plotBeta function

plotBeta

Plots heatmaps of parameter estimates or posterior support values of species' environmental responses, i.e. how species in Y responds to covariates in X

plotBeta(
  hM,
  post,
  param = "Support",
  plotTree = FALSE,
  SpeciesOrder = "Original",
  SpVector = NULL,
  covOrder = "Original",
  covVector = NULL,
  spNamesNumbers = c(TRUE, TRUE),
  covNamesNumbers = c(TRUE, TRUE),
  supportLevel = 0.9,
  split = 0.3,
  cex = c(0.7, 0.7, 0.8),
  colors = colorRampPalette(c("blue", "white", "red")),
  colorLevels = NULL,
  mar = NULL,
  marTree = c(6, 0, 2, 0),
  mgp = c(3, 2, 0),
  main = NULL,
  smallplot = NULL,
  bigplot = NULL,
  newplot = TRUE
)

Arguments

• hM: a fitted Hmsc model object
• post: posterior summary of Beta parameters obtained from getPostEstimate
• param: controls which parameter is plotted, current options include "Mean" for posterior mean estimate, "Support" for the level of statistical support measured by posterior probability for a positive or negative response, and "Sign" to indicate whether the response is positive, negative, or neither of these given the chosen supportLevel
• plotTree: logical. Whether species' environmental responses is to be mapped onto the phylogeny used in model fitting
• SpeciesOrder: controls the ordering of species, current options are "Original", "Tree", and "Vector". If SpeciesOrder = "Vector", an ordering vector must be provided (see SpVector). If plotTree = TRUE, SpeciesOrder is ignored
• SpVector: controls the ordering of species if SpeciesOrder = "Vector". If a subset of species are listed, only those will be plotted. For alphabetic ordering, try match(1:hM$ns, as.numeric(as.factor(colnames(hM$Y))))
• covOrder: controls the ordering of covariates, current options are "Original" and "Vector". If covOrder = "Vector", an ordering vector must be provided (see covVector)
• covVector: controls the ordering of covariates if covOrder = "Vector". If a subset of covariates are listed, only those will be plotted
• spNamesNumbers: logical of length 2, where first entry controls whether species names are added to axes, and second entry controls whether species numbers are added
• covNamesNumbers: logical of length 2, where first entry controls whether covariate names are added to axes, and second entry controls whether covariate numbers are added
• supportLevel: controls threshold posterior support for plotting
• split: if plotTree = TRUE, controls the division of the plotting window between the tree and the heatmap.
• cex: controls character expansion (font size). Three values, controlling covariate names, species names, and color legend axis labels
• colors: controls the colors of the heatmap, default value colorRampPalette(c("blue","white","red"))
• colorLevels: number of color levels used in the heatmap
• mar: plotting margins
• marTree: plotting margins for phylogenetic tree
• mgp: can be used to set the location of the scale bar
• main: main title for the plot.
• smallplot: passed to image.plot
• bigplot: passed to image.plot
• newplot: set to false if the plot will be part of multi-panel plot initialized with par(mfrow)

Examples

# Plot posterior support values of species' environmental responses
betaPost=getPostEstimate(TD$m, "Beta")
plotBeta(TD$m, post=betaPost, param="Support")

# Plot parameter estimates of species' environmental responses together with the phylogenetic tree
betaPost=getPostEstimate(TD$m, "Beta")
plotBeta(TD$m, post=betaPost, param="Mean", plotTree=TRUE)