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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]])
#> $scale.prop.zos
#>       X counts_ label_              type_     value label bootstrap    response
#> 1 -1.75     449  class partial dependence 0.1625835 class         1 Hzosteropis
#> 2 -1.25     449  class partial dependence 0.1625835 class         1 Hzosteropis
#> 3 -0.75     449  class partial dependence 0.5623608 class         1 Hzosteropis
#> 4 -0.25     449  class partial dependence 0.5298441 class         1 Hzosteropis
#> 5  0.25     449  class partial dependence 0.5458797 class         1 Hzosteropis
#> 6  0.75     449  class partial dependence 0.0247216 class         1 Hzosteropis
#> 7  1.25     449  class partial dependence 0.0247216 class         1 Hzosteropis
#> 8  1.75     449  class partial dependence 0.4048998 class         1 Hzosteropis
#> 9  2.25     449  class partial dependence 0.4048998 class         1 Hzosteropis
#> 
#> $Hkillangoi
#>   X counts_ label_              type_      value label bootstrap    response
#> 1 0     449  class partial dependence 0.22761693 class         1 Hzosteropis
#> 2 1     449  class partial dependence 0.04944321 class         1 Hzosteropis
#> 
#> $Plas
#>   X counts_ label_              type_     value label bootstrap    response
#> 1 0     449  class partial dependence 0.2394209 class         1 Hzosteropis
#> 2 1     449  class partial dependence 0.1209354 class         1 Hzosteropis
#> 
#> $Microfilaria
#>   X counts_ label_              type_     value label bootstrap    response
#> 1 0     449  class partial dependence 0.1302895 class         1 Hzosteropis
#> 2 1     449  class partial dependence 0.6171492 class         1 Hzosteropis
#> 
#> $scale.prop.zos
#>       X counts_ label_              type_     value label bootstrap    response
#> 1 -1.75     449  class partial dependence 0.2387528 class         2 Hzosteropis
#> 2 -1.25     449  class partial dependence 0.3182628 class         2 Hzosteropis
#> 3 -0.75     449  class partial dependence 0.4436526 class         2 Hzosteropis
#> 4 -0.25     449  class partial dependence 0.6420935 class         2 Hzosteropis
#> 5  0.25     449  class partial dependence 0.7093541 class         2 Hzosteropis
#> 6  0.75     449  class partial dependence 0.0935412 class         2 Hzosteropis
#> 7  1.25     449  class partial dependence 0.0935412 class         2 Hzosteropis
#> 8  1.75     449  class partial dependence 0.1757238 class         2 Hzosteropis
#> 9  2.25     449  class partial dependence 0.1757238 class         2 Hzosteropis
#> 
#> $Hkillangoi
#>   X counts_ label_              type_      value label bootstrap    response
#> 1 0     449  class partial dependence 0.28151448 class         2 Hzosteropis
#> 2 1     449  class partial dependence 0.04521158 class         2 Hzosteropis
#> 
mrIML_rf_PD[[2]]