R/jomo.glmer.MCMCchain.R

Defines functions jomo.glmer.MCMCchain

Documented in jomo.glmer.MCMCchain

jomo.glmer.MCMCchain <-
  function(formula, data, level=rep(1,ncol(data)), beta.start=NULL, l2.beta.start=NULL, u.start=NULL, l1cov.start=NULL, l2cov.start=NULL, l1cov.prior=NULL, l2cov.prior=NULL, a.start=NULL, a.prior=NULL, betaY.start=NULL, varY.start=NULL, covuY.start=NULL, uY.start=NULL, nburn=1000, meth="common", start.imp=NULL, start.imp.sub=NULL, l2.start.imp=NULL, output=1, out.iter=10, family="binomial") {
    cat("This function is beta software. Please use carefully and report any bug to the package mantainer\n")
    if (family!="gaussian"&family!="binomial") cat("ERROR: choose either family binomial or gaussian\n")
    if (family=="gaussian") {
      jomo.lmer.MCMCchain(formula, data, level=level, beta.start=beta.start, l2.beta.start=l2.beta.start, u.start=u.start, l1cov.start=l1cov.start, l2cov.start=l2cov.start, l1cov.prior=l1cov.prior, l2cov.prior=l2cov.prior, a.start=a.start, a.prior=a.prior, betaY.start=betaY.start, varY.start=varY.start, covuY.start=covuY.start, uY.start=uY.start, nburn=nburn, meth=meth, start.imp=start.imp, start.imp.sub=start.imp.sub, l2.start.imp=l2.start.imp, output=output, out.iter=out.iter)
    }
    if (family=="binomial") {
      stopifnot(is.data.frame(data))
      stopifnot(any(grepl("~",deparse(formula))))
      fit.cr<-glmer(formula,data=data, family=binomial, na.action = na.omit)
      if (is.null(betaY.start)) betaY.start<-fixef(fit.cr)
      if (is.null(varY.start)) varY.start<-1
      varY.prior<-1
      colnamysub<-all.vars(formula[[2]])
      Ysub<-get(colnamysub,pos=data)
      Ycov<-data.frame(mget(all.vars(formula[[3]]), envir =as.environment(data)))
      level<-data.frame(matrix(level,1,ncol(data)))
      colnames(level)<-colnames(data)
      terms.sub<-attr(terms(formula), "term.labels")
      split.terms<-strsplit(terms.sub,":")
      length.sub<-length(terms.sub)
      order.sub<-attr(terms(formula), "order")
      submod<-matrix(1,4,sum(order.sub)-1)
      Y.con<-NULL
      Y.cat<-NULL
      Y.numcat<-NULL
      Y2.con<-NULL
      Y2.cat<-NULL
      Y2.numcat<-NULL
      Y2i<-NULL
      Y2imp2<-NULL
      for (j in 1:ncol(Ycov)) {
        if (level[1, which(colnames(level)==colnames(Ycov)[j])]==1) {
          if (is.numeric(Ycov[,j])) {
            if (is.null(Y.con)) Y.con<-data.frame(Ycov[,j,drop=FALSE])
            else Y.con<-data.frame(Y.con,Ycov[,j,drop=FALSE])
          }
          if (is.factor(Ycov[,j])) {
            if (is.null(Y.cat)) Y.cat<-data.frame(Ycov[,j,drop=FALSE])
            else Y.cat<-data.frame(Y.cat,Ycov[,j,drop=FALSE])
            Y.numcat<-cbind(Y.numcat,nlevels(Ycov[,j]))
          }
        } else {
          if (is.numeric(Ycov[,j])) {
            if (is.null(Y2.con)) Y2.con<-data.frame(Ycov[,j,drop=FALSE])
            else Y2.con<-data.frame(Y2.con,Ycov[,j,drop=FALSE])
          }
          if (is.factor(Ycov[,j])) {
            if (is.null(Y2.cat)) Y2.cat<-data.frame(Ycov[,j,drop=FALSE])
            else Y2.cat<-data.frame(Y2.cat,Ycov[,j,drop=FALSE])
            Y2.numcat<-cbind(Y2.numcat,nlevels(Ycov[,j]))
          }
        }
        
        
      }
      h<-1
      for ( j in 1:length.sub) {
        for ( k in 1:order.sub[j]) {
          current.term<-split.terms[[j]][k]
          if (grepl("\\|", deparse(current.term))) {
            j.tbd<-j
            clus.name<-sub(".*\\|","",current.term)
            clus.name<-gsub(" ","",clus.name)
            current.term<-sub("\\|.*$","",current.term)
            random.terms<-strsplit(current.term,"+", fixed=T)
            length.ran<-length(random.terms[[1]])
            submod.ran<-matrix(1,3,length.ran)
            for (t in 1:length.ran) {
              ct<-gsub(" ","",random.terms[[1]][t])
              if (ct==1) {
                submod.ran[1:2,t]<-0
              } else if (length(which(colnames(Y.cat)==ct))!=0) {
                submod.ran[1,t]<-which(colnames(Y.cat)==ct)
                submod.ran[2,t]<-2
                submod.ran[3,t]<-Y.numcat[submod.ran[1,t]]-1
              } else if (length(which(colnames(Y.con)==ct))!=0) {
                submod.ran[1,t]<-which(colnames(Y.con)==ct)
                submod.ran[2,t]<-1
              }
            }
          } else {
            current.term<-sub(".*I\\(","",current.term)
            current.term<-sub("\\)","",current.term)
            if (grepl("\\^",current.term)) {
              submod[3,h]<-as.integer(sub(".*\\^","",current.term))
              current.term<-sub("\\^.*","",current.term)
            } else {
              submod[3,h]<-1
            }
            if (length(which(colnames(Y.cat)==current.term))!=0) {
              submod[1,h]<-which(colnames(Y.cat)==current.term)
              submod[2,h]<-2
              submod[4,h]<-Y.numcat[submod[1,h]]-1
            } else if (length(which(colnames(Y.con)==current.term))!=0) {
              submod[1,h]<-which(colnames(Y.con)==current.term)
              submod[2,h]<-1
            } else if (length(which(colnames(Y2.cat)==current.term))!=0) {
              submod[1,h]<-which(colnames(Y2.cat)==current.term)
              submod[2,h]<-4
              submod[4,h]<-Y2.numcat[submod[1,h]]-1
            } else if (length(which(colnames(Y2.con)==current.term))!=0) {
              submod[1,h]<-which(colnames(Y2.con)==current.term)
              submod[2,h]<-3
            }
            h<-h+1  
          }
          
