CLAUDE.md

In sbalci/ClinicoPathDescriptives: Descriptive Analysis Tools for Clinicopathological Research

CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

ClinicoPathDescriptives is a hybrid R package