ordinate.jsdgam: Latent variable ordination plots from jsdgam objects

In nicholasjclark/mvgam: Multivariate (Dynamic) Generalized Additive Models

Latent variable ordination plots from jsdgam objects

Description

Plot an ordination of latent variables and their factor loadings from jsdgam models

Usage

ordinate(object, ...)

## S3 method for class 'jsdgam'
ordinate(
  object,
  which_lvs = c(1, 2),
  biplot = TRUE,
  alpha = 0.5,
  label_sites = TRUE,
  ...
)

Arguments

object	list object of class jsdgam resulting from a call to jsdgam()
...	ignored
which_lvs	A vector of indices indicating the two latent variables to be plotted (if number of the latent variables specified in the model was more than 2). Defaults to c(1, 2)
biplot	Logical. If TRUE, both the site and the species scores will be plotted, with names for the taxa interpreted based on the species argument in the original call to jsdgam(). If FALSE, only the site scores will be plotted
alpha	A proportional numeric scalar between 0 and 1 that controls the relative scaling of the latent variables and their loading coefficients
label_sites	Logical flag. If TRUE, site scores will be plotted as labels using names based on the unit argument in the original call to jsdgam(). If FALSE, site scores will be shown as points only

Details

This function constructs a two-dimensional scatterplot in ordination space. The chosen latent variables are first re-rotated using singular value decomposition, so that the first plotted latent variable does not have to be the first latent variable that was estimated in the original model. Posterior median estimates of the variables and the species' loadings on these variables are then used to construct the resulting plot. Some attempt at de-cluttering the resulting plot is made by using geom_label_repel() and geom_text_repel from the ggrepel package, but if there are many sites and/or species then some labels may be removed automatically. Note that you can typically get better, more readable plot layouts if you also have the ggarrow and ggpp packages installed

Value

An ggplot object

Author(s)

Nicholas J Clark

See Also

jsdgam(), residual_cor()

Examples

# Fit a JSDGAM to the portal_data captures
mod <- jsdgam(
  formula = captures ~
    # Fixed effects of NDVI and mintemp, row effect as a GP of time
    ndvi_ma12:series + mintemp:series + gp(time, k = 15),
  factor_formula = ~ -1,
  data = portal_data,
  unit = time,
  species = series,
  family = poisson(),
  n_lv = 2,
  silent = 2,
  chains = 2
)

# Plot a residual ordination biplot
ordinate(
  mod,
  alpha = 0.7
)

# Compare to a residual correlation plot
plot(
  residual_cor(mod)
)

nicholasjclark/mvgam documentation built on April 17, 2025, 9:39 p.m.