plotGamma: plotGamma

In Hmsc: Hierarchical Model of Species Communities

plotGamma

Description

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

Usage

plotGamma(
  hM,
  post,
  param = "Support",
  trOrder = "Original",
  trVector = NULL,
  covOrder = "Original",
  covVector = NULL,
  trNamesNumbers = c(TRUE, TRUE),
  covNamesNumbers = c(TRUE, TRUE),
  supportLevel = 0.9,
  main = NULL,
  cex = c(0.8, 0.8, 0.8),
  colors = colorRampPalette(c("blue", "white", "red")),
  colorLevels = NULL,
  mar = c(6, 9, 2, 0),
  smallplot = NULL,
  bigplot = NULL,
  newplot = TRUE
)

Arguments

hM	a fitted Hmsc model object
post	posterior summary of Gamma 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
trOrder	controls the ordering of traits, current options are "Original", and "Vector". If trOrder = "Vector", an ordering vector must be provided (see trVector)
trVector	controls the ordering of traits if trOrder = "Vector". If a subset of traits are listed, only those will be plotted
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
trNamesNumbers	logical of length 2, where first entry controls whether trait names are added to axes, and second entry controls whether traits 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
main	main title for the plot
cex	controls character expansion (font size). Three values, controlling covariate names, trait 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
smallplot	passed to image.plot
bigplot	passed to image.plot
newplot	set to false if the plot will be part of multi-panel plot

Examples

# Plot posterior support values of trait effects on environmental responses
gammaPost=getPostEstimate(TD$m, "Gamma")
plotGamma(TD$m, post=gammaPost, param="Support")

# Plot parameter estimates of trait effects on environmental responses
gammaPost=getPostEstimate(TD$m, "Gamma")
plotGamma(TD$m, post=gammaPost, param="Mean")

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