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Investigate partial dependencies of a covariate for mrIML JSDMs (Joint Species Distribution Models)

Source: R/mrCovar.R
mrCovar.Rd

This function is a wrapper around mrFlashlight() that plots the covariate partial dependencies for a specified environmental/host variable. It also filters the taxa based on standard deviation thresholds.

Usage

mrCovar(mrIMLobj, var, sdthresh = 0.05, ...)

Arguments

mrIMLobj

A list object output by mrIMLpredicts().

var

The variable of interest for calculating the profile.

sdthresh

The standard deviation threshold for filtering taxa (default: 0.05).

...

Arguments passed to flashlight::light_profile()

Value

A list of figures:

  • $partial_dep_curves: The covariate partial dependence profiles for those models that meet the sdthresh requirement.

  • $partial_dep_avg: The average partial dependence profile for all models. All individual model partial dependence profiles are silhouetted in the background.

  • $partial_dep_diff: The distribution of the rates of change in probability for the specified variable (the derivatives of the PD curves). Useful to identify key threshold values in the variable.

Examples

mrIML_rf <-  mrIML::mrIML_bird_parasites_RF

covar_results <- mrIML_rf %>%
  mrCovar(var = "scale.prop.zos", sdthresh = 0.05)