R/plot.TPmsm.R

In TPmsm: Estimation of Transition Probabilities in Multistate Models

plot.TPmsm <- function(x, tr.choice, xlab="Time", ylab="Transition probability", col, lty, xlim, ylim, conf.int=FALSE, ci.col, ci.lty, legend=TRUE, legend.pos, curvlab, legend.bty="n", ...) {
	if ( !inherits(x, "TPmsm") ) {stop("'x' must be of class 'TPmsm'");}
	if ( missing(tr.choice) ) {tr.choice <- colnames(x$est);}
	lt <- length(tr.choice);
	if (sum( tr.choice %in% colnames(x$est) ) != lt) {stop("Argument 'tr.choice' and possible transitions must match");}
	if ( anyDuplicated(tr.choice) ) {stop("Argument 'tr.choice' must be unique");}
	if ( missing (xlim) ) {xlim <- c( 0, max(x$time) );}
	if ( missing(ylim) ) {ylim <- c(0, 1);}
	if ( missing(col) ) {col <- rep(1, lt);}
	else if (length(col) < lt) {col <- col*rep(1, lt);}
	if ( missing(lty) ) {lty <- seq_len(lt);}
	else if (length(lty) < lt) {lty <- lty*rep(1, lt);}
	itr <- match( tr.choice, colnames(x$est) );
	plot(xlim, ylim, xlab=xlab, ylab=ylab, xlim=xlim, ylim=ylim, type="n", ...);
	for ( i in seq_len(lt) ) {
		lines(x=x$time, y=x$est[,itr[i]], type="s", col=col[i], lty=lty[i], ...);
	}
	if ( conf.int & !is.null(x$inf) & !is.null(x$sup) ) {
		if ( missing(ci.col) ) {ci.col <- col;}
		if (length(ci.col) < lt) {ci.col <- ci.col*rep(1, lt);}
		if ( missing(ci.lty) ) {ci.lty <- 3;}
		if (length(ci.lty) < lt) {ci.lty <- ci.lty*rep(1, lt);}
		for ( i in seq_len(lt) ) {
			lines(x=x$time, y=x$inf[,itr[i]], type="s", col=ci.col[i], lty=ci.lty[i], ...);
			lines(x=x$time, y=x$sup[,itr[i]], type="s", col=ci.col[i], lty=ci.lty[i], ...);
		}
	}
	if (legend) {
		if ( missing(legend.pos) ) {legend.pos <- "topleft";}
		if ( missing(curvlab) ) {curvlab <- tr.choice;}
		addlegend(legend.pos, curvlab, col=col, lty=lty, legend.bty=legend.bty, ...);
	}
	invisible();
} # plot.TPmsm