Merge pull request #7 from PennLINC/add_qc_classifier

Post-replication fixes

Author: smeisler

reproducibility_guide/12_supplement.md

@@ -1,6 +1,6 @@
 # Supplemental Figures And Analyses
 
-This chapter documents the scripts and notebooks in `scripts/8_supplement` used to generate supplemental figures (S2-S16) and supporting supplementary tables.
+This chapter documents the scripts and notebooks in `scripts/8_supplement` used to generate supplemental figures (S2-S18) and supporting supplementary tables.
 
 ```{important}
 Many supplemental analyses require the **full modeling run** across all configured microstructural metrics and quality covariates.  
@@ -20,7 +20,7 @@ Before running supplement notebooks, make sure you have completed:
 - Assembled quality effects:
   - `data/quality_effects/quality_effects_all_outputs.rds`
 
-In practice, this usually means running the modeling scripts in Chapter 8 without limiting to the main-text subset arrays.
+In practice, this usually means running the modeling scripts in Chapter 9 without limiting to the main-text subset arrays.
 
 ## Running supplement notebooks
 
@@ -39,7 +39,7 @@ Or execute from CLI:
 
 ```bash
 cd "${PROJECT_ROOT}/scripts/8_supplement"
-for nb in FigureS2_S6.ipynb FigureS7_S9.ipynb FigureS10.ipynb FigureS11.ipynb FigureS12.ipynb FigureS13.ipynb FigureS14.ipynb FigureS15.ipynb FigureS16.ipynb; do
+for nb in FigureS2_S6.ipynb FigureS7_S9.ipynb FigureS10.ipynb FigureS11.ipynb FigureS12.ipynb FigureS13.ipynb FigureS14.ipynb FigureS15.ipynb FigureS16.ipynb FigureS17.ipynb FigureS18.ipynb; do
   "${PY_ENV}/bin/jupyter" nbconvert --to notebook --execute --inplace "$nb"
 done
 ```
@@ -55,10 +55,10 @@ Outputs are written to `${PROJECT_ROOT}/figures/Supplement/FigureS*/`.
 - `FigureS12.ipynb`: cross-vendor correspondence of bundlewise age effects, pre/post harmonization, across all configured microstructural metrics.
 - `FigureS13.ipynb`: cross-metric age-effect correlation heatmap across all configured microstructural metrics.
 - `FigureS14.ipynb`: winner-take-all maximum quality-effect heatmap across all configured microstructural metrics and bundles.
-- `FigureS15.ipynb`: IQM covariance/correlation heatmap from harmonized data.
-- `FigureS16.ipynb`: FA/MD software comparison panels for batch, age, and quality effects.
-
-`FigureS14_old.ipynb` and `FigureS15_old.ipynb` are legacy versions retained in the directory and are not part of the current supplemental figure workflow.
+- `FigureS15.ipynb`: full-dataset supplemental version of Figure 7 (batch mediation/sensitivity grid), with row-2 age-by-IQM scatters colored by scanner vendor and software version encoded as marker shape.
+- `FigureS16.ipynb`: IQM covariance/correlation heatmap from harmonized data.
+- `FigureS17.ipynb`: FA/MD software comparison panels for batch, age, and quality effects.
+- `FigureS18.ipynb`: supplementary panel combining vendor-stratified manual-vs-predicted scatter relationships with SHAP summary.
 
 ## Supplementary tables in `scripts/8_supplement`
 

reproducibility_guide/7_replication_setup.md

@@ -70,21 +70,36 @@ A computational environment must have the following packages (and dependencies):
 ```
 install.packages(c(
   "arrow",
+  "cowplot",
   "dplyr",
+  "forcats",
   "fs",
   "gamm4",
+  "ggpattern",
   "ggplot2",
+  "grid",
+  "hexbin",
   "IRkernel",
   "jsonlite",
+  "knitr",
   "lme4",
   "mgcv",
+  "nlme",
+  "patchwork",
   "purrr",
   "readr",
   "remotes",
+  "scales",
+  "showtext",
   "stringr",
+  "sysfonts",
   "systemfonts",
   "tibble",
-  "tidyr"
+  "tidyr",
+  "tidyselect",
+  "tidyverse",
+  "tools",
+  "viridis"
 ))
 ```
 
@@ -134,4 +149,3 @@ To make that fallback reliable, launch Jupyter from the project root:
 cd "${PROJECT_ROOT}"
 "${PY_ENV}/bin/jupyter" lab
 ```
-

scripts/1_munge_data/munge_data.R

@@ -97,20 +97,28 @@ final_output_file <- fs::path(output_dir, "merged_data.parquet")
 # AutoTrack bundle geometry metrics to extract from bundlestats files
 shape_metrics <- c(
   "bundle_name",
+  "number_of_tracts",
+  "mean_length_mm",
+  "span_mm",
+  "curl",
+  "elongation",
+  "total_volume_mm3",
   "1st_quarter_volume_mm3",
   "2nd_and_3rd_quarter_volume_mm3",
   "4th_quarter_volume_mm3",
+  "total_surface_area_mm2",
+  "total_radius_of_end_regions_mm",
+  "total_area_of_end_regions_mm2",
+  "irregularity",
   "area_of_end_region_1_mm2",
+  "radius_of_end_region_1_mm",
+  "volume_of_end_branches_1",
   "area_of_end_region_2_mm2",
-  "curl",
-  "elongation",
-  "irregularity",
-  "mean_length_mm",
-  "number_of_tracts",
-  "span_mm",
-  "total_volume_mm3"
+  "radius_of_end_region_2_mm",
+  "volume_of_end_branches_2"
 )
 
+
 # Scanner QC columns that should be treated as numeric
 qc_numeric_cols <- c(
   "raw_dimension_x", "raw_dimension_y", "raw_dimension_z",