        }
      }
      order.sub<-order.sub[-j.tbd]
      if (!is.null(Y.con)&sum((colnames(Y.con)==clus.name)==1)) Y.con<-data.frame(Y.con[,-which(colnames(Y.con)==clus.name), drop=FALSE])
      if (!is.null(Y.cat)&sum((colnames(Y.cat)==clus.name)==1)) Y.cat<-data.frame(Y.cat[,-which(colnames(Y.cat)==clus.name), drop=FALSE])
      Y.auxiliary<-data.frame(data[,-c(which(colnames(data)%in%colnames(Y.con)),which(colnames(data)%in%colnames(Y.cat)),which(colnames(data)%in%colnames(Y2.con)),which(colnames(data)%in%colnames(Y2.cat)),which(colnames(data)==clus.name),which(colnames(data)==colnamysub)), drop=FALSE])
      Y.aux.con<-NULL
      Y.aux.cat<-NULL
      Y.aux.numcat<-NULL
      Y2.aux.con<-NULL
      Y2.aux.cat<-NULL
      Y2.aux.numcat<-NULL
      if (ncol(Y.auxiliary)>0) {
        for (j in 1:ncol(Y.auxiliary)) {
          if (level[1, which(colnames(level)==colnames(Y.auxiliary)[j])]==1) {
            if (is.numeric(Y.auxiliary[,j])) {
              if (is.null(Y.aux.con)) Y.aux.con<-data.frame(Y.auxiliary[,j,drop=FALSE])
              else Y.aux.con<-data.frame(Y.aux.con,Y.auxiliary[,j,drop=FALSE])
            }
            if (is.factor(Y.auxiliary[,j])) {
              if (is.null(Y.aux.cat)) Y.aux.cat<-data.frame(Y.auxiliary[,j,drop=FALSE])
              else Y.aux.cat<-data.frame(Y.aux.cat,Y.auxiliary[,j,drop=FALSE])
              Y.aux.numcat<-cbind(Y.aux.numcat,nlevels(Y.auxiliary[,j]))
            }
          } else {
            if (is.numeric(Y.auxiliary[,j])) {
              if (is.null(Y2.aux.con)) Y2.aux.con<-data.frame(Y.auxiliary[,j,drop=FALSE])
              else Y2.aux.con<-data.frame(Y2.aux.con,Y.auxiliary[,j,drop=FALSE])
            }
            if (is.factor(Y.auxiliary[,j])) {
              if (is.null(Y2.aux.cat)) Y2.aux.cat<-data.frame(Y.auxiliary[,j,drop=FALSE])
              else Y2.aux.cat<-data.frame(Y2.aux.cat,Y.auxiliary[,j,drop=FALSE])
              Y2.aux.numcat<-cbind(Y2.aux.numcat,nlevels(Y.auxiliary[,j]))
            }
          }
          
          
        }
      }
      X=matrix(1,max(nrow(Y.cat),nrow(Y.con)),1)
      if (!is.null(Y2.con)|!is.null(Y2.cat)|!is.null(Y2.aux.con)|!is.null(Y2.aux.cat)) {
        #cat("Level 2 variables must be fully observed for valid inference. \n")
        X2=matrix(1,max(nrow(Y2.cat),nrow(Y2.con),nrow(Y2.aux.cat),nrow(Y2.aux.con)),1)
        if (is.null(l2.beta.start)) l2.beta.start=matrix(0,ncol(X2),(max(as.numeric(!is.null(Y2.con)),ncol(Y2.con))+max(0,(sum(Y2.numcat)-length(Y2.numcat)))+max(as.numeric(!is.null(Y2.aux.con)),ncol(Y2.aux.con))+max(0,(sum(Y2.aux.numcat)-length(Y2.aux.numcat)))))
      }
      Z=matrix(1,nrow(X),1)
      if (is.null(beta.start)) beta.start=matrix(0,ncol(X),(max(as.numeric(!is.null(Y.con)),ncol(Y.con))+max(0,(sum(Y.numcat)-length(Y.numcat)))+max(as.numeric(!is.null(Y.aux.con)),ncol(Y.aux.con))+max(0,(sum(Y.aux.numcat)-length(Y.aux.numcat)))))
      
