R/jomo.coxph.R

In jomo: Multilevel Joint Modelling Multiple Imputation

jomo.coxph <-
  function(formula, data, beta.start=NULL, l1cov.start=NULL, l1cov.prior=NULL, nburn=1000, nbetween=1000, nimp=5, output=1, out.iter=10) {
    cat("This function is beta software. Use carefully and please report any bug to the package mantainer\n")
    if (nimp<2) {
      nimp=2
      cat("Minimum number of imputations:2. For single imputation using function jomo.coxph.MCMCchain\n")
    }
    stopifnot(is.data.frame(data))
    if (is_tibble(data)) {
      data<-data.frame(data)
      warning("tibbles not supported. data converted to standard data.frame. ")
    }
    
    if (isTRUE(any(sapply(df, is.character)))) stop("Character variables not allowed in data\n")
    stopifnot(any(grepl("~",deparse(formula))))
    fit.cr<-coxph(formula,data=data, na.action = na.omit)
    betaY.start<-as.numeric(coef(fit.cr))
    colnamysub<-all.vars(formula[[2]])
    data <- data[order(data[, colnamysub[1]]), ]
    Ysub <- as.matrix(data[, colnamysub])    
    Ycov<-data.frame(mget(all.vars(formula[[3]]), envir =as.environment(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))
    Y.con<-NULL
    Y.cat<-NULL
    Y.numcat<-NULL
    for (j in 1:ncol(Ycov)) {
      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]))
      }
    }
    h<-1
    for ( j in 1:length.sub) {
      for ( k in 1:order.sub[j]) {
        current.term<-split.terms[[j]][k]
        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
        } 
        h<-h+1  
      }
    }
    Y.auxiliary<-data.frame(data[,-c(which(colnames(data)%in%colnames(Y.con)),which(colnames(data)%in%colnames(Y.cat)),which(colnames(data)%in%colnamysub)), drop=FALSE])
    Y.aux.con<-NULL
    Y.aux.cat<-NULL
    Y.aux.numcat<-NULL
    if (ncol(Y.auxiliary)>0) {
      for (j in 1:ncol(Y.auxiliary)) {
        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]))
        }
      }
    }
    X=matrix(1,max(nrow(Y.cat),nrow(Y.con)),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)))))
    
    if (is.null(l1cov.start)) {
      l1cov.start=diag(1,ncol(beta.start))
    }
    if (is.null(l1cov.prior)) l1cov.prior=diag(1,ncol(l1cov.start))
    ncolYcon<-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))
    ncolYcon[2]=max(as.numeric(!is.null(Y.con)),ncol(Y.con))
    ncolYcon[3]=ncolYcon[1]+max(0,(sum(Y.numcat)-length(Y.numcat)))
    ncolYcon[4]=max(0,ncol(Y.cat))
    stopifnot(((!is.null(Y.con))||(!is.null(Y.cat)&!is.null(Y.numcat))))
    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
    } 
    
    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)))))
    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))
    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]
    }
    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]
    }   
    if (!is.null(Y.con)) {
      colnamycon<-colnames(Y.con)
      Y.con<-data.matrix(Y.con)
      storage.mode(Y.con) <- "numeric"  
    } else {
      colnamycon<-NULL
    }
    if (isnullcat == 0) {
      colnamycat <- colnames(Y.cat)
      Y.cat <- data.matrix(Y.cat)
      storage.mode(Y.cat) <- "numeric"
      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 (!is.null(Y.aux.con)) {
      colnamyauxcon<-colnames(Y.aux.con)
      Y.aux.con<-data.matrix(Y.aux.con)
      storage.mode(Y.aux.con) <- "numeric"  
    }  else {
      colnamyauxcon<-NULL
    }
    if (isnullcataux == 0) {
      colnamyauxcat <- colnames(Y.aux.cat)
      Y.aux.cat <- data.matrix(Y.aux.cat)
      storage.mode(Y.aux.cat) <- "numeric"
      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
    }
    colnamx<-colnames(X)
    X<-data.matrix(X)
    storage.mode(X) <- "numeric"    
    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))
    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
      }
    }
    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 (output == 0) out.iter=nburn+nbetween
    imp=matrix(0,nrow(Y)*(nimp+1),ncol(Y)+4)
    imp[1:nrow(Y),1:2]=Ysub
    imp[1:nrow(Y),3:(2+ncol(Y))]=Y
    imp[1:nrow(X), (ncol(Y)+3)]=c(1:nrow(Y))
    Yimp=Yi
    Yimp2=matrix(Yimp, nrow(Yimp),ncol(Yimp))
    imp[(nrow(X)+1):(2*nrow(X)), (ncol(Y)+3)]=c(1:nrow(Y))
    imp[(nrow(X)+1):(2*nrow(X)), (ncol(Y)+4)]=1  
    betapost<- array(0, dim=c(nrow(beta.start),ncol(beta.start),(nimp-1)))
    betaYpost<- array(0, dim=c(1,length(betaY.start),(nimp-1)))
    bpost<-matrix(0,nrow(beta.start),ncol(beta.start))
    bYpost<-matrix(0,1,length(betaY.start))
    omegapost<- array(0, dim=c(nrow(l1cov.start),ncol(l1cov.start),(nimp-1)))
    opost<-matrix(0,nrow(l1cov.start),ncol(l1cov.start))
    meanobs<-colMeans(Yi,na.rm=TRUE)
    for (i in 1:nrow(Yi)) for (j in 1:ncol(Yi)) if (is.na(Yimp[i,j])) Yimp2[i,j]=meanobs[j]

