pglmm-plot-data function

Plot the original dataset and predicted values (optional)

Plots a representation of the marginal posterior distribution of model parameters. Note this function requires the packages ggplot2 and ggridges to be installed.

plot_data(
  x,
  sp.var = "sp",
  site.var = "site",
  show.sp.names = FALSE,
  show.site.names = FALSE,
  digits = max(3, getOption("digits") - 3),
  predicted = FALSE,
  ...
)

## S3 method for class 'communityPGLMM'
plot_bayes(x, n_samp = 1000, sort = TRUE, ...)

Arguments

• x: A communityPGLMM object fit with bayes = TRUE.
• sp.var: The variable name of "species"; y-axis of the image.
• site.var: The variable name of "site"; x-axis of the image.
• show.sp.names: Whether to print species names as y-axis labels.
• show.site.names: Whether to print site names as x-axis labels.
• digits: Not used.
• predicted: Whether to plot predicted values side by side with observed ones.
• ...: Further arguments to pass to or from other methods.
• n_samp: Number of sample from the marginal posterior to take in order to estimate the posterior density.
• sort: Whether to plot different terms in the order of their estimations. Default is 'TRUE'.

Returns

A ggplot object

Note

The underlying plot grid object is returned but invisible. It can be saved for later uses.