Skip to contents

Trace and density plots for coevfit objects

Source: R/plot.R
plot.coevfit.Rd

Trace and density plots for coevfit objects

Usage

# S3 method for class 'coevfit'
plot(
  x,
  parameters = NULL,
  combo = c("dens", "trace"),
  npars = 5,
  plot = TRUE,
  ...
)

Arguments

x

An object of class coevfit.

parameters

If NULL (default), the function returns plots for the main parameters from the model (the selection matrix "A", the drift matrix "Q", and the continuous time intercepts "b"). Otherwise, a character vector declaring the parameters to plot (strictly case-sensitive).

combo

A character vector with at least two elements. Each element of combo corresponds to a column in the resulting plot and should be the name of one of the available MCMC functions (omitting the mcmc_ prefix).

npars

Number of parameters displayed per page (default = 5).

plot

Logical. If TRUE (default), plots are plotted in the active graphic device. If FALSE, plots are not plotted.

...

Not used.

Value

A list of ggplot objects

Examples

if (FALSE) { # \dontrun{
# fit dynamic coevolutionary model
fit <- coev_fit(
  data = authority$data,
  variables = list(
    political_authority = "ordered_logistic",
    religious_authority = "ordered_logistic"
  ),
  id = "language",
  tree = authority$phylogeny,
  # additional arguments for cmdstanr::sample()
  chains = 4,
  parallel_chains = 4,
  seed = 1
  )

# print trace and density plots
plot(fit)
} # }