      clus<-factor(data[,clus.name])
      previous_levels_clus<-levels(clus)
      levels(clus)<-0:(nlevels(clus)-1)
      if (is.null(uY.start)) uY.start<-matrix(0,nlevels(clus),ncol(VarCorr(fit.cr)[[1]]))
      if (is.null(l1cov.start)) {
        if (meth=="common") {
          l1cov.start=diag(1,ncol(beta.start))
        } else {
          l1cov.start=matrix(diag(1,ncol(beta.start)),nlevels(clus)*ncol(beta.start),ncol(beta.start),2)
        }
      }
      if (is.null(l1cov.prior)) l1cov.prior=diag(1,ncol(l1cov.start))
      diagVar<-as.data.frame(VarCorr(fit.cr))[1:ncol(VarCorr(fit.cr)[[1]]),4]
      if (is.null(covuY.start)) covuY.start<-VarCorr(fit.cr)[[1]][1:ncol(VarCorr(fit.cr)[[1]]),1:ncol(VarCorr(fit.cr)[[1]])]
      covuY.prior<-VarCorr(fit.cr)[[1]][1:ncol(VarCorr(fit.cr)[[1]]),1:ncol(VarCorr(fit.cr)[[1]])]
      if (kappa(covuY.start)>10^8) {
        covuY.prior<-diag(1, ncol(VarCorr(fit.cr)[[1]]))
        covuY.start<-diag(1, ncol(VarCorr(fit.cr)[[1]]))
      }
      ncolYcon<-rep(NA,4)
      ncolY2con<-rep(NA,4)
      ncolYcon[1]=max(as.numeric(!is.null(Y.con)),ncol(Y.con))+max(as.numeric(!is.null(Y.aux.con)),ncol(Y.aux.con))
      ncolY2con[1]=max(as.numeric(!is.null(Y2.con)),ncol(Y2.con))+max(as.numeric(!is.null(Y2.aux.con)),ncol(Y2.aux.con))
      ncolYcon[2]=max(as.numeric(!is.null(Y.con)),ncol(Y.con))
      ncolY2con[2]=max(as.numeric(!is.null(Y2.con)),ncol(Y2.con))
      ncolYcon[3]=ncolYcon[1]+max(0,(sum(Y.numcat)-length(Y.numcat)))
      ncolY2con[3]=ncolY2con[1]+max(0,(sum(Y2.numcat)-length(Y2.numcat)))
      ncolYcon[4]=max(0,ncol(Y.cat))
      ncolY2con[4]=max(0,ncol(Y2.cat))
      stopifnot(((!is.null(Y.con))||(!is.null(Y.cat)&!is.null(Y.numcat)))||((!is.null(Y2.con))||(!is.null(Y2.cat)&!is.null(Y2.numcat))))
      if (is.null(u.start)) u.start = matrix(0, nlevels(clus), ncol(Z)*(ncolYcon[1]+max(0,(sum(Y.numcat)-length(Y.numcat)))+max(0,(sum(Y.aux.numcat)-length(Y.aux.numcat))))+(ncolY2con[1]+max(0,(sum(Y2.numcat)-length(Y2.numcat)))+max(0,(sum(Y2.aux.numcat)-length(Y2.aux.numcat)))))
      Ysub<-as.factor(Ysub)
      previous_levelssub<-levels(Ysub)
      levels(Ysub)<-1:2
      if (is.null(l2cov.start)) l2cov.start = diag(1, ncol(u.start))
      if (is.null(l2cov.prior)) l2cov.prior = diag(1, ncol(l2cov.start))
      if (!is.null(Y.cat)) {
        isnullcat=0
        previous_levels<-list()
        Y.cat<-data.frame(Y.cat)
        for (i in 1:ncol(Y.cat)) {
          Y.cat[,i]<-factor(Y.cat[,i])
          previous_levels[[i]]<-levels(Y.cat[,i])
          levels(Y.cat[,i])<-1:nlevels(Y.cat[,i])
        }
      } else {
        isnullcat=1
      }
      if (!is.null(Y.aux.cat)) {
        isnullcataux=0
        previous_levelsaux<-list()
        Y.aux.cat<-data.frame(Y.aux.cat)
        for (i in 1:ncol(Y.aux.cat)) {
          Y.aux.cat[,i]<-factor(Y.aux.cat[,i])
          previous_levelsaux[[i]]<-levels(Y.aux.cat[,i])
          levels(Y.aux.cat[,i])<-1:nlevels(Y.aux.cat[,i])
        }
      } else {
        isnullcataux=1
      } 
      if (!is.null(Y2.cat)) {
        isnullcat2=0
        previous_levels2<-list()
        Y2.cat<-data.frame(Y2.cat)
        for (i in 1:ncol(Y2.cat)) {
          Y2.cat[,i]<-factor(Y2.cat[,i])
          previous_levels2[[i]]<-levels(Y2.cat[,i])
          levels(Y2.cat[,i])<-1:nlevels(Y2.cat[,i])
        }
      } else {
        isnullcat2=1
      }
      if (!is.null(Y2.aux.cat)) {
        isnullcat2aux=0
        previous_levels2aux<-list()
        Y2.aux.cat<-data.frame(Y2.aux.cat)
        for (i in 1:ncol(Y2.aux.cat)) {
          Y2.aux.cat[,i]<-factor(Y2.aux.cat[,i])
          previous_levels2aux[[i]]<-levels(Y2.aux.cat[,i])
          levels(Y2.aux.cat[,i])<-1:nlevels(Y2.aux.cat[,i])
        }
      } else {
        isnullcat2aux=1
      }
      if (!is.null(Y.con)) {
        stopifnot(nrow(Y.con)==nrow(clus),nrow(Y.con)==nrow(X), nrow(Z)==nrow(Y.con))
      }
      if (isnullcat==0) {
        stopifnot(nrow(Y.cat)==nrow(clus),nrow(Y.cat)==nrow(X), nrow(Z)==nrow(Y.cat))
      }
      if (!is.null(Y2.con)) {
        stopifnot(nrow(Y2.con)==nrow(clus),nrow(Y2.con)==nrow(X), nrow(Z)==nrow(Y2.con))
      }
      if (isnullcat2==0) {
        stopifnot(nrow(Y2.cat)==nrow(clus),nrow(Y2.cat)==nrow(X), nrow(Z)==nrow(Y2.cat))
      }
      stopifnot(nrow(beta.start)==ncol(X), ncol(beta.start)==(ncolYcon[1]+max(0,(sum(Y.numcat)-length(Y.numcat)))+max(0,(sum(Y.aux.numcat)-length(Y.aux.numcat)))))
      if (!is.null(Y2.con)||isnullcat2==0||!is.null(Y2.aux.con)||isnullcat2aux==0) stopifnot(nrow(l2.beta.start)==ncol(X2), ncol(l2.beta.start)==(ncolY2con[3]+max(0,(sum(Y2.aux.numcat)-length(Y2.aux.numcat)))))
      stopifnot(ncol(u.start)==ncol(Z)*(ncolYcon[1]+max(0,(sum(Y.numcat)-length(Y.numcat)))+max(0,(sum(Y.aux.numcat)-length(Y.aux.numcat))))+(ncolY2con[1]+max(0,(sum(Y2.numcat)-length(Y2.numcat)))+max(0,(sum(Y2.aux.numcat)-length(Y2.aux.numcat)))))
      if (meth=="common") stopifnot(nrow(l1cov.start)==ncol(l1cov.start),nrow(l1cov.prior)==nrow(l1cov.start),nrow(l1cov.start)==ncol(beta.start))
      stopifnot(nrow(l1cov.prior)==ncol(l1cov.prior))
