plot-DLcurve: Plotting Posterior Distribution of the Double Logistic...

In jasonacollins/bayesTFR1: Bayesian Fertility Projection

Description

The functions plot the posterior distribution of the double logistic function used in the simulation of Phase II, including their median and given probability intervals.

Usage

DLcurve.plot(mcmc.list, country, burnin = NULL, pi = 80, tfr.max = 10, 
    nr.curves = NULL, predictive.distr = FALSE, ylim = NULL, 
    xlab = 'TFR (reversed)', ylab = 'TFR decrement', main = NULL, 
    show.legend = TRUE, col=c('black', 'red', "#00000020"), ...)
	
DLcurve.plot.all(mcmc.list = NULL, sim.dir = NULL, 
    output.dir = file.path(getwd(), 'DLcurves'),
    output.type = "png", burnin = NULL, verbose = FALSE, ...)

Arguments

mcmc.list	List of bayesTFR.mcmc objects, an object of class bayesTFR.mcmc.set or of class bayesTFR.prediction. In case of DLcurve.plot.all if it si NULL, it is loaded from sim.dir.
country	Name or numerical code of a country.
burnin	Number of iterations to be discarded from the beginning of parameter traces.
pi	Probability interval. It can be a single number or an array.
tfr.max	Maximum TFR to be shown in the plot.
nr.curves	Number of curves to be plotted. If NULL, all curves are plotted.
predictive.distr	Logical. If TRUE, an error term is added to each trajectory.
ylim, xlab, ylab, main	Graphical parameters passed to the plot function.
show.legend	Logical determining if the legend should be shown.
col	Vector of colors in this order: 1. observed data points, 2. quantiles, 3. trajectories
...	Additional graphical parameters. For DLcurve.plot.all, ... contains also arguments pi, tfr.max and nr.curves.
sim.dir	Directory with the simulation results. Only relevant, if mcmc.list is NULL.
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”.
verbose	Logical switching log messages on and off.

Details

DLcurve.plot plots double logistic curves for the given country. DLcurve.plot.all creates such plots for all countries and stores them in output.dir. Parameters inputting the double logistic function are either thinned traces created by the tfr.predict function (if mcmc.list is an object of class bayesTFR.prediction), or they are selected by equal spacing from the MCMC traces. In the former case, burnin is set automatically; in the latter case, burnin defaults to 0. If nr.curves is smaller than 2000, the median and probability intervals are computed on a sample of 2000 equally spaced data points, otherwise on all plotted curves.

Author(s)

Hana Sevcikova, Leontine Alkema

Examples

## Not run: 
sim.dir <- file.path(find.package("bayesTFR"), "ex-data", "bayesTFR.output")
mcmc.set <- get.tfr.mcmc(sim.dir=sim.dir)
DLcurve.plot(country="Burkina Faso", mcmc.set, burnin=15)

## End(Not run)

jasonacollins/bayesTFR1 documentation built on May 23, 2019, 7:34 a.m.