Problem

The plot.sivs() function was excluding the top 2 most important features from the Recursive Feature Elimination (RFE) plot. This happened because:

1. In the RFE step (sivs.R), the algorithm intentionally skips testing the top 2 features since they are considered too important to remove
2. The plotting function (plot.sivs.R) was removing these same features to match the RFE data structure using tmp.vimp <- head(x = tmp.vimp, n = -2)

This meant users couldn't see the complete picture of all features with positive Variable Importance (VIMP) scores.

Solution

Modified the plotting logic to include ALL features with positive VIMP scores:

Key Changes

1. Removed feature exclusion: Eliminated the line that removed the top 2 features
2. Added placeholder data handling: For features not tested in RFE (typically the top 2), added empty numeric vectors as placeholders
3. Fixed data alignment: Ensured tmp.rfe and tmp.vimp arrays are properly aligned for plotting
4. Updated feature count labels: Corrected the top axis labels to reflect the actual number of features shown

Code Example

Before (only showed features tested in RFE):

tmp.vimp <- head(x = tmp.vimp, n = -2)  # Excluded top 2 features

After (shows all features):

# Add placeholder entries for features not tested in RFE
missing_features <- vimp_names[!vimp_names %in% rfe_names]
for(feature_name in missing_features) {
    tmp.rfe[[feature_name]] <- numeric(0)
}
tmp.rfe <- tmp.rfe[vimp_names]  # Reorder to match VIMP order

Impact

• Users now see ALL features with positive VIMP scores in the RFE plot
• The plot provides a complete view of feature importance, including the most critical features
• Maintains backward compatibility with existing functionality
• Features not tested in RFE are clearly distinguished in the visualization

Testing

Verified the changes work correctly through comprehensive testing:

• Syntax validation passed
• Logic tests confirmed all features are included
• Mock data tests verified proper handling of missing RFE data

The fix ensures that the RFE plot now shows the complete feature landscape as requested.

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