# GRM Forests for Robust DIF Detection

# Introduction

GRM Forests extend GRM Trees by creating ensembles of trees to provide more robust variable importance measures. This vignette covers:

- GRM Forest implementation

- Variable importance and variable importance plot.

See the vignette on getting started with grmtree package for a more detailed walkthrough of the tree-based graded response theory model (GRMTree).

# Install and Load required packages

To implement the tree-based GRM (GRMTree), you will install the following packages if not previously installed.

    ## Install packages from CRAN repository
    install.packages(c("dplyr", "grmtree"))

Once installed, load the packages as follows:

    library(dplyr)        # For data manipulation
    library(grmtree)      # For tree-based GRM DIF Test

# Import and prepare the data

The data set used in this demonstration is a test/sample data for the package.

    ## Load the data
    data("grmtree_data", package = "grmtree")

    ## Take a glimpse at the data
    glimpse(grmtree_data)
    #> Rows: 3,500
    #> Columns: 17
    #> $ MOS_Listen        <chr> "5", "4", "5", "3", "5", "2", "5", "5", "2", "3", "3…
    #> $ MOS_Info          <chr> "5", "3", "5", "3", "5", "3", "5", "5", "2", "4", "3…
    #> $ MOS_Advice_Crisis <chr> "5", "3", "5", "3", "5", "5", "5", "5", "4", "4", "3…
    #> $ MOS_Confide       <chr> "5", "4", "4", "2", "4", "4", "5", "5", "2", "3", "3…
    #> $ MOS_Advice_Want   <chr> "5", "2", "4", "3", "4", "3", "5", "5", "4", "3", "3…
    #> $ MOS_Fears         <chr> "5", "2", "5", "4", "5", "4", "5", "5", "1", "2", "1…
    #> $ MOS_Personal      <chr> "5", "2", "5", "1", "5", "2", "5", "5", "4", "2", "3…
    #> $ MOS_Understand    <chr> "5", "2", "5", "1", "4", "3", "5", "5", "4", "2", "3…
    #> $ sex               <chr> "Male", "Male", "Male", "Male", "Male", "Female", "M…
    #> $ age               <dbl> 69, 66, 72, 52, 61, 57, 61, 71, 77, 65, 55, 64, 45, …
    #> $ residency         <chr> "urban", "urban", "urban", "urban", "urban", "rural"…
    #> $ depressed         <chr> "No", "No", "No", "Yes", "No", "No", "Yes", "No", "N…
    #> $ bmi               <dbl> 22.85714, 33.59375, 24.38272, 31.14187, 25.88057, 24…
    #> $ Education         <chr> "Primary/High school", "College/University", "Colleg…
    #> $ job               <chr> "Unemployed", "Unemployed", "Unemployed", "Unemploye…
    #> $ smoker            <chr> "No", "No", "Yes", "No", "No", "No", "Yes", "Yes", "…
    #> $ multimorbidity    <chr> "2+", "2+", "1", "1", "2+", "2+", "2+", "1", "2+", "…

    ## Prepare the data
    resp.data <- grmtree_data %>%
      mutate_at(vars(starts_with("MOS")), as.ordered) %>%
      mutate_at(vars(c(sex, residency, depressed,
                       Education, job, smoker,
                       multimorbidity)), as.factor)

    ## Explore the data
    head(resp.data)
    #> # A tibble: 6 × 17
    #>   MOS_Listen MOS_Info MOS_Advice_Crisis MOS_Confide MOS_Advice_Want MOS_Fears
    #>   <ord>      <ord>    <ord>             <ord>       <ord>           <ord>
    #> 1 5          5        5                 5           5               5
    #> 2 4          3        3                 4           2               2
    #> 3 5          5        5                 4           4               5
    #> 4 3          3        3                 2           3               4
    #> 5 5          5        5                 4           4               5
    #> 6 2          3        5                 4           3               4
    #> # ℹ 11 more variables: MOS_Personal <ord>, MOS_Understand <ord>, sex <fct>,
    #> #   age <dbl>, residency <fct>, depressed <fct>, bmi <dbl>, Education <fct>,
    #> #   job <fct>, smoker <fct>, multimorbidity <fct>

