object$mothers,by.x="CandidateMum1",by.y="mother")
Offspring<-merge(Offspring,colony.object$fathers,by.x="CandidateDad1",by.y="father")


			xx<-as.data.frame(table(Offspring$CandidateMum1,Offspring$CandidateDad1))
			names(xx)<-c("mums","dads","Freq")

			xx2<-expand.grid(mums=colony.object$mothers$motherID,dads=colony.object$fathers$fatherID)
			xx2$Freq<-rep(0,dim(xx2)[1])

			omit.these<-paste(xx$mums,xx$dads)

			temp<-paste(xx2$mums,xx2$dads)

			xx2<-xx2[!(temp%in%omit.these),]

			xx<-rbind(xx2,xx)

			return(xx)
		}}