R/GetVarCov.R

In CovCombR: Combine Partial Covariance / Relationship Matrices

GetVarCov <- function(Hmat, Klist, nu = 100, w=1) {
    
    Hmatinv<-solve(Hmat)
    nrowe<-nrow(Hmat)^2
    namesinH<-rownames(Hmat)
    
    geterrorsonesample<-function(K){
    INFmat<-matrix(0,nrowe,nrowe)
    namesforerrormat<-apply(expand.grid(x=namesinH,y=namesinH),1,function(inp){paste(inp[1], inp[2],sep="_.._")})
    rownames(INFmat)<-colnames(INFmat)<-namesforerrormat
    namesinK<-rownames(K[[1]])
    m=length(Klist)
    
    for (i in 1:(length(namesforerrormat))){
        name11<-strsplit(namesforerrormat[i], "_.._")[[1]][1]  
        name12<-strsplit(namesforerrormat[i], "_.._")[[1]][2]  
        mat1<-matrix(0,nrow=nrow(Hmat), ncol=ncol(Hmat))
        rownames(mat1)<-colnames(mat1)<-namesinH
        mat1[name11, name12]<-1
        for (j in 1:length(namesforerrormat)){
          name21<-strsplit(namesforerrormat[j], "_.._")[[1]][1]  
          name22<-strsplit(namesforerrormat[j], "_.._")[[1]][2]  
          mat2<-matrix(0,nrow=nrow(Hmat), ncol=ncol(Hmat))
          rownames(mat2)<-colnames(mat2)<-namesinH
          mat2[name21, name22]<-1
          Hmata <- Hmatfunc(Hmat, K[[1]], w = K[[2]], 
                                           nu = nu)
          colnames(Hmata) <- rownames(Hmata) <- rownames(Hmatinv)
          Hmatainv<-solve(Hmata)
          INFmat[namesforerrormat[i],namesforerrormat[j]]<- (nu/(2))*sum(diag({Hmatainv*(nu)}%*%mat1%*%{Hmatainv*(nu)}%*%mat2))
        }
    }
    return(INFmat)
    }
   if (length(w)<2){
      wvec<-rep(w,length(Klist))
    } else{
      wvec<-w
    }
    for (k in 1:length(Klist)){
      Klist[[k]]<-list(Klist[[k]],wvec[k])
    }
    listout<-lapply(Klist, geterrorsonesample)
    outfunc <- Reduce("+", listout)
    namesforerrormat<-apply(expand.grid(x=namesinH,y=namesinH),1,function(inp){paste(inp[1], inp[2],sep="_")})
    rownames(outfunc)<-colnames(outfunc)<-namesforerrormat
    outfunc<-outfunc[order(rownames(outfunc)),order(colnames(outfunc))]
    outfunc<-nu^2*solve(outfunc)
    return(outfunc)
}