      stopifnot(ncol(l2cov.start)==ncol(u.start), nrow(l2cov.prior)==nrow(l2cov.start), nrow(l2cov.prior)==ncol(l2cov.prior))
      betait=matrix(0,nrow(beta.start),ncol(beta.start))
      for (i in 1:nrow(beta.start)) {
        for (j in 1:ncol(beta.start)) betait[i,j]=beta.start[i,j]
      }
      if (!is.null(Y2.con)||isnullcat2==0||!is.null(Y2.aux.con)||isnullcat2aux==0) {
        beta2it=matrix(0,nrow(l2.beta.start),ncol(l2.beta.start))
        for (i in 1:nrow(l2.beta.start)) {
          for (j in 1:ncol(l2.beta.start)) beta2it[i,j]=l2.beta.start[i,j]
        }
      }
      covit=matrix(0,nrow(l1cov.start),ncol(l1cov.start))
      for (i in 1:nrow(l1cov.start)) {
        for (j in 1:ncol(l1cov.start)) covit[i,j]=l1cov.start[i,j]
      }   
      uit=matrix(0,nrow(u.start),ncol(u.start))
      for (i in 1:nrow(u.start)) {
        for (j in 1:ncol(u.start)) uit[i,j]=u.start[i,j]
      }
      covuit=matrix(0,nrow(l2cov.start),ncol(l2cov.start))
      for (i in 1:nrow(l2cov.start)) {
        for (j in 1:ncol(l2cov.start)) covuit[i,j]=l2cov.start[i,j]
      }   
      if (!is.null(Y.con)) {
        colnamycon<-colnames(Y.con)
        Y.con<-data.matrix(Y.con)
        storage.mode(Y.con) <- "numeric"  
      }
      if (isnullcat==0) {
        colnamycat<-colnames(Y.cat)
        Y.cat<-data.matrix(Y.cat)
        storage.mode(Y.cat) <- "numeric"  
      }
      if (!is.null(Y2.con)) {
        colnamy2con<-colnames(Y2.con)
        Y2.con<-data.matrix(Y2.con)
        storage.mode(Y2.con) <- "numeric"  
      }
      if (isnullcat2==0) {
        colnamy2cat<-colnames(Y2.cat)
        Y2.cat<-data.matrix(Y2.cat)
        storage.mode(Y2.cat) <- "numeric"  
      }
      if (!is.null(Y.aux.con)) {
        colnamyauxcon<-colnames(Y.aux.con)
        Y.aux.con<-data.matrix(Y.aux.con)
        storage.mode(Y.aux.con) <- "numeric"  
      }
      if (isnullcataux==0) {
        colnamyauxcat<-colnames(Y.aux.cat)
        Y.aux.cat<-data.matrix(Y.aux.cat)
        storage.mode(Y.aux.cat) <- "numeric"  
      }
      if (!is.null(Y2.aux.con)) {
        colnamy2auxcon<-colnames(Y2.aux.con)
        Y2.aux.con<-data.matrix(Y2.aux.con)
        storage.mode(Y2.aux.con) <- "numeric"  
      }
      if (isnullcat2aux==0) {
        colnamy2auxcat<-colnames(Y2.aux.cat)
        Y2.aux.cat<-data.matrix(Y2.aux.cat)
        storage.mode(Y2.aux.cat) <- "numeric"  
      }
      Y.cat.tot<-cbind(Y.cat,Y.aux.cat)
      colnamx<-colnames(X)
      colnamz<-colnames(Z)
      X<-data.matrix(X)
      storage.mode(X) <- "numeric"    
      Z<-data.matrix(Z)
      storage.mode(Z) <- "numeric" 
      if (!is.null(Y2.con)||isnullcat2==0||!is.null(Y2.aux.con)||isnullcat2aux==0) {
        colnamx2<-colnames(X2)
        X2<-data.matrix(X2)
        storage.mode(X2) <- "numeric"
      }
      clus <- matrix(as.integer(levels(clus))[clus], ncol=1)
      Y=cbind(Y.con,Y.aux.con,Y.cat, Y.aux.cat)
      Yi=cbind(Y.con, Y.aux.con, switch(is.null(Y.cat)+1, matrix(0,nrow(Y),(sum(Y.numcat)-length(Y.numcat))), NULL), switch(is.null(Y.aux.cat)+1, matrix(0,nrow(Y.aux.cat),(sum(Y.aux.numcat)-length(Y.aux.numcat))), NULL))
      Y2=cbind(Y2.con,Y2.aux.con,Y2.cat, Y2.aux.cat)
      Y2i=cbind(Y2.con, Y2.aux.con, switch(is.null(Y2.cat)+1, matrix(0,nrow(Y2),(sum(Y2.numcat)-length(Y2.numcat))), NULL), switch(is.null(Y2.aux.cat)+1, matrix(0,nrow(Y2.aux.cat),(sum(Y2.aux.numcat)-length(Y2.aux.numcat))), NULL))
      h=1
      if (isnullcat==0) {
        for (i in 1:length(Y.numcat)) {
          for (j in 1:nrow(Y)) {
            if (is.na(Y.cat[j,i])) {
              Yi[j,(ncolYcon[1]+h):(ncolYcon[1]+h+Y.numcat[i]-2)]=NA
            }
          } 
          h=h+Y.numcat[i]-1
        }
      }
      if (isnullcataux==0) {
        for (i in 1:length(Y.aux.numcat)) {
          for (j in 1:nrow(Y)) {
            if (is.na(Y.aux.cat[j,i])) {
              Yi[j,(ncolYcon[1]+h):(ncolYcon[1]+h+Y.aux.numcat[i]-2)]=NA
            }
          } 
          h=h+Y.aux.numcat[i]-1
        }
      }
      h=1
      if (isnullcat2==0) {
        for (i in 1:length(Y2.numcat)) {
          for (j in 1:nrow(Y2)) {
            if (is.na(Y2.cat[j,i])) {
              Y2i[j,(ncolY2con[1]+h):(ncolY2con[1]+h+Y2.numcat[i]-2)]=NA
            }
          } 
          h=h+Y2.numcat[i]-1
        }
      }
      if (isnullcat2aux==0) {
        for (i in 1:length(Y2.aux.numcat)) {
          for (j in 1:nrow(Y2)) {
            if (is.na(Y2.aux.cat[j,i])) {
              Y2i[j,(ncolY2con[1]+h):(ncolY2con[1]+h+Y2.aux.numcat[i]-2)]=NA
            }
          } 
          h=h+Y2.aux.numcat[i]-1
        }
      }
      if (isnullcat==0||isnullcataux==0) {
        Y.cat.tot<-cbind(Y.cat,Y.aux.cat)
        Y.numcat.tot<-c(Y.numcat, Y.aux.numcat)
      } else {
        Y.cat.tot=-999
        Y.numcat.tot=-999
      }
      if (isnullcat2==0||isnullcat2aux==0) {
        Y2.cat.tot<-cbind(Y2.cat,Y2.aux.cat)
        Y2.numcat.tot<-c(Y2.numcat, Y2.aux.numcat)
      } else {
        Y2.cat.tot=-999
        Y2.numcat.tot=-999
      }
      ncY2<-max(0,ncol(Y2))
      Ysubimp<-Ysub
      if (is.null(a.start)) a.start=50+ncol(Y)
      if (is.null(a.prior)) a.prior=a.start
      
