Nothing
tolongformat <- function(d, mpl){
all.d <- d
d <- d$msm.basics
## with pmX:
# if(length(all.d) > 3.5){
# d <- data.frame(d$msm.basics, d$pmX)
# ## number of covariates:
# p <- ncol(d) - 7
# for(i in 1:nrow(d)){
# ## current line:
# d.i <- d[i, ]
# all.to.i <- as.vector(mpl[[d.i$from]]$all.to)
# for(k in 1:length(all.to.i)){
# if(!(all.to.i[k] == d.i$to)){
# d <- rbind(d, d.i)
# d[nrow(d), ]$to <- all.to.i[k]
# d[nrow(d), ]$delta <- 0
# d[nrow(d), ]$trans <- paste(d[nrow(d), ]$from, all.to.i[k], sep = "")
# all.d$pmX <- rbind(all.d$pmX, all.d$pmX[i, ])
# all.d$ttsce <- rbind(all.d$ttsce, all.d$ttsce[i, ])
# q.old <- d.i$trans
# q.new <- d[nrow(d), ]$trans
# index.old <- grepl(pattern = paste(".", q.old, sep = ""), names(all.d$ttsce))
# index.new <- grepl(pattern = paste(".", q.new, sep = ""), names(all.d$ttsce))
# all.d$ttsce[nrow(all.d$ttsce), ] <- 0
# all.d$ttsce[nrow(all.d$ttsce), index.new] <- all.d$ttsce[i, index.old]
# }
# }
# }
# relevant.order <- order(d$id, d$entry)
# d <- d[relevant.order, ]
# all.d$pmX <- all.d$pmX[relevant.order, ]
# }
## without pmX:
#if(length(all.d) < 3.5){
## number of covariates:
p <- ncol(d) - 7
for(i in 1:nrow(d)){
## current line:
d.i <- d[i, ]
all.to.i <- as.vector(mpl[[d.i$from]]$all.to)
for(k in 1:length(all.to.i)){
if(!(all.to.i[k] == d.i$to)){
d <- rbind(d, d.i)
d[nrow(d), ]$to <- all.to.i[k]
d[nrow(d), ]$delta <- 0
d[nrow(d), ]$trans <- paste(d[nrow(d), ]$from, all.to.i[k], sep = "")
## all.d$pmX <- rbind(all.d$pmX, all.d$pmX[i, ])
all.d$ttsce <- rbind(all.d$ttsce, all.d$ttsce[i, ])
q.old <- d.i$trans
q.new <- d[nrow(d), ]$trans
index.old <- grepl(pattern = paste(".", q.old, sep = ""), names(all.d$ttsce), fixed = TRUE)
index.new <- grepl(pattern = paste(".", q.new, sep = ""), names(all.d$ttsce), fixed = TRUE)
all.d$ttsce[nrow(all.d$ttsce), ] <- 0
all.d$ttsce[nrow(all.d$ttsce), index.new] <- all.d$ttsce[i, index.old]
}
}
}
relevant.order <- order(d$id, d$entry)
d <- d[relevant.order, ]
## all.d$pmX <- all.d$pmX[relevant.order, ]
#}
all.d$ttsce <- all.d$ttsce[relevant.order, ]
all.d$msm.basics <- d
## transition-type indicators:
tt.indicators <- tt.indicator.names <- NULL
for(index in 1:length(mpl)){
q <- c(paste(mpl[[index]]$from, mpl[[index]]$all.to, sep = ""))
if(!is.null(mpl[[index]]$all.to)){
for(q.index in q){
tt.indicators <- cbind(tt.indicators, as.integer(d$trans == q.index))
tt.indicator.names <- c(tt.indicator.names, paste("trans", q.index, sep = ""))
}
}
}
tt.indicators[which(all.d$msm.basics$delta == 0), ] <- rep(0, ncol (tt.indicators))
tt.indicators <- data.frame(tt.indicators)
names(tt.indicators) <- tt.indicator.names
rownames(tt.indicators) <- rownames(all.d$ttsce)
all.d$tt.indicators <- tt.indicators
rownames(all.d$msm.basics) <- rownames(all.d$ttsce) <- rownames(all.d$tt.indicators) <- 1:nrow(all.d$msm.basics)
#if(length(all.d) > 3.5){
# rownames(all.d$pmX) <- 1:nrow(all.d$msm.basics)
#}
return(all.d)
}
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