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Bootstrap Partial Dependence Plots

Source: R/mrPdPlotBootstrap.R
mrPdPlotBootstrap.Rd

This function extracts and plots the bootrapped partial dependence functions calculated by mrBootstrap() for each response variable.

Usage

mrPdPlotBootstrap(
  mrIML_obj,
  mrBootstrap_obj,
  vi_obj = NULL,
  target,
  global_top_var = 2
)

Arguments

mrIML_obj

A list object returned by mrIMLpredicts().

mrBootstrap_obj

A list object returned by mrBootstrap().

vi_obj

A list object returned by mrVip(). If vi_obj is not provided, then it is created inside mrPD_bootstrap by running mrVip().

target

The target variable for generating plots.

global_top_var

The number of top variables to consider (default: 2).

Value

A list with two elements:

  • [[1]]: A data frame of the partial dependence grid for each response model, predictor variable, and bootstrap.

  • [[2]]: A list of partial dependence plots for each predictor variable in the target response model.

Examples

mrIML_rf <- mrIML::mrIML_bird_parasites_RF

mrIML_rf_boot <- mrIML_rf %>%
  mrBootstrap(num_bootstrap = 50)
#> 
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mrIML_rf_PD <- mrPdPlotBootstrap(
  mrIML_rf,
  mrIML_rf_boot,
  target = "Plas",
  global_top_var = 4
)

head(mrIML_rf_PD[[1]])
#>              var     X counts     value label               type bootstrap
#> 1 scale.prop.zos -1.75    449 0.1625835 class partial dependence         1
#> 2 scale.prop.zos -1.25    449 0.1625835 class partial dependence         1
#> 3 scale.prop.zos -0.75    449 0.5623608 class partial dependence         1
#> 4 scale.prop.zos -0.25    449 0.5298441 class partial dependence         1
#> 5 scale.prop.zos  0.25    449 0.5458797 class partial dependence         1
#> 6 scale.prop.zos  0.75    449 0.0247216 class partial dependence         1
#>      response
#> 1 Hzosteropis
#> 2 Hzosteropis
#> 3 Hzosteropis
#> 4 Hzosteropis
#> 5 Hzosteropis
#> 6 Hzosteropis
mrIML_rf_PD[[2]]