checkESS: Check if any parameters in an mcmc chain have an ESS value <...

In laduplessis/beastio: Functions for pre- and post-processing of BEAST and BEAST2 files.

Description

Check if any parameters in an mcmc chain have an ESS value < cutoff Constant (unsampled) parameters are ignored.

Usage

checkESS(data, cutoff = 200, value = TRUE, ignored = c(), plot = FALSE, ...)

Arguments

data	The object containing the MCMC sample - usually of class "mcmc" or "mcmc.list"
cutoff	The cutoff ESS value (default = 200)
value	If value == TRUE the parameters with ESS < cutoff and their ESS values are returned If value == FALSE only the column indices of those parameters are returned
ignored	Parameters in the chain that should be ignored
plot	If plot == TRUE draw a barplot of the ESS values and mark parameters with ESS < cutoff
...	Extra parameters to be passed to the plotESS() function

laduplessis/beastio documentation built on Dec. 14, 2021, 7:04 p.m.