plot_data {phyr}

Plot the original dataset and predicted values (optional)

Description

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

Usage

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'.

Value

A ggplot object

Note

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