#' @export
#'
predictL.multlcmm <- function(x,newdata,var.time,na.action=1,confint=FALSE,...)
{
if(missing(newdata)) stop("The argument newdata should be specified")
if(missing(x)) stop("The argument x should be specified")
if (!inherits(x, "multlcmm")) stop("use only with \"multlcmm\" objects")
# ad 2/04/2012 Xnames2
if (!all(x$Xnames2 %in% colnames(newdata))) {
stop(paste(c("newdata should at least include the following covariates: ","\n",x$Xnames2),collapse=" "))}
if (!inherits(newdata, "data.frame")) stop("newdata should be a data.frame object")
# if(missing(var.time)) stop("missing argument 'var.time'")
# if(!(var.time %in% colnames(newdata))) stop("'var.time' should be included in newdata")
if(x$conv==1 | x$conv==2 | x$conv==3)
{
if(!(na.action%in%c(1,2)))stop("only 1 for 'na.omit' or 2 for 'na.fail' are required in na.action argument")
call_fixed <- x$call$fixed[3]
if(is.null(x$call$random)) {call_random <- -1} else call_random <- x$call$random[2]
if(is.null(x$call$classmb)) {call_classmb <- -1} else call_classmb <- x$call$classmb[2]
if(is.null(x$call$mixture)) {call_mixture <- -1} else call_mixture <- x$call$mixture[2]
if(!(na.action%in%c(1,2)))stop("only 1 for 'na.omit' or 2 for 'na.fail' are required in na.action argument")
if(na.action==1){
na.action=na.omit
}else{
na.action=na.fail
}
## transform to factor is the variable appears in levels$levelsdata
for(v in colnames(newdata))
{
if(v %in% names(x$levels$levelsdata))
{
if(!is.null(x$levels$levelsdata[[v]]))
{
newdata[,v] <- factor(newdata[,v], levels=x$levels$levelsdata[[v]])
}
}
}
call_fixed <- gsub("factor","",call_fixed)
call_fixed <- gsub("contrast","",call_fixed)
call_random <- gsub("factor","",call_random)
call_classmb <- gsub("factor","",call_classmb)
call_mixture <- gsub("factor","",call_mixture)
call_mixture <- formula(paste("~",call_mixture,sep=""))
call_random <- formula(paste("~",call_random,sep=""))
call_classmb <- formula(paste("~",call_classmb,sep=""))
## Traitement des donnees manquantes
mcall <- match.call()[c(1,match(c("data","subset","na.action"),names(match.call()),0))]
mcall$na.action <- na.action
mcall$data <- newdata
## fixed
m <- mcall
m$formula <- formula(paste("~",call_fixed,sep=""))
m[[1]] <- as.name("model.frame")
m <- eval(m, sys.parent())
na.fixed <- attr(m,"na.action")
## mixture
na.mixture <- NULL
if(call_mixture != -1)
{
m <- mcall
m$formula <- call_mixture
m[[1]] <- as.name("model.frame")
m <- eval(m, sys.parent())
na.mixture <- attr(m,"na.action")
}
## random
na.random <- NULL
if(call_random != -1)
{
m <- mcall
m$formula <- call_random
m[[1]] <- as.name("model.frame")
m <- eval(m, sys.parent())
na.random <- attr(m,"na.action")
}
## classmb
na.classmb <- NULL
if(call_classmb != -1)
{
m <- mcall
m$formula <- call_classmb
m[[1]] <- as.name("model.frame")
m <- eval(m, sys.parent())
na.classmb <- attr(m,"na.action")
}
## cor
na.cor <- NULL
if(x$N[7]>0)
{
z <- which(x$idcor0==1)
var.cor <- newdata[,x$Xnames[z]]
na.cor <- which(is.na(var.cor))
}
##var.time
if(!missing( var.time))
{
if(!(var.time %in% colnames(newdata))) stop("'var.time' should be included in newdata")
times <- newdata[,var.time,drop=FALSE]
}
else
{
times <- newdata[,1,drop=FALSE]
}
## Table sans donnees manquante: newdata
na.action <- unique(c(na.fixed,na.mixture,na.random,na.classmb,na.cor))
if(length(na.action)){
newdata1 <- newdata[-na.action,]