      if (output!=1) out.iter=nburn+2
      nimp=1
      imp=matrix(0,nrow(Y)*(nimp+1),ncol(Y)+ncY2+4)
      imp[1:nrow(Y),1]=Ysub
      imp[1:nrow(Y),2:(1+ncol(Y))]=Y
      if (!is.null(Y2)) imp[1:nrow(Y2),(ncol(Y)+2):(ncol(Y)+ncY2+1)]=Y2
      imp[1:nrow(clus), (ncol(Y)+ncY2+2)]=clus
      imp[1:nrow(X), (ncol(Y)+ncY2+3)]=c(1:nrow(Y))
      Yimp=Yi
      Yimp2=matrix(Yimp, nrow(Yimp),ncol(Yimp))
      if (!is.null(Y2)) {
        Y2imp=Y2i
        Y2imp2=matrix(Y2imp, nrow(Y2imp),ncol(Y2imp))
      }
      imp[(nrow(clus)+1):(2*nrow(clus)), (ncol(Y)+ncY2+2)]=clus
      imp[(nrow(X)+1):(2*nrow(X)), (ncol(Y)+ncY2+3)]=c(1:nrow(Y))
      imp[(nrow(X)+1):(2*nrow(X)), (ncol(Y)+ncY2+4)]=1  
      betapost<- array(0, dim=c(nrow(beta.start),ncol(beta.start),(nburn)))
      betaYpost<- array(0, dim=c(1,length(betaY.start),(nburn)))
      if (!is.null(Y2)) {
        beta2post<- array(0, dim=c(nrow(l2.beta.start),ncol(l2.beta.start),(nburn)))
      }
      upostall<-array(0, dim=c(nrow(u.start),ncol(u.start),(nburn)))
      uYpostall<-array(0, dim=c(nrow(uY.start),ncol(uY.start),(nburn)))
      omegapost<- array(0, dim=c(nrow(l1cov.start),ncol(l1cov.start),(nburn)))
      varYpost<-rep(0,(nburn))
      covupost<- array(0, dim=c(nrow(l2cov.start),ncol(l2cov.start),(nburn)))
      covuYpost<-array(0, dim=c(nrow(as.matrix(covuY.start)),ncol(as.matrix(covuY.start)),(nburn)))
      meanobs<-colMeans(Yi,na.rm=TRUE)
      if (!is.null(Y2)) {
        meanobs2<-colMeans(Y2i,na.rm=TRUE)
      }
      if (!is.null(start.imp)) {
        start.imp<-as.matrix(start.imp)
        if ((nrow(start.imp)!=nrow(Yimp2))||(ncol(Yimp2)!=ncol(start.imp))) {
          cat("start.imp dimensions incorrect. Not using start.imp as starting value for the imputed dataset.\n")
          start.imp=NULL
        } else {
          Yimp2<-start.imp
        }
      }
      if (is.null(start.imp)) {
        for (i in 1:nrow(Yi)) for (j in 1:ncol(Yi)) if (is.na(Yimp[i,j])) Yimp2[i,j]=meanobs[j]
      }
      if (!is.null(l2.start.imp)) {
        l2.start.imp<-as.matrix(l2.start.imp)
        if ((nrow(l2.start.imp)!=nrow(Y2imp2))||(ncol(Y2imp2)!=ncol(l2.start.imp))) {
          cat("l2.start.imp dimensions incorrect. Not using l2.start.imp as starting value for the level 2 imputed dataset.\n")
          l2.start.imp=NULL
        } else {
          Y2imp2<-l2.start.imp
        }
      }
      if (!is.null(Y2i)&is.null(l2.start.imp)) {
        for (i in 1:nrow(Y2i)) for (j in 1:ncol(Y2i)) if (is.na(Y2imp[i,j])) Y2imp2[i,j]=meanobs2[j]
      }
      if (!is.null(start.imp.sub)) {
        start.imp<-as.matrix(start.imp)
        if (!is.vector(start.imp.sub)) {
          cat("start.imp.sub must be a vector. Not using start.imp as starting value for the imputed dataset.\n")
          start.imp.sub=NULL
        } else {
          Ysubimp=start.imp.sub
        }
      }
      if (is.null(start.imp.sub)) {
        for (i in 1:length(Ysubimp)) if (is.na(Ysubimp[i])) Ysubimp[i]=mean(Ysubimp, na.rm = TRUE)
      }
      Ysubcat <- c(Ysub)
      if (!is.null(Y2)) {
        if (meth=="common") {
          .Call("MCMCjomo2glmerbin", Ysub, Ysubimp, Ysubcat, submod, order.sub, submod.ran, Y, Yimp, Yimp2, Y.cat.tot, Y2, Y2imp, Y2imp2, Y2.cat.tot, X, X2, Z, clus,betaY.start,betaYpost, betait,beta2it,uit,uY.start,betapost, upostall, uYpostall, beta2post, varY.start, varYpost, covit,omegapost, covuY.start, covuYpost, covuit, covupost, nburn, varY.prior, covuY.prior, l1cov.prior,l2cov.prior,Y.numcat.tot, Y2.numcat.tot, ncolYcon,ncolY2con, out.iter, PACKAGE = "jomo")

