R/as.CMM.R

In arturstat/genSurv: Generating Multi-State Survival Data

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

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

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

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

as.CMM.TDCM <- function(x) {
	if ( !is.TDCM(x) ) {stop("'x' must be of class 'TDCM'");}
	data <- cbind(x$id, x$start, x$stop, x$event, x$covariate, x$tdcov);
	data <- data.frame(data, row.names=NULL);
	names(data) <- c("id", "start", "stop", "event", "covariate", "tdcov");
	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) {
			aux1 <- c(data[i,1], 0, data[i,3], 0, data[i,5], 1);
			aux2 <- c(data[i,1], 0, data[i,3], 0, data[i,5], 2);
			data2 <- rbind(data2, aux1, aux2);
			i <- i+1;
		}
		if (i <= (nrow(data)-1) & data[i,1] != data[i+1,1] & data[i,4] == 1) {
			aux1 <- c(data[i,1], 0, data[i,3], 1, data[i,5], 1);
			aux2 <- c(data[i,1], 0, data[i,3], 0, data[i,5], 2);
			data2 <- rbind(data2, aux1, aux2);
			i <- i+1;
		}
		if (i <= (nrow(data)-1) & data[i,1] == data[i+1,1] & data[i,4] == 0) {
			if (data[i+1,4] == 0) {
				aux1 <- c(data[i,1], 0, data[i,3], 0, data[i,5], 1);
				aux2 <- c(data[i,1], 0, data[i,3], 1, data[i,5], 2);
				aux3 <- c(data[i,1], data[i,3], data[i+1,3], 0, data[i,5], 3);
				data2 <- rbind(data2, aux1, aux2, aux3);
			} else if (data[i+1,4] == 1) {
				aux1 <- c(data[i,1], 0, data[i,3], 0, data[i,5], 1);
				aux2 <- c(data[i,1], 0, data[i,3], 1, data[i,5], 2);
				aux3 <- c(data[i,1], data[i,3], data[i+1,3], 1, data[i,5], 3);
				data2 <- rbind(data2, aux1, aux2, aux3);
			}
			i <- i+2;
		}
	}
	if ( i == nrow(data) ) {
		if (data[i,4] == 0) {
			aux1 <- c(data[i,1], 0, data[i,3], 0, data[i,5], 1);
			aux2 <- c(data[i,1], 0, data[i,3], 0, data[i,5], 2);
			data2 <- rbind(data2, aux1, aux2);
		} else if (data[i,4] == 1) {
			aux1 <- c(data[i,1], 0, data[i,3], 1, data[i,5], 1);
			aux2 <- c(data[i,1], 0, data[i,3], 0, data[i,5], 2);
			data2 <- rbind(data2, aux1, aux2);
		}
	}
	data2 <- data.frame(data2, row.names=NULL);
	names(data2) <- c("id", "start", "stop", "event", "covariate", "trans");
	data2 <- data2[-1,];
	row.names(data2) <- as.integer( 1:nrow(data2) );
	class(data2) <- c(class(data2), "CMM");
	return(data2);
} # as.CMM.TDCM

as.CMM.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)-1) ) {
		if (data[i,2] != 0) {i <- i+1;}
		if (data[i,2] == 0 & data[i+1,3] == 1) {
			aux1 <- c(data[i,1], 0, data[i+1,2], 0, data[i,4], 1);
			aux2 <- c(data[i,1], 0, data[i+1,2], 0, data[i,4], 2);
			data2 <- rbind(data2, aux1, aux2);
		}
		if(data[i,2] == 0 & data[i+1,3] == 3) {
			aux1 <- c(data[i,1], 0, data[i+1,2], 1, data[i,4], 1);
			aux2 <- c(data[i,1], 0, data[i+1,2], 0, data[i,4], 2);
			data2 <- rbind(data2, aux1, aux2);
		}
		if (data[i,2] == 0 & (i+2) <= nrow(data) & data[i+1,3] == 2) {
			if (data[i+2,3] == 2) {
				aux1 <- c(data[i,1], 0, data[i+1,2], 0, data[i,4], 1);
				aux2 <- c(data[i,1], 0, data[i+1,2], 1, data[i,4], 2);
				aux3 <- c(data[i,1], data[i+1,2], data[i+2,2], 0, data[i,4], 3);
				data2 <- rbind(data2, aux1, aux2, aux3);
			}
			if (data[i+2,3] == 3) {
				aux1 <- c(data[i,1], 0, data[i+1,2], 0, data[i,4], 1);
				aux2 <- c(data[i,1], 0, data[i+1,2], 1, data[i,4], 2);
				aux3 <- c(data[i,1], data[i+1,2], data[i+2,2], 1, data[i,4], 3);
				data2 <- rbind(data2, aux1, aux2, aux3);
			}
		}
		i <- i+1;
	}
	data2 <- data.frame(data2, row.names=NULL);
	names(data2) <- c("id", "start", "stop", "event", "covariate", "trans");
	data2 <- data2[-1,];
	row.names(data2) <- as.integer( 1:nrow(data2) );
	class(data2) <- c(class(data2), "CMM");
	return(data2);
} # as.CMM.THMM