plotGamma function

plotGamma

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

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")