coda_neff: Create effective sample size diagnostic graphic

In MichaelMalick/r-codatools: codatools

Description

coda_neff creates a graphic of the effective sample size. The left-hand y-axis is the total effective size and the right-hand y-axis is the effective size scaled by the total number of MCMC draws.

Usage

coda_neff(neff, samps, thresh = 0.5, cex.labels = 0.5)

Arguments

neff	named vector of Neff values
samps	total number of MCMC draws (N chains * N draws)
thresh	threshold used to flag parameters with low effective sample sizes, as a percentage of total MCMC draws
cex.labels	scaling for parameters plotted by name

Value

Invisibly returns a vector of the effective sample size for each parameter sorted from lowest (first) to highest (last) and prints a plot of the effective sample sizes.

Author(s)

Michael Malick

See Also

effectiveSize

Examples

library(coda)
data(line)

neff  <- coda::effectiveSize(line)
samps <- coda::niter(line) * coda::nchain(line)
coda_neff(neff, samps)

MichaelMalick/r-codatools documentation built on May 8, 2019, 9:56 a.m.