stanDxplot: Diagnostic Trace Plots

In rmsb: Bayesian Regression Modeling Strategies

Diagnostic Trace Plots

Description

For an rms Bayesian fit object, uses by default the stored posterior draws to check convergence properties of posterior sampling. If instead rstan=TRUE, calls the rstan traceplot function on the rstan object inside the rmsb object, to check properties of posterior sampling. If rstan=TRUE and the rstan object has been removed and previous=TRUE, attempts to find an already existing plot created by a previous run of the knitr chunk, assuming it was the plotno numbered plot of the chunk.

Usage

stanDxplot(
  x,
  which = NULL,
  rstan = FALSE,
  previous = TRUE,
  plotno = 1,
  rev = FALSE,
  stripsize = 8,
  ...
)

Arguments

x	an rms Bayesian fit object
which	names of parameters to plot, defaulting to all non-intercepts. When rstan=FALSE these are the friendly rms names, otherwise they are the rstan parameter names. If the model fit was run through stackMI for multiple imputation, the number of traces is multiplied by the number of imputations. Set to 'ALL' to plot all parameters.
rstan	set to TRUE to use rstan::traceplot() on a (presumed) stored rstan object in x, otherwise only real iterations are plotted and parameter values are shown as points instead of lines, with chains separated
previous	see details
plotno	see details
rev	set to TRUE to reverse direction for faceting chains
stripsize	specifies size of chain facet label text, default is 8
...	passed to rstan::traceplot()

Value

ggplot2 object if rstan object was in x

Author(s)

Frank Harrell

rmsb documentation built on Sept. 26, 2023, 5:11 p.m.