plotBeta: plotBeta

In Hmsc: Hierarchical Model of Species Communities

plotBeta

Description

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

Usage

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)

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