biPlot function

biPlot

Constructs an ordination biplot based on the fitted model

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))