times <- times[-na.action,,drop=FALSE]
} else {
newdata1 <- newdata
}
## create one data frame for each formula (useful with factors)
newdata1fixed <- newdata1
for(v in colnames(newdata1fixed))
{
if(v %in% names(x$levels$levelsfixed))
{
if(!is.null(x$levels$levelsfixed[[v]]))
{
newdata1fixed[,v] <- factor(newdata1fixed[,v], levels=x$levels$levelsfixed[[v]])
if(any(is.na(newdata1fixed[,v]))) stop(paste("Wrong factor level in variable",v))
}
}
}
newdata1mixture <- newdata1
for(v in colnames(newdata1mixture))
{
if(v %in% names(x$levels$levelsmixture))
{
if(!is.null(x$levels$levelsmixture[[v]]))
{
newdata1mixture[,v] <- factor(newdata1mixture[,v], levels=x$levels$levelsmixture[[v]])
if(any(is.na(newdata1mixture[,v]))) stop(paste("Wrong factor level in variable",v))
}
}
}
newdata1random <- newdata1
for(v in colnames(newdata1random))
{
if(v %in% names(x$levels$levelsrandom))
{
if(!is.null(x$levels$levelsrandom[[v]]))
{
newdata1random[,v] <- factor(newdata1random[,v], levels=x$levels$levelsrandom[[v]])
if(any(is.na(newdata1random[,v]))) stop(paste("Wrong factor level in variable",v))
}
}
}
newdata1classmb <- newdata1
for(v in colnames(newdata1classmb))
{
if(v %in% names(x$levels$levelsclassmb))
{
if(!is.null(x$levels$levelsclassmb[[v]]))
{
newdata1classmb[,v] <- factor(newdata1classmb[,v], levels=x$levels$levelsclassmb[[v]])
if(any(is.na(newdata1classmb[,v]))) stop(paste("Wrong factor level in variable",v))
}
}
}
## Construction de nouvelles var eplicatives sur la nouvelle table
X_fixed <- X_mixture <- X_random <- X_classmb <- NULL
## fixed
X_fixed <- model.matrix(formula(paste("~",call_fixed,sep="")),data=newdata1fixed)
if(colnames(X_fixed)[1]=="(Intercept)"){
colnames(X_fixed)[1] <- "intercept"
}
## mixture
if(call_mixture != ~-1){
X_mixture <- model.matrix(call_mixture,data=newdata1mixture)
if(colnames(X_mixture)[1]=="(Intercept)"){
colnames(X_mixture)[1] <- "intercept"
}
}
## random
if(call_random != ~-1){
X_random <- model.matrix(call_random,data=newdata1random)
if(colnames(X_random)[1]=="(Intercept)"){
colnames(X_random)[1] <- "intercept"
}
}
## classmb
if(call_classmb != ~-1){
X_classmb <- model.matrix(call_classmb,data=newdata1classmb)
colnames(X_classmb)[1] <- "intercept"
}
##cor
if(x$N[7]>0) #on reprend la variable de temps de cor (sans NA)
{
z <- which(x$idcor0==1)
var.cor <- newdata1[,x$Xnames[z]]
}
## pour mettre les var dans le bon ordre
newdata1 <- X_fixed
colX <- colnames(X_fixed)
if(!is.null(X_mixture)){
for(i in 1:length(colnames(X_mixture))){
if((colnames(X_mixture)[i] %in% colnames(newdata1))==FALSE){
newdata1 <- cbind(newdata1,X_mixture[,i])
colnames(newdata1) <- c(colX,colnames(X_mixture)[i])
colX <- colnames(newdata1)
}
}
}
if(!is.null(X_random)){
for(i in 1:length(colnames(X_random))){
if((colnames(X_random)[i] %in% colnames(newdata1))==FALSE){
newdata1 <- cbind(newdata1,X_random[,i])
colnames(newdata1) <- c(colX,colnames(X_random)[i])
colX <- colnames(newdata1)
}
}
}
if(!is.null(X_classmb)){
for(i in 1:length(colnames(X_classmb))){
if((colnames(X_classmb)[i] %in% colnames(newdata1))==FALSE){
newdata1 <- cbind(newdata1,X_classmb[,i])
colnames(newdata1) <- c(colX,colnames(X_classmb)[i])
colX <- colnames(newdata1)
}
}
}
if(x$N[7]>0)
{
if( x$idg0[z]==0 & x$idea0[z]==0 & x$idprob0[z]==0)
{
newdata1 <- cbind(newdata1,var.cor)
colnames(newdata1) <- c(colX,x$Xnames[z])
