arguments show.mean and traj.index in e0.tajectories.plot

ChangeLog

@@ -10,6 +10,9 @@ Added argument use.wpp.data to run.e0.mcmc().
 
 Added the mean variant into sumary output.
 
+e0.trajectories.plot() got arguments to plot the means (show.mean), 
+as well as selected trajectories (traj.index).
+
 5.2-0 (09/15/2023)
 -----
 Annual subnational projections are now possible, via the argument "annual"

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bayesLife
 Type: Package
 Title: Bayesian Projection of Life Expectancy
-Version: 5.2-0.9008
+Version: 5.2-0.9009
 Date: 2024-06-05
 Author: Hana Sevcikova, Adrian Raftery, Jennifer Chunn 
 Maintainer: Hana Sevcikova <[email protected]>

R/plot_functions.R

@@ -200,6 +200,7 @@ e0.trajectories.plot.all <- function(e0.pred,
 
 e0.trajectories.plot <- function(e0.pred, country, pi=c(80, 95), both.sexes=FALSE,
 								  nr.traj=NULL, adjusted.only = TRUE, typical.trajectory=FALSE,
+								  traj.index = NULL, show.mean = FALSE,
 								  xlim=NULL, ylim=NULL, type='b', 
 								  xlab='Year', ylab='Life expectancy at birth', main=NULL, 
 								  lwd=c(2,2,2,2,1), col=c('black', 'green', 'red', 'red', '#00000020'),
@@ -325,13 +326,20 @@ e0.trajectories.plot <- function(e0.pred, country, pi=c(80, 95), both.sexes=FALS
 		e0pred <- pred[[ipred]]
 		this.col <- plotcols[[ipred]]
 		meta <- e0pred$mcmc.set$meta
+		if(!is.null(traj.index)) nr.traj <- length(traj.index)
 		if(do.average) {
 			trajectories <- get.e0.trajectories.object(pred, country$code, nr.traj=nr.traj, typical.trajectory=typical.trajectory, pi=pi)
 			e0.median <- trajectories$median
+			if(show.mean)
+			    e0.mean <- apply(trajectories$trajectories, 1, mean, na.rm=TRUE)
 		} else {
 			trajectories <- get.e0.trajectories.object(e0pred, country$code, nr.traj=nr.traj, typical.trajectory=typical.trajectory)
 			e0.median <- bayesTFR::get.median.from.prediction(e0pred, country$index, country$code)
+			if(show.mean)
+			    e0.mean <- bayesTFR::get.mean.from.prediction(e0pred, country$index, country$code)
 		}
+		if(!is.null(traj.index) && !is.null(trajectories$trajectories)) trajectories$index <- traj.index
+
 		cqp <- list()
 		if(ipred > 1) add <- TRUE
 		if(!add)
@@ -418,6 +426,16 @@ e0.trajectories.plot <- function(e0.pred, country, pi=c(80, 95), both.sexes=FALS
 			lwds <- c(lwds, lwd[3])
 			lty <- c(lty, max(lty)+1)
 		}
+		if(show.mean){
+		    # plot mean
+		    lines(plot.data[[ipred]]$pred.x, e0.mean, type='l', col=this.col[3], lwd=1, lty=max(lty)+1)
+		    mean.leg <- 'mean'
+		    if(do.both.sexes) mean.leg <- paste(lowerize(get.sex.label(meta)), mean.leg)
+		    legend <- c(legend, mean.leg)
+		    cols <- c(cols, this.col[3])
+		    lwds <- c(lwds, 1)
+		    lty <- c(lty, max(lty)+1)
+		}
 		if(lpart2 > 0) {
 			legend <- c(legend, paste('imputed', if(do.both.sexes) paste(lowerize(get.sex.label(meta)), 'e0') else 'e0'))
 			cols <- c(cols, this.col[2])

man/e0.trajectories.plot.Rd

@@ -12,6 +12,7 @@ The functions plot/tabulate the posterior distribution of trajectories of the li
 \usage{
 e0.trajectories.plot(e0.pred, country, pi = c(80, 95), both.sexes = FALSE,
     nr.traj = NULL, adjusted.only = TRUE, typical.trajectory = FALSE, 
+    traj.index = NULL, show.mean = FALSE,
     xlim = NULL, ylim = NULL, type = "b", 
     xlab = "Year", ylab = "Life expectancy at birth", main = NULL, 
     lwd = c(2, 2, 2, 2, 1), col = c('black', 'green', 'red', 'red', '#00000020'),
@@ -34,6 +35,8 @@ e0.trajectories.table(e0.pred, country, pi = c(80, 95),
   \item{nr.traj}{Number of trajectories to be plotted. If \code{NULL}, all trajectories are plotted, otherwise they are thinned evenly. If \code{both.sexes} is \code{TRUE} the default is zero.}
   \item{adjusted.only}{Logical. By default, if the projection median is adjusted using e.g. \code{\link{e0.median.set}}, the function plots the adjusted median. If \code{adjusted.only=FALSE} the original (non-adjusted) median is plotted as well.}
   \item{typical.trajectory}{Logical. If \code{TRUE} one trajectory is shown  for which the median absolute deviation from the median e0 projection is the median among all the trajectories.}
+  \item{traj.index}{Vector of trajectory indices to show. If not given, the trajectories are selected using equidistant spacing.}
+  \item{show.mean}{Logical indicating if the mean of the distribution should be shown.}
   \item{xlim, ylim, type, xlab, ylab, main}{Graphical parameters passed to the \code{plot} function.}
   \item{lwd, col, col2}{Vector of five elements giving the line width and color for: 1. observed data, 2. imputed missing data, 3. median, 4. quantiles, 5. trajectories. \code{col2} is only used if \code{both.sexes} is \code{TRUE}. In such a case, \code{col2} is used for female lines and \code{col} is used for male lines, which in this case defaults to 
   	\code{c('black', 'green', 'darkgreen', 'darkgreen', 'gray')}.}