R/make.ctable.R

In dmm: Dyadic Mixed Model for Pedigree Data

make.ctable <-
function(){
#  make.ctable() - setup lists of components
#                - VarGa() and VarGs() added
  cohortvar <- c("VarE(C)","VarE(M&C)","VarE(M&!C)")
  cohortcov <- c("CovE(I,M&!C)","CovE(M&!C,I)")
  cohort <- c(cohortvar,cohortcov)
  evar <- c("VarE(I)","VarE(M)")
  ecov <- c("CovE(I,M)","CovE(M,I)")
  e <- c(evar,ecov)

  sexlinaddgvar <- c("VarGs(Ia)","VarGs(Ma)")
  addgvar <- c("VarG(Ia)","VarG(Ma)",sexlinaddgvar)
  domgvar <- c("VarG(Id)","VarG(Md)")
  epiaddgvar <- c("VarG(Ia:a)","VarG(Ma:a)")
  epidomgvar <- c("VarG(Ia:d)","VarG(Ma:d)","VarG(Id:d)","VarG(Md:d)")
  matcgvar <- c("VarGlm(I)")
  patygvar <- c("VarGlp(I)")

  gvar <- c(addgvar,domgvar,epiaddgvar,epidomgvar,matcgvar,patygvar)
  allvar <- c(evar,gvar,cohortvar)

  sexlinaddgcov <- c("CovGs(Ia,Ma)","CovGs(Ma,Ia)")
  addgcov <- c("CovG(Ia,Ma)","CovG(Ma,Ia)",sexlinaddgcov)
  domgcov <- c("CovG(Id,Md)","CovG(Md,Id)")
  epiaddgcov <- c("CovG(Ia:a,Ma:a)","CovG(Ma:a,Ia:a)")
  epidomgcov <- c("CovG(Ia:d,Ma:d)","CovG(Ma:d,Ia:d)","CovG(Id:d,Md:d)","CovG(Md:d,Id:d)")

  gcov <- c(addgcov,domgcov,epiaddgcov,epidomgcov)
  g <- c(gvar,gcov)
  sexlinaddg <- c(sexlinaddgvar,sexlinaddgcov)
  allcov <- c(ecov,gcov,cohortcov)
  addg <- c(addgvar,addgcov)
  domg <- c(domgvar,domgcov)
  epiaddg <- c(epiaddgvar,epiaddgcov)
  epidomg <- c(epidomgvar,epidomgcov)
  matcg <- c(matcgvar)
  patyg <- c(patygvar)

  indvar <- c("VarE(I)","VarG(Ia)","VarG(Id)","VarG(Ia:a)","VarG(Ia:d)","VarG(Id:d)","VarGs(Ia)","VarGlm(I)","VarGlp(I)")
  indcov <- NULL  
  # if indcov is NULL matcov is same as allcov
  ind <- c(indvar,indcov)

  matvar <- c("VarE(M)","VarG(Ma)","VarG(Md)","VarG(Ma:a)","VarG(Ma:d)","VarG(Md:d)","VarE(M&C)","VarE(M&!C)","VarGs(Ma)")
  matcov <- c("CovE(I,M)","CovE(M,I)","CovG(Ia,Ma)","CovG(Ma,Ia)","CovG(Id,Md)","CovG(Md,Id)","CovG(Ia:a,Ma:a)","CovG(Ma:a,Ia:a)","CovG(Ia:d,Ma:d)","CovG(Ma:d,Ia:d)","CovG(Id:d,Md:d)","CovG(Md:d,Id:d)",cohortcov,"CovGs(Ia,Ma)","CovGs(Ma,Ia)")
  mat <- c(matvar,matcov)

  all <- c(allvar,allcov)

  allzpre <- c("zi","zm","zi","zm","zi","zm","zi","zm","zi","zm","zi","zm","zi","zm","zy","zp","zc","S","S","zi","zm","zi","zm","zi","zm","zi","zm","zi","zm","zi","zm","zi","zm","S","S")

  allzpost <- c("zi","zm","zi","zm","zi","zm","zi","zm","zi","zm","zi","zm","zi","zm","zy","zp","zc","S","S","zm","zi","zm","zi","zm","zi","zm","zi","zm","zi","zm","zi","zm","zi","S","S")

  allrel <- c("e","e","a","a","s","s","d","d","aa","aa","ad","ad","dd","dd","I","I","I","S","S","e","e","a","a","s","s","d","d","aa","aa","ad","ad","dd","dd","S","S")

  allindenv <- c("VarE(I)","CovE(I,M)","CovE(M,I)","CovE(I,M&!C)","CovE(M&!C,I)")

  cohortzpre1 <- c("zc","zm","zm","zi","zm")
  cohortzpost1 <- c("zc","zm","zm","zm","zi")
  cohortzpre2 <- c(NA,"zc","zc","zc","zc")
  cohortzpost2 <- c(NA,"zc","zc","zc","zc")
  cohortop <- c(NA,"&","&!","&!","&!")

  ctable <- list(cohortvar=cohortvar, cohortcov=cohortcov, cohort=cohort, evar = evar, ecov=ecov, e=e, addgvar=addgvar, domgvar=domgvar, epiaddgvar=epiaddgvar, epidomgvar=epidomgvar, matcgvar=matcgvar, patygvar=patygvar, sexlinaddgvar=sexlinaddgvar, gvar=gvar, allvar=allvar, addgcov=addgcov, domgcov=domgcov, epiaddgcov=epiaddgcov, epidomgcov=epidomgcov, sexlinaddgcov=sexlinaddgcov, gcov=gcov, g=g,  allcov=allcov, addg=addg, domg=domg, epiaddg=epiaddg, epidomg=epidomg, matcg=matcg, patyg=patyg, sexlinaddg=sexlinaddg, indvar=indvar, indcov=indcov, ind=ind,  matvar=matvar, matcov=matcov, mat=mat,  all=all, allzpre=allzpre, allzpost=allzpost, allrel=allrel, allindenv=allindenv, cohortzpre1=cohortzpre1, cohortzpost1=cohortzpost1, cohortzpre2=cohortzpre2, cohortzpost2=cohortzpost2, cohortop=cohortop)
  return(ctable)
}