          } else {
          .Call("MCMCjomo2glmerbinhr", Ysub, Ysubimp, Ysubcat, submod, order.sub, submod.ran, Y, Yimp, Yimp2, Y.cat.tot, Y2, Y2imp, Y2imp2, Y2.cat.tot, X, X2, Z, clus,betaY.start,betaYpost, betait,beta2it,uit,uY.start,betapost, upostall, uYpostall, beta2post, varY.start, varYpost, covit,omegapost, covuY.start, covuYpost, covuit, covupost, nburn, varY.prior, covuY.prior, l1cov.prior,l2cov.prior,Y.numcat.tot, Y2.numcat.tot, ncolYcon,ncolY2con,a.start, a.prior, out.iter, PACKAGE = "jomo")
        }
      } else {
        if (meth=="common") {
          .Call("MCMCjomo1glmerbin", Ysub, Ysubimp, Ysubcat, submod, order.sub, submod.ran, Y, Yimp, Yimp2, Y.cat.tot, X, Z, clus,betaY.start,betaYpost, betait,uit,uY.start,betapost, upostall, uYpostall, varY.start, varYpost, covit,omegapost, covuY.start, covuYpost, covuit, covupost, nburn, varY.prior, covuY.prior, l1cov.prior,l2cov.prior,Y.numcat.tot, ncolYcon,out.iter, PACKAGE = "jomo")

