Supplementary Materials

This directory contains supplementary materials and supporting information.

Usage

From project root:

# Basic compilation
./scripts/shell/compile_supplementary.sh

# Skip figures
./scripts/shell/compile_supplementary.sh --no_figs

# Quiet mode
./scripts/shell/compile_supplementary.sh --quiet

# Draft mode
./scripts/shell/compile_supplementary.sh --draft

Directory Structure

02_supplementary/
├── base.tex                  # Main supplementary LaTeX document
├── contents/
│   ├── figures/
│   │   ├── caption_and_media/   # Supplementary figures
│   │   └── captions/            # Figure captions
│   ├── tables/
│   │   ├── caption_and_media/   # Supplementary tables
│   │   └── captions/            # Table captions
│   ├── latex_styles/            # LaTeX formatting (00_shared)
│   └── supplementary_*.tex     # Supplementary sections
├── archive/                    # Version history
├── logs/                       # Compilation logs
└── docs/                       # Documentation

Output Files

After successful compilation:
- supplementary.pdf - Compiled supplementary materials
- supplementary.tex - Processed LaTeX source
- supplementary_diff.pdf - PDF with tracked changes
- supplementary_diff.tex - LaTeX with change tracking

Adding Supplementary Figures

Place files in contents/figures/caption_and_media/
Use naming: Supplementary_.XX_description.ext
XX: Two-digit number (01, 02, ...)
Common extensions: png, jpg, tif, svg, mmd

Example: Supplementary_.01_additional_analysis.png

Adding Supplementary Tables

Place files in contents/tables/caption_and_media/
Use naming: Supplementary_.XX_description.tex

Compilation Options

-nf, --no_figs - Skip figure processing
-nt, --no_tables - Skip table processing
-nd, --no_diff - Skip diff generation
-d, --draft - Single-pass compilation
-dm, --dark_mode - Black background, white text
-p2t, --ppt2tif - Convert PowerPoint to TIF (WSL)
-c, --crop_tif - Auto-crop TIF images
-q, --quiet - Suppress detailed output
--force - Force full recompilation
-h, --help - Show help

Notes

Shares bibliography and LaTeX styles with main manuscript
Word counting and diff generation enabled

# Supplementary Materials
This directory contains supplementary materials and supporting information.
## Usage
From project root:
```bash
# Basic compilation
./scripts/shell/compile_supplementary.sh
# Skip figures
./scripts/shell/compile_supplementary.sh --no_figs
# Quiet mode
./scripts/shell/compile_supplementary.sh --quiet
# Draft mode
./scripts/shell/compile_supplementary.sh --draft
```
## Directory Structure
```
02_supplementary/
├── base.tex                  # Main supplementary LaTeX document
├── contents/
│   ├── figures/
│   │   ├── caption_and_media/   # Supplementary figures
│   │   └── captions/            # Figure captions
│   ├── tables/
│   │   ├── caption_and_media/   # Supplementary tables
│   │   └── captions/            # Table captions
│   ├── latex_styles/            # LaTeX formatting (00_shared)
│   └── supplementary_*.tex     # Supplementary sections
├── archive/                    # Version history
├── logs/                       # Compilation logs
└── docs/                       # Documentation
```
## Output Files
After successful compilation:
- `supplementary.pdf` - Compiled supplementary materials
- `supplementary.tex` - Processed LaTeX source
- `supplementary_diff.pdf` - PDF with tracked changes
- `supplementary_diff.tex` - LaTeX with change tracking
## Adding Supplementary Figures
1. Place files in `contents/figures/caption_and_media/`
2. Use naming: `Supplementary_.XX_description.ext`
   - XX: Two-digit number (01, 02, ...)
   - Common extensions: png, jpg, tif, svg, mmd
Example: `Supplementary_.01_additional_analysis.png`
## Adding Supplementary Tables
1. Place files in `contents/tables/caption_and_media/`
2. Use naming: `Supplementary_.XX_description.tex`
## Compilation Options
- `-nf, --no_figs` - Skip figure processing
- `-nt, --no_tables` - Skip table processing
- `-nd, --no_diff` - Skip diff generation
- `-d, --draft` - Single-pass compilation
- `-dm, --dark_mode` - Black background, white text
- `-p2t, --ppt2tif` - Convert PowerPoint to TIF (WSL)
- `-c, --crop_tif` - Auto-crop TIF images
- `-q, --quiet` - Suppress detailed output
- `--force` - Force full recompilation
- `-h, --help` - Show help
## Notes
- Shares bibliography and LaTeX styles with main manuscript
- Word counting and diff generation enabled
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