ordiplot: Plotting an ordination plot for a GLLVM model

In fseaton/jsdmstan: Fitting jSDMs in Stan

Plotting an ordination plot for a GLLVM model

Description

This function takes a GLLVM model fit and plots an ordination plot with a random (or specified) selection of draws

Usage

ordiplot(
  object,
  choices = c(1, 2),
  type = "species",
  summary_stat = "median",
  ndraws = 0,
  draw_ids = NULL,
  size = c(2, 1),
  alpha = c(1, 0.5),
  shape = c(18, 16),
  geom = "point",
  errorbar_range = 0.75,
  errorbar_linewidth = 1
)

Arguments

object	The jsdmStanFit model object
choices	Which latent variables to plot as dimensions, by default c(1,2)
type	Whether to plot sites or species, default "species".
summary_stat	The summary statistic used to plot overall averages of the posterior sample. By default this is "median", and NULL will result in no summary being included
ndraws	How many individual draws to include in plot, by default 0. Setting this to 0 will result in no individual draws being included
draw_ids	Which draws to include in plot (overrides ndraws)
size	The size of the points in the graph, specified as a two-element vector with the first being used for the summary points and the second the individual draws, default c(2,1)
alpha	The transparency/alpha of the points in the graph, specified as a two-element vector with the first being used for the summary points and the second the individual draws, default c(1,0.5)
shape	The shape of the points in the graph, specified as a two-element vector with the first being used for the summary points and the second the individual draws, default c(18,16)
geom	Which geom from ggplot2 is used for the summary statistic by default "point", or alternatively can be "text"
errorbar_range	If specified, the central range of the data that is covered by the errorbar. Needs to be given as either NULL (i.e. no errorbar), or a number between 0 and 1, default 0.75.
errorbar_linewidth	The linewidth of the error bar, by default 1.

Value

A ggplot object that can be customised using the ggplot2 package

Examples

## Not run: 
# First simulate data and fit the model:
gllvm_data <- jsdm_sim_data(
  method = "gllvm", N = 100, S = 6, D = 3,
  family = "bernoulli"
)
gllvm_fit <- stan_jsdm(
  dat_list = gllvm_data, method = "gllvm",
  family = "bernoulli"
)

ordiplot(gllvm_fit)
# now plot the 1st and 3rd latent variables against each other for the sites:
ordiplot(gllvm_fit, choices = c(1, 3), type = "sites")

## End(Not run)

fseaton/jsdmstan documentation built on June 12, 2025, 7:02 a.m.