    .Call("jomo1smcC", Ysub, 0, 0, submod, order.sub, Y, Yimp, Yimp2, Y.cat.tot, X, betaY.start, bYpost, betait,bpost, 0, 0, covit,opost, nburn, 0, l1cov.prior,Y.numcat.tot,1, ncolYcon,out.iter, 0, 2, PACKAGE = "jomo")
    #betapost[,,1]=bpost
    #omegapost[,,(1)]=opost
    bpost<-matrix(0,nrow(beta.start),ncol(beta.start))
    bYpost<-matrix(0,1,length(betaY.start))
    opost<-matrix(0,nrow(l1cov.start),ncol(l1cov.start))
    imp[(nrow(Y)+1):(2*nrow(Y)),1:2]=as.matrix(Ysub)
    if (!is.null(Y.con)|!is.null(Y.aux.con)) {
      imp[(nrow(Y)+1):(2*nrow(Y)),3:(2+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]+3):(2+ncol(Y))]=Y.cat.tot
    }
    if (output>0) cat("First imputation registered.", "\n")
    for (i in 2:nimp) {
      #Yimp2=matrix(0, nrow(Yimp),ncol(Yimp))
      imp[(i*nrow(X)+1):((i+1)*nrow(X)), (ncol(Y)+3)]=c(1:nrow(Y))
      imp[(i*nrow(X)+1):((i+1)*nrow(X)), (ncol(Y)+4)]=i
      .Call("jomo1smcC", Ysub, 0, 0, submod, order.sub, Y, Yimp, Yimp2, Y.cat.tot, X, betaY.start, bYpost, betait,bpost, 0, 0, covit,opost, nbetween, 0, l1cov.prior,Y.numcat.tot, 1, ncolYcon,out.iter, 0, 2, PACKAGE = "jomo")
      betapost[,,(i-1)]=bpost
      betaYpost[,,(i-1)]=bYpost
      omegapost[,,(i-1)]=opost
      bpost<-matrix(0,nrow(beta.start),ncol(beta.start))
      bYpost<-matrix(0,1,length(betaY.start))
      opost<-matrix(0,nrow(l1cov.start),ncol(l1cov.start))
      imp[(i*nrow(X)+1):((i+1)*nrow(X)),1:2]=as.matrix(Ysub)
      if (!is.null(Y.con)|!is.null(Y.aux.con)) {
        imp[(i*nrow(X)+1):((i+1)*nrow(X)),3:(2+max(0,ncol(Y.con))+max(0,ncol(Y.aux.con)))]=Yimp2[,1:(max(0,ncol(Y.aux.con))+max(0,ncol(Y.con)))]
      }
      if (isnullcat==0|isnullcataux==0) {
        imp[(i*nrow(X)+1):((i+1)*nrow(X)),(ncolYcon[1]+3):(2+ncol(Y))]=Y.cat.tot
      }
      if (output>0) cat("Imputation number ", i, "registered", "\n")
    }
    
    cnamycomp<-c(colnamycon, colnamyauxcon, cnycatcomp, cnyauxcatcomp)
    dimnames(betapost)[1] <- list("(Intercept)")
    dimnames(betapost)[2] <- list(cnamycomp)
    dimnames(omegapost)[1] <- list(cnamycomp)
    dimnames(omegapost)[2] <- list(cnamycomp)
    betaYpostmean<-apply(betaYpost, c(1,2), mean)
    betapostmean<-apply(betapost, c(1,2), mean)
    omegapostmean<-apply(omegapost, c(1,2), mean)
    colnames(betaYpostmean)<-names(fit.cr$coefficients)
    if (output>0) {
      cat("The posterior mean of the substantive model fixed effects estimates is:\n")
      print(betaYpostmean)
      if (output==2) {
        cat("The posterior mean of the fixed effects estimates is:\n")
        print(betapostmean)
        cat("The posterior mean of the level 1 covariance matrix is:\n")
        print(omegapostmean)
      }
    }
    imp<-data.frame(imp)
    if (isnullcat==0) {
      for (i in 1:ncol(Y.cat)) {
        imp[,(2+ncolYcon[1]+i)]<-as.factor(imp[,(2+ncolYcon[1]+i)]) 
        levels(imp[,(2+ncolYcon[1]+i)])<-previous_levels[[i]]
      }
    }
    if (isnullcataux==0) {
      for (i in 1:ncol(Y.aux.cat)) {
        imp[,(2+ncolYcon[1]+ncolYcon[4]+i)]<-as.factor(imp[,(2+ncolYcon[1]+ncolYcon[4]+i)]) 
        levels(imp[,(2+ncolYcon[1]+ncolYcon[4]+i)])<-previous_levelsaux[[i]]
      }
    }
    if (ncolYcon[1]>0) {
      for (j in 1:(ncolYcon[1])) {
        imp[,j+2]=as.numeric(imp[,j+2])
      }
    }
     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 (is.null(colnamysub)) colnamysub=c("time","status")
    colnames(imp)<-c(colnamysub,colnamycon,colnamyauxcon,colnamycat,colnamyauxcat,"id","Imputation")
    return(imp)
  }