tfr.trajectories.plot: Output of Posterior Distribution of TFR Trajectories

Description

The functions plot/tabulate the posterior distribution of TFR trajectories for a given country, or for all countries, including their median and given probability intervals.

Usage

tfr.trajectories.plot(tfr.pred, country, pi = c(80, 95), 
    half.child.variant = TRUE, nr.traj = NULL, 
    adjusted.only = TRUE, typical.trajectory = FALSE, 
    mark.estimation.points = FALSE,
    xlim = NULL, ylim = NULL, type = 'b', xlab = 'Year', ylab = 'TFR', 
    main = NULL, lwd = c(2, 2, 2, 2, 2, 1), 
    col=c('black', 'green', 'red', 'red', 'blue', '#00000020'),
    show.legend = TRUE, add = FALSE, uncertainty = FALSE, 
    col_unc = "purple", ...)
	
tfr.trajectories.plot.all(tfr.pred, 
    output.dir = file.path(getwd(), 'TFRtrajectories'),
    output.type = "png", main = NULL, verbose = FALSE, ...)
	
tfr.trajectories.table(tfr.pred, country, pi = c(80, 95), 
    half.child.variant = TRUE, adjusted = TRUE)

Arguments

tfr.pred: Object of class bayesTFR.prediction.
country: Name or numerical code of a country. It can also be given as ISO-2 or ISO-3 characters.
pi: Probability interval. It can be a single number or an array.
half.child.variant: If TRUE the United Nations variant of “+/-0.5 child” (relative to the median) is shown.
nr.traj: Number of trajectories to be plotted. If NULL, all trajectories are plotted, otherwise they are thinned evenly.
adjusted.only: Logical. By default, if the projection or estimation median is adjusted using e.g. tfr.median.set or tfr.median.set.all, the function plots the adjusted median. If adjusted.only=FALSE the original (non-adjusted) median is plotted as well.
typical.trajectory: Logical. If TRUE one trajectory is shown that has the smallest distance to the median.
mark.estimation.points: Logical. If TRUE, points that were not used in the estimation (phase I) are shown in lighter color than points in phase II and III.
xlim, ylim, type, xlab, ylab: Graphical parameters passed to the plot function.
lwd, col: Vector of six elements giving the line width and color for: 1. observed data, 2. imputed missing data, 3. median, 4. quantiles, 5. half-child variant, 6. trajectories.
show.legend: Logical controlling whether the legend should be drawn.
add: Logical controlling whether the trajectories should be plotted into a new graphic device (FALSE) or into an existing device (TRUE). One can use this argument to plot trajectories from multiple countries into one graphics.
...: Additional graphical parameters. In addition, for tfr.trajectories.plot.all, ... contains any of the arguments of tfr.trajectories.plot.
output.dir: Directory into which resulting graphs are stored.
output.type: Type of the resulting files. It can be “png”, “pdf”, “jpeg”, “bmp”, “tiff”, or “postscript”.
main: Main title for the plot(s). In tfr.trajectories.plot.all any occurence of the string “XXX” is replaced by the country name.
verbose: Logical switching log messages on and off.
uncertainty: Logical: TRUE means uncertainty of past TFR should be plotted with the same level of uncertainty interval.
col_unc: Color of past TFR estimation uncertainty plot.
adjusted: Logical. If FALSE the unadjusted values are returned.

Author

Hana Sevcikova, Leontine Alkema, Peiran Liu

Details

tfr.trajectories.plot plots posterior distribution of TFR trajectories for a given country. tfr.trajectories.table gives the same output as a table. tfr.trajectories.plot.all creates a set of graphs (one per country) that are stored in output.dir.

The median and given probability intervals are computed using all available trajectories. Thus, nr.traj does not influence those values - it is used only to control the number of trajectories plotted.

Examples

Run this code

if (FALSE) {
sim.dir <- file.path(find.package("bayesTFR"), "ex-data", "bayesTFR.output")
pred <- get.tfr.prediction(sim.dir)
tfr.trajectories.plot(pred, country="Burkina Faso", pi=c(80, 95))
tfr.trajectories.table(pred, country="Burkina Faso", pi=c(80, 95))
}