colX <- colnames(newdata1)
}
}
###calcul des predictions
X1 <- NULL
X2 <- NULL
b1 <- NULL
b2 <- NULL
placeV <- list() #places pour les variances
placeV$commun <- NA
for(i in 1:x$ng)
{
placeV[paste("class",i,sep="")] <- NA
}
kk<-0
for(k in 1:length(x$idg0))
{
if(x$idg0[k]==1)
{
X1 <- cbind(X1,newdata1[,k])
if (k==1) b1 <- c(b1,0)
if (k>1)
{
place <- x$N[1]+kk
b1 <- c(b1,x$best[place+1])
placeV$commun <- c(placeV$commun,place+1)
kk <- kk+1
}
}
if(x$idg0[k]==2)
{
X2 <- cbind(X2,newdata1[,k])
if (k==1)
{
place1 <- x$N[1]+kk+1
place2 <- x$N[1]+kk+x$ng-1
b2 <- rbind(b2,c(0,x$best[place1:place2]))
for(i in 2:x$ng)
{
placeV[[paste("class",i,sep="")]] <- c(placeV[[paste("class",i,sep="")]],x$N[1]+kk+i-1)
}
kk <- kk+x$ng-1
}
if (k>1)
{
place1 <- x$N[1]+kk+1
place2 <- x$N[1]+kk+x$ng
b2 <- rbind(b2,x$best[place1:place2])
for(i in 1:x$ng)
{
placeV[[paste("class",i,sep="")]] <- c(placeV[[paste("class",i,sep="")]],x$N[1]+kk+i)
}
kk <- kk+x$ng
}
}
}
Y<-matrix(0,length(newdata1[,1]),x$ng)
colnames(Y) <- paste("class",1:x$ng,sep="")
for(g in 1:x$ng)
{
if(length(b1) != 0)
{
Y[,g]<- X1 %*% b1
}
if(length(b2) != 0)
{
Y[,g]<- Y[,g] + X2 %*% b2[,g]
}
}
ny <- length(x$Ynames)
#extraction de Var(beta)
Vbeta <- matrix(0,x$N[3]-x$N[2]-x$N[1],x$N[3]-x$N[2]-x$N[1])
npm <- length(x$best)
indice <- 1:npm * (1:npm+1) /2
indtmp <- indice[(x$N[1]+1):(x$N[3]-x$N[2])]
indtmp <- cbind(indtmp-0:(length(indtmp)-1),indtmp)
indV <- NULL
for(i in 1:nrow(indtmp))
{
indV <- c(indV,seq(indtmp[i,1],indtmp[i,2]))
}
Vbeta[upper.tri(Vbeta, diag=TRUE)] <- x$V[indV]
Vbeta <- t(Vbeta)
Vbeta[upper.tri(Vbeta, diag=TRUE)] <- x$V[indV]
#IC pour les predictions
lower <- matrix(0,nrow(Y),ncol(Y))
upper <- matrix(0,nrow(Y),ncol(Y))
colnames(lower) <- paste("lower.class",1:x$ng,sep="")
colnames(upper) <- paste("upper.class",1:x$ng,sep="")
if(x$ng==1)
{
#varpred <- diag(X1[,-1,drop=FALSE] %*% Vbeta %*% t(X1[,-1,drop=FALSE]))
varpred <- apply(X1[,-1,drop=FALSE],1,function(x) matrix(x,nrow=1) %*% Vbeta %*% matrix(x,ncol=1))
# browser()
lower[,1] <- Y[,1] -1.96 * sqrt(varpred)
upper[,1] <- Y[,1] +1.96 * sqrt(varpred)
}
else
{
for(g in 1:x$ng)
{
ind <- na.omit(c(placeV[["commun"]],placeV[[paste("class",g,sep="")]]))
if(g==1)
{
if(x$idg0[1]==1)
{
X12 <- X12 <- cbind(X1[,-1,drop=FALSE],X2)
}
if(x$idg0[1]==2)
{
X12 <- X12 <- cbind(X1,X2[,-1,drop=FALSE])
}
}
else
{
X12 <- cbind(X1,X2)
}
X12 <- X12[,order(ind),drop=FALSE]
varclass <- Vbeta[sort(ind)-x$N[1],sort(ind)-x$N[1]]
varpred <- apply(X12,1,function(x) matrix(x,nrow=1) %*% varclass %*% matrix(x,ncol=1))
lower[,g] <- Y[,g] -1.96 * sqrt(varpred)
upper[,g] <- Y[,g] +1.96 * sqrt(varpred)
}
}
if(confint==TRUE)
{
res <- cbind(Y,lower,upper)
if(x$ng==1) colnames(res) <- c("pred","lower.pred","upper.pred")
if(x$ng>1) colnames(res) <- c(paste("pred_class",1:x$ng,sep=""),paste("lower.pred_class",1:x$ng,sep=""),paste("upper.pred_class",1:x$ng,sep=""))
res.list <- NULL
res.list$pred <- res
res.list$times <- times
}
if(confint==FALSE)
{
if(x$ng==1) colnames(Y) <- "pred"
if(x$ng>1) colnames(Y) <- paste("pred_class",1:x$ng,sep="")
res.list <- NULL
res.list$pred <- Y
res.list$times <- times
}
}
else
{
cat("Output can not be produced since the program stopped abnormally.")
res.list <- list(pred=NA,times=NA)
}
class(res.list) <- "predictL"
return(res.list)
}
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