Heatmaps for the beta and omega parameters of the Hmsc model

The mod_heatmap_beta() and mod_heatmap_omega() functions generate heatmaps using ggplot2 to visualise parameter estimates or posterior support values for species' environmental responses (beta parameters, which describes how species (Y) respond to various covariates (X); see Hmsc::plotBeta) and residual associations (omega parameter), respectively.

Usage

mod_heatmap_beta(
  path_model = NULL,
  support_level = 0.95,
  width = 25,
  height = 35
)

mod_heatmap_omega(
  path_model = NULL,
  support_level = 0.95,
  width = 26,
  height = 22.5
)

Arguments

path_model

Character. Path to the fitted Hmsc model object.

support_level

Numeric. The posterior support threshold for determining which values are considered significant in the heatmap. Defaults to 0.95, indicating 95% posterior support. Values above this threshold (or below 1 - threshold for negative associations) are considered significant and will be plotted (see Hmsc::plotBeta).

width, height

Integer. The width and height of the generated heatmaps in centimetres. Defaults to 26×22.5 for omega; 25×35 for beta.

Value

Both functions do not return a value but saves heatmap plots as JPEG files in the model_postprocessing/parameters_summary subdirectory.

Details

The functions exports three types of visualisations (see Hmsc::plotBeta):

• mean: posterior mean estimate,

• support: statistical support level, measured by the posterior probability for a positive or negative response,

• sign: indicates whether the response is positive, negative, or neither of these based on the chosen support_level.

For the omega parameter, the mod_heatmap_omega() function generates two JPEG files: signs and mean values. While for the beta parameter, the mod_heatmap_beta() function generates four JPEG files : support, signs, mean values (including and excluding the intercept).

Author

Ahmed El-Gabbas. The mod_heatmap_beta() function is adapted from Hmsc::plotBeta