biPlot: biPlot

In Hmsc: Hierarchical Model of Species Communities

biPlot

Description

Constructs an ordination biplot based on the fitted model

Usage

biPlot(
  hM,
  etaPost,
  lambdaPost,
  factors = c(1, 2),
  colVar = NULL,
  colors = NULL,
  spNames = hM$spNames,
  ...
)

Arguments

hM	a fitted Hmsc model object
etaPost	posterior distribution of site loadings (Eta)
lambdaPost	posterior distribution of species loadings (Lambda)
factors	indices of the two factors to be plotted
colVar	the environmental covariate from XData according to which the sites are to be coloured
colors	controls the colors of the heatmap. For continuous covariates, colors should be given as a name of palette, with default value colorRampPalette(c("blue","white","red")), or as a vector of colours. For factors, colors should be given as a vector of colours, e.g. c("blue","red").
spNames	a vector of species names to be added to the ordination diagram
...	other parameters passed to the function.

Examples

# Construct an ordination biplot using two chosen latent factors from a previously fitted HMSC model
etaPost = getPostEstimate(TD$m, "Eta")
lambdaPost=getPostEstimate(TD$m, "Lambda")
biPlot(TD$m, etaPost = etaPost, lambdaPost=lambdaPost, factors=c(1,2))

Hmsc documentation built on Aug. 11, 2022, 5:11 p.m.