        } else {
          .Call("MCMCjomo1glmerbinhr", Ysub, Ysubimp, Ysubcat, submod, order.sub, submod.ran, Y, Yimp, Yimp2, Y.cat.tot, X, Z, clus,betaY.start,betaYpost, betait,uit,uY.start,betapost, upostall, uYpostall, varY.start, varYpost, covit,omegapost, covuY.start, covuYpost, covuit, covupost, nburn, varY.prior, covuY.prior, l1cov.prior,l2cov.prior,Y.numcat.tot, ncolYcon,a.start, a.prior, out.iter, PACKAGE = "jomo")
          }
      }
      imp[(nrow(Y)+1):(2*nrow(Y)),1]=Ysubcat
      if (!is.null(Y.con)|!is.null(Y.aux.con)) {
        imp[(nrow(Y)+1):(2*nrow(Y)),2:(1+max(0,ncol(Y.con))+max(0,ncol(Y.aux.con)))]=Yimp2[,1:(max(0,ncol(Y.con))+max(0,ncol(Y.aux.con)))]
      }
      if (isnullcat==0|isnullcataux==0) {
        imp[(nrow(Y)+1):(2*nrow(Y)),(ncolYcon[1]+2):(1+ncol(Y))]=Y.cat.tot
      }
      if (!is.null(Y2.con)|!is.null(Y2.aux.con)) {
        imp[(nrow(Y2)+1):(2*nrow(Y2)),(ncol(Y)+2):(1+ncol(Y)+max(0,ncol(Y2.con))+max(0,ncol(Y2.aux.con)))]=Y2imp2[,1:(max(0,ncol(Y2.con))+max(0,ncol(Y2.aux.con)))]
      }
      if (isnullcat2==0|isnullcat2aux==0) {
        imp[(nrow(Y2)+1):(2*nrow(Y2)),(ncolY2con[1]+ncol(Y)+2):(ncol(Y)+ncY2+1)]=Y2.cat.tot
      }
      if (output==1) cat("First imputation registered.", "\n")
      betaYpostmean<-apply(betaYpost, c(1,2), mean)
      varYpostmean<-mean(varYpost)
      covuYpostmean<-apply(covuYpost, c(1,2), mean)
      uYpostmean<-apply(uYpostall, c(1,2), mean)
      betapostmean<-apply(betapost, c(1,2), mean)
      if (!is.null(Y2)) beta2postmean<-apply(beta2post, c(1,2), mean)
      upostmean<-apply(upostall, c(1,2), mean)
      omegapostmean<-apply(omegapost, c(1,2), mean)
      covupostmean<-apply(covupost, c(1,2), mean)
      if (output==1) {
        cat("The posterior mean of the substantive model fixed effects estimates is:\n")
        print(betaYpostmean)
        cat("The posterior mean of the substantive model residual variance is:\n")
        print(varYpostmean)
        cat("The posterior mean of the substantive model random effects covariance matrix is:\n")
        print(covuYpostmean)
        cat("The posterior mean of the substantive model random effects estimates is:\n")
        print(uYpostmean)
        cat("The posterior mean of the fixed effects estimates is:\n")
        print(betapostmean)
        if (!is.null(Y2)) {
          cat("The posterior mean of the level 2 fixed effects estimates is:\n")
          print(beta2postmean)
        }
        cat("The posterior mean of the random effects estimates is:\n")
        print(upostmean)
        cat("The posterior mean of the level 1 covariance matrix is:\n")
        print(omegapostmean)
        cat("The posterior mean of the level 2 covariance matrix is:\n")
        print(covupostmean)
      }
      imp<-data.frame(imp)
      imp[,1]<-as.factor(imp[,1])
      levels(imp[,1])<-previous_levelssub
      if (isnullcat==0) {
        for (i in 1:ncol(Y.cat)) {
          imp[,(1+ncolYcon[1]+i)]<-as.factor(imp[,(1+ncolYcon[1]+i)]) 
          levels(imp[,(1+ncolYcon[1]+i)])<-previous_levels[[i]]
        }
      }
      if (isnullcataux==0) {
        for (i in 1:ncol(Y.aux.cat)) {
          imp[,(1+ncolYcon[1]+ncolYcon[4]+i)]<-as.factor(imp[,(1+ncolYcon[1]+ncolYcon[4]+i)]) 
          levels(imp[,(1+ncolYcon[1]+ncolYcon[4]+i)])<-previous_levelsaux[[i]]
        }
      }
      if (isnullcat2==0) {
        for (i in 1:ncol(Y2.cat)) {
          imp[,(1+ncol(Y)+ncolY2con[1]+i)]<-as.factor(imp[,(1+ncol(Y)+ncolY2con[1]+i)]) 
          levels(imp[,(1+ncol(Y)+ncolY2con[1]+i)])<-previous_levels2[[i]]
        }
      }
      if (isnullcat2aux==0) {
        for (i in 1:ncol(Y2.aux.cat)) {
          imp[,(1+ncol(Y)+ncolY2con[1]+ncolY2con[4]+i)]<-as.factor(imp[,(1+ncol(Y)+ncolY2con[1]+ncolY2con[4]+i)]) 
          levels(imp[,(1+ncol(Y)+ncolY2con[1]+ncolY2con[4]+i)])<-previous_levels2aux[[i]]
        }
      }
      imp[,(ncol(Y)+ncY2+2)]<-factor(imp[,(ncol(Y)+ncY2+2)])
      levels(imp[,(ncol(Y)+ncY2+2)])<-previous_levels_clus
      clus<-factor(clus)
      levels(clus)<-previous_levels_clus
      if (ncolYcon[1]>0) {
        for (j in 1:(ncolYcon[1])) {
          imp[,j+1]=as.numeric(imp[,j+1])
        }
      }
      if (ncolY2con[1]>0) {
        for (j in 1:(ncolY2con[1])) {
          imp[,ncol(Y)+j+1]=as.numeric(imp[,ncol(Y)+j+1])
        }
      }
      if (isnullcat==0) {
        if (is.null(colnamycat)) colnamycat=paste("Ycat", 1:ncol(Y.cat), sep = "")
      } else {
        colnamycat=NULL
        Y.cat=NULL
        Y.numcat=NULL
      }
      if (isnullcataux==0) {
        if (is.null(colnamyauxcat)) colnamyauxcat=paste("Ycat.aux", 1:ncol(Y.aux.cat), sep = "")
      } else {
        colnamyauxcat=NULL
        Y.aux.cat=NULL
        Y.aux.numcat=NULL
      }
      if (!is.null(Y.con)) {
        if (is.null(colnamycon)) colnamycon=paste("Ycon", 1:ncol(Y.con), sep = "")
      } else {
        colnamycon=NULL
      }
      if (!is.null(Y.aux.con)) {
        if (is.null(colnamyauxcon)) colnamyauxcon=paste("Ycon.aux", 1:ncol(Y.aux.con), sep = "")
      } else {
        colnamyauxcon=NULL
      }
      if (isnullcataux==0) {
        if (is.null(colnamyauxcat)) colnamyauxcat=paste("Ycat.aux", 1:ncol(Y.aux.cat), sep = "")
      } else {
        colnamyauxcat=NULL
        Y.aux.cat=NULL
        Y.aux.numcat=NULL
      }
      if (isnullcat2==0) {
        if (is.null(colnamy2cat)) colnamy2cat=paste("Y2cat", 1:ncol(Y2.cat), sep = "")
      } else {
        colnamy2cat=NULL
        Y2.cat=NULL
        Y2.numcat=NULL
      }
      if (isnullcat2aux==0) {
        if (is.null(colnamy2auxcat)) colnamy2auxcat=paste("Y2cat.aux", 1:ncol(Y2.aux.cat), sep = "")
      } else {
        colnamy2auxcat=NULL
        Y2.aux.cat=NULL
        Y2.aux.numcat=NULL
      }
      if (!is.null(Y2.con)) {
        if (is.null(colnamy2con)) colnamy2con=paste("Y2con", 1:ncol(Y2.con), sep = "")
      } else {
        colnamy2con=NULL
      }
      if (!is.null(Y2.aux.con)) {
        if (is.null(colnamy2auxcon)) colnamy2auxcon=paste("Y2con.aux", 1:ncol(Y2.aux.con), sep = "")
      } else {
        colnamy2auxcon=NULL
      }
      if (is.null(colnamysub)) colnamysub="Ysub"
      colnames(imp)<-c(colnamysub,colnamycon,colnamyauxcon,colnamycat,colnamyauxcat,colnamy2con,colnamy2auxcon,colnamy2cat,colnamy2auxcat,"clus","id","Imputation")
      if (isnullcat==0) {
        cnycatcomp<-rep(NA,(sum(Y.numcat)-length(Y.numcat)))
        count=0
        for ( j in 1:ncol(Y.cat)) {
          for (k in 1:(Y.numcat[j]-1)) {
            cnycatcomp[count+k]<-paste(colnamycat[j],k,sep=".")
          }
          count=count+Y.numcat[j]-1
        }
        
