Trace and histogram plots of draws — plot.frmtmb

brms's plot() of a fit: for each selected parameter a histogram and a trace of its draws, nvariables parameters to a page, drawn with bayesplot::mcmc_combo(). The arguments are brms's, in brms's order and with brms's defaults. Without pars or variable the parameters are the model's outer parameters (no group-level coefficients), as brms leaves out its r_ draws.

Usage

# S3 method for class 'frmtmb_draws'
plot(
  x,
  pars = NA,
  combo = c("hist", "trace"),
  nvariables = 5,
  N = NULL,
  variable = NULL,
  regex = FALSE,
  fixed = FALSE,
  bins = 30,
  theme = NULL,
  plot = TRUE,
  ask = TRUE,
  newpage = TRUE,
  ...
)

Arguments

x: A frmtmb_draws from frm_sample().
pars, variable, regex, fixed: Which parameters, by brms's rule: variable is exact names unless regex = TRUE; pars is a regular expression unless fixed = TRUE, and wins when both are given.
combo: The two bayesplot panel types, as in brms.
nvariables: Parameters per page.
N: brms's deprecated alias of nvariables, with brms's warning.
bins: Histogram bins.
theme: A ggplot2 theme for the panels.
plot: If FALSE, return the pages without drawing them.
ask: Whether to ask before each page after the first.
newpage: Whether the first page starts a new page.
...: Passed to bayesplot::mcmc_combo().

Value

The pages, a list of bayesplot grids, invisibly.

Examples

# \donttest{
if (requireNamespace("tmbstan", quietly = TRUE) &&
    requireNamespace("rstan", quietly = TRUE) &&
    requireNamespace("bayesplot", quietly = TRUE) &&
    !frmtmb.sample:::tmbstan_build_broken()) {
  set.seed(1)
  dd <- data.frame(x = rnorm(40))
  dd$y <- rnorm(40, 1 + 0.5 * dd$x, 1)
  ds <- frm_sample(bf(y ~ x), family = gaussian(), data = dd,
                   chains = 1, iter = 400, refresh = 0)
  plot(ds, variable = "^b_", regex = TRUE, ask = FALSE)
}
#> frm_sample(): default priors (brms 2.23 defaults; prior = "flat" puts brms's (flat) in every slot)
#>   Intercept          student_t(3, 1.1, 2.5)
#>   sigma              student_t(3, 0, 2.5)  [natural scale]
#>   b                  (flat), as brms leaves slopes
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> https://mc-stan.org/misc/warnings.html#bulk-ess

# }