chainsPlot {basicMCMCplots} | R Documentation |
Overlays trace plots from each MCMC chain, for each parameter
chainsPlot(samplesList, var = NULL, ind = NULL, burnin = NULL, scale = FALSE, ncols = NULL, width = 7, height = NULL, legend = !is.null(names(samplesList)), legend.location = "topright", cex = 1, traceplot = TRUE, densityplot = TRUE, file = NULL)
samplesList |
List of arrays of MCMC samples from different chains |
var |
Parameter names to plot |
ind |
Indices of MCMC samples to plot |
burnin |
Number of initial samples to discard from each MCMC chain (default: 0) |
scale |
Logical, whether to normalize each posterior chain (default: FALSE) |
ncols |
Number of columns in grid of parameter traceplots or densityplots |
width |
Width of the plot |
height |
Height of the plot |
legend |
Logical, whether to include a legend of chain names |
legend.location |
Legend location |
cex |
Expansion coefficient for text (default: 1) |
traceplot |
Logical, whether to generate posterior trace plots (default: TRUE) |
densityplot |
Logical, whether to generate posterior density plots (default: TRUE) |
file |
Filename for saving figure to a file |
samples1 <- cbind(rnorm(1000, 1), rgamma(1000, 1), rpois(1000, 1)) colnames(samples1) <- c('alpha', 'beta', 'gamma') samples2 <- cbind(rnorm(1000, 2), rgamma(1000, 2), rpois(1000, 2)) colnames(samples2) <- c('alpha', 'beta', 'gamma') samplesList <- list(chain1 = samples1, chain2 = samples2) chainsPlot(samplesList) chainsPlot(samplesList, densityplot = FALSE, burnin = 500) chainsPlot(samplesList, traceplot = FALSE, legend.location = 'topleft', cex = 0.7)