      } else {
        cnycatcomp<-NULL
      }
      if (isnullcataux==0) {
        cnyauxcatcomp<-rep(NA,(sum(Y.aux.numcat)-length(Y.aux.numcat)))
        count=0
        for ( j in 1:ncol(Y.aux.cat)) {
          for (k in 1:(Y.aux.numcat[j]-1)) {
            cnyauxcatcomp[count+k]<-paste(colnamyauxcat[j],k,sep=".")
          }
          count=count+Y.aux.numcat[j]-1
        }
        
      } else {
        cnyauxcatcomp<-NULL
      }
      cnamycomp<-c(colnamycon,colnamyauxcon,cnycatcomp,cnyauxcatcomp)
      if (isnullcat2==0) {
        cny2catcomp<-rep(NA,(sum(Y2.numcat)-length(Y2.numcat)))
        count=0
        for ( j in 1:ncol(Y2.cat)) {
          for (k in 1:(Y2.numcat[j]-1)) {
            cny2catcomp[count+k]<-paste(colnamy2cat[j],k,sep=".")
          }
          count=count+Y2.numcat[j]-1
        }
        
      } else {
        cny2catcomp<-NULL
      }
      if (isnullcat2aux==0) {
        cny2auxcatcomp<-rep(NA,(sum(Y2.aux.numcat)-length(Y2.aux.numcat)))
        count=0
        for ( j in 1:ncol(Y2.aux.cat)) {
          for (k in 1:(Y2.aux.numcat[j]-1)) {
            cny2auxcatcomp[count+k]<-paste(colnamy2auxcat[j],k,sep=".")
          }
          count=count+Y2.aux.numcat[j]-1
        }
        
      } else {
        cny2auxcatcomp<-NULL
      }
      cnamy2comp<-c(colnamy2con,colnamy2auxcon,cny2catcomp,cny2auxcatcomp)
      dimnames(betapost)[1] <- list(colnamx)
      dimnames(betapost)[2] <- list(cnamycomp)
      if (!is.null(Y2)) {
        dimnames(beta2post)[1] <- list(colnamx2)
        dimnames(beta2post)[2] <- list(cnamy2comp)
      }
      if (meth=="random") {
        dimnames(omegapost)[1] <- list(paste(rep(cnamycomp, nrow(u.start)),rep(previous_levels_clus,each=ncol(omegapost)))) 
      } else  {
        dimnames(omegapost)[1] <- list(cnamycomp)
      } 
      dimnames(omegapost)[2] <- list(cnamycomp)
      dimnames(Yimp2)[2] <- list(cnamycomp)
      return(list("finimp"=imp,"collectbeta"=betapost,"collectu"=upostall,"collectomega"=omegapost, "collectcovu"=covupost, "finimp.latnorm" = Yimp2, "l2.finimp.latnorm" = Y2imp2, "collectbetaY"=betaYpost, "collectvarY"=varYpost, "collectcovuY"=covuYpost, "collectuY"=uYpostall))    }
  }

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jomo documentation built on Aug. 7, 2018, 9:02 a.m.