RFGLS (version 1.1)

rescovmtx: Residual variance-covariance matrix.

Description

The residual covariance matrix used in package examples. In the previous package version, its name was "resVCmtx".

Usage

data(rescovmtx)

Format

An object of class bdsmatrix (from package bdsmatrix). It is a 4050-by-4050 block-diagonal sparse matrix, with off-diagonal elements of 0. It has six slots, the descriptions of which may be found in the documentation for bdsmatrix-class.

Details

It is perhaps most instructive to see the syntax by which rescovmtx can be reproduced from datasets pheno, geno, and pedigree:

data(pheno)
data(geno)
data(pedigree)
foo <- gls.batch.get(
  phenfile=pheno,genfile=data.frame(t(geno)),pedifile=pedigree,
  covmtxfile.in=NULL,theta=NULL,snp.names=NULL,input.mode=c(1,2,3),
  pediheader=FALSE,pedicolname=c("FAMID","ID","PID","MID","SEX"),
  sep.phe=" ",sep.gen=" ",sep.ped=" ",
  phen="Zscore",covars="IsFemale",med=c("UN","VC"),
  outfile,col.names=TRUE,return.value=FALSE,
  covmtxfile.out=NULL,
  covmtxparams.out=NULL,
  sizeLab=NULL,Mz=NULL,Bo=NULL,Ad=NULL,Mix=NULL,indobs=NULL)
bar <- fgls(
  Zscore ~ IsFemale, data=foo$test.dat, tlist=foo$tlist,
  sizelist=foo$sizelist,med=c("UN","VC"), 
  vmat=NULL, 
  start=NULL, theta=NULL, drop=NULL, get.hessian=FALSE, 
  optim.method="BFGS", control=list(), weights=NULL,
  sizeLab=NULL,Mz=NULL,Bo=NULL,Ad=NULL,Mix=NULL,indobs=NULL)

Then, bar$sigma is identical to rescovmtx.

Examples

data(rescovmtx)
str(rescovmtx)
##Also see examples for functions fgls() and gls.batch().