R/as.TDCM.R

In arturstat/genSurv: Generating Multi-State Survival Data

is.TDCM <- function(x) {
	return( is.data.frame(x) & inherits(x, "TDCM") );
} # is.TDCM

as.TDCM <- function(x) {
	UseMethod("as.TDCM");
} # as.TDCM

as.TDCM.default <- function(x) {
	stop(gettextf( "cannot coerce class '%s' into class 'TDCM'", deparse( class(x) ) ), domain = NA);
} # as.TDCM.default

as.TDCM.TDCM <- function(x) {
	if ( !is.TDCM(x) ) {stop("'x' must be of class 'TDCM'");}
	return(x);
} # as.TDCM.TDCM

as.TDCM.CMM <- function(x) {
	if ( !is.CMM(x) ) {stop("'x' must be of class 'CMM'");}
	data <- cbind(x$id, x$start, x$stop, x$event, x$covariate, x$trans);
	data <- data.frame(data, row.names=NULL);
	names(data) <- c("id", "start", "stop", "event", "covariate", "trans");
	data2 <- matrix(ncol=6, nrow=1);
	i <- 1;
	while ( i <= (nrow(data)-1) ) {
		if (data[i,1] == data[i+1,1] & data[i,4] == 0 & data[i+1,4]==0) {
			aux1 <- c(data[i,1], 0, data[i,3], 0, data[i,5], 0);
			data2 <- rbind(data2, aux1);
			i <- i+2;
		}
		if (i <= (nrow(data)-1) & data[i,6]==1 & data[i,4]==1) {
			aux1 <- c(data[i,1], 0, data[i,3], 1, data[i,5], 0);
			data2 <- rbind(data2, aux1);
			i <- i+2;
		}
		if (i <= (nrow(data)-1) & data[i,1] == data[i+1,1] & data[i,4] == 0 & data[i+1,4] == 1) {
			if (data[i+2,4] == 0) {
				aux1 <- c(data[i,1], 0, data[i,3], 0, data[i,5], 0);
				aux2 <- c(data[i,1], data[i,3], data[i+2,3], 0, data[i,5], 1);
				data2 <- rbind(data2, aux1, aux2);
			}
			if (data[i+2,4] == 1) {
				aux1 <- c(data[i,1], 0, data[i,3], 0, data[i,5], 0);
				aux2 <- c(data[i,1], data[i,3], data[i+2,3], 1, data[i,5], 1);
				data2 <- rbind(data2, aux1, aux2);
			}
			i <- i+3;
		}
	}
	data2 <- data.frame(data2, row.names=NULL);
	names(data2) <- c("id", "start", "stop", "event", "covariate", "tdcov");
	data2 <- data2[-1,];
	row.names(data2) <- as.integer( 1:nrow(data2) );
	class(data2) <- c(class(data2), "TDCM");
	return(data2);
} # as.TDCM.CMM

as.TDCM.THMM <- function(x) {
	if ( !is.THMM(x) ) {stop("'x' must be of class 'THMM'");}
	data <- cbind(x$PTNUM, x$time, x$state, x$covariate);
	data <- data.frame(data, row.names=NULL);
	names(data) <- c("PTNUM", "time", "state", "covariate");
	data2 <- matrix(ncol=6, nrow=1);
	i <- 1;
	while( i <= nrow(data) ) {
		if (data[i,3] == data[i+1,3] & data[i+1,3] == 1) {
			aux <- c(data[i,1], 0, data[i+1,2], 0, data[i,4], 0);
			data2 <- rbind(data2, aux);
			i <- i+2;
		} else {
			if (data[i,3] == 1 & data[i+1,3] == 3) {
				aux <- c(data[i,1], 0, data[i+1,2], 1, data[i,4], 0);
				data2 <- rbind(data2, aux);
				i <- i+2;
			} else {
				aux <- c(data[i,1], 0, data[i+1,2], 0, data[i,4], 0);
				data2 <- rbind(data2, aux);
				i <- i+2;
				if (data[i,3] == 2) {
					aux <- c(data[i,1], data[i-1,2], data[i,2], 0, data[i,4], 1);
					data2 <- rbind(data2, aux);
					i <- i+1;
				} else {
					aux <- c(data[i,1], data[i-1,2], data[i,2], 1, data[i,4], 1);
					data2 <- rbind(data2, aux);
					i <- i+1;
				}
			}
		}
	}
	data2 <- data.frame(data2, row.names=NULL);
	names(data2) <- c("id", "start", "stop", "event", "covariate", "tdcov");
	data2 <- data2[-1,];
	row.names(data2) <- as.integer( 1:nrow(data2) );
	class(data2) <- c(class(data2), "TDCM");
	return(data2);
} # as.TDCM.THMM