    ## Check the structure of the data
    glimpse(resp.data)
    #> Rows: 3,500
    #> Columns: 17
    #> $ MOS_Listen        <ord> 5, 4, 5, 3, 5, 2, 5, 5, 2, 3, 3, 4, 5, 2, 5, 3, 5, 4…
    #> $ MOS_Info          <ord> 5, 3, 5, 3, 5, 3, 5, 5, 2, 4, 3, 4, 5, 2, 4, 4, 4, 3…
    #> $ MOS_Advice_Crisis <ord> 5, 3, 5, 3, 5, 5, 5, 5, 4, 4, 3, 4, 2, 2, 4, 4, 4, 3…
    #> $ MOS_Confide       <ord> 5, 4, 4, 2, 4, 4, 5, 5, 2, 3, 3, 4, 5, 2, 5, 4, 5, 3…
    #> $ MOS_Advice_Want   <ord> 5, 2, 4, 3, 4, 3, 5, 5, 4, 3, 3, 4, 2, 2, 5, 4, 4, 2…
    #> $ MOS_Fears         <ord> 5, 2, 5, 4, 5, 4, 5, 5, 1, 2, 1, 4, 5, 2, 5, 4, 4, 4…
    #> $ MOS_Personal      <ord> 5, 2, 5, 1, 5, 2, 5, 5, 4, 2, 3, 4, 5, 2, 5, 4, 4, 3…
    #> $ MOS_Understand    <ord> 5, 2, 5, 1, 4, 3, 5, 5, 4, 2, 3, 4, 5, 2, 5, 4, 4, 3…
    #> $ sex               <fct> Male, Male, Male, Male, Male, Female, Male, Female, …
    #> $ age               <dbl> 69, 66, 72, 52, 61, 57, 61, 71, 77, 65, 55, 64, 45, …
    #> $ residency         <fct> urban, urban, urban, urban, urban, rural, urban, urb…
    #> $ depressed         <fct> No, No, No, Yes, No, No, Yes, No, No, No, Yes, No, N…
    #> $ bmi               <dbl> 22.85714, 33.59375, 24.38272, 31.14187, 25.88057, 24…
    #> $ Education         <fct> Primary/High school, College/University, College/Uni…
    #> $ job               <fct> Unemployed, Unemployed, Unemployed, Unemployed, Unem…
    #> $ smoker            <fct> No, No, Yes, No, No, No, Yes, Yes, No, No, No, Yes, …
    #> $ multimorbidity    <fct> 2+, 2+, 1, 1, 2+, 2+, 2+, 1, 2+, 2+, 2+, 2+, 1, 2+, …

    ## Create response as outcomes
    resp.data$resp <- data.matrix(resp.data[, 1:8])

# GRM Forests Implementation

## Define the forest control parameters

    ## Get help on the control parameter
    # ?grmforest.control

    ## GRMTree control parameters with Benjamini-Hochberg
    grm_control <- grmtree.control(
      minbucket = 350,
      p_adjust = "BH", alpha = 0.05)

    ## Define the forest control parameters
    forest_control <- grmforest.control(
      n_tree = 3, # Number of trees (Reduced for vignette build time)
      sampling = "bootstrap",  # Bootstrap method; resampling also available
      sample_fraction = 0.632,
      mtry = sqrt(9),  # Usually the square root of the number of covariates
      control = grm_control,
      remove_dead_trees = TRUE, # Remove any null GRMTree
      seed = 123
    )

## Grow the GRM Forest

    ## Fit the GRM forest
    mos_forest <- grmforest(
      resp ~ sex + age + bmi + Education +
      residency + depressed + job + multimorbidity + smoker,
      data = resp.data,
      control = forest_control
    )

    ## Get the summary of the fitted forest
    summary(mos_forest)
    print(mos_forest)

    ## Plot a tree in the forest
    plot(mos_forest$trees[[1]])

# Variable Importance

## Compute the variable importance of each covariate

    ## Calculate the variable importance
    importance <- varimp(mos_forest, seed = 123, verbose = T)

    ## Print the result of the variable importance
    print(importance)

Example output:

               age         smoker            bmi multimorbidity            sex
         403.07554      220.37908       39.02621       37.00120       32.06389
         Education      residency      depressed            job
           0.00000        0.00000        0.00000        0.00000

## Plot the variable importance of each variable

Here `plot.varimp` creates a bar plot of variable importance scores with options for both ggplot2 and base R graphics.

    ## Plot the variable importance scores (ggplot is the default)
    plot(importance)

    ## Plot onlt the top 5 importance variables
    plot(importance, xlab = "", top_n = 5)

    ## Plot the base R version
    plot(importance, use_ggplot = FALSE)

    ## Custom colors
    plot(importance, col = c("green", "red"))

    ## Rename the variable names in the order from the variable importance result
    names(importance) <- c("Age", "Smoking Status", "BMI",
                           "Multimorbidity", "Sex", "Education",
                           "Residency", "Depression", "Employment")

    ## Now create the plot with informative names
    plot(importance)

# Conclusion

GRM Forests provide more stable DIF detection by aggregating across many trees. Key advantages include robust variable importance measures, reduced overfitting, and better handling of complex interactions.