pglmm-plot-data: Plot the original dataset and predicted values (optional)

In phyr: Model Based Phylogenetic Analysis

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.

phyr documentation built on Jan. 13, 2021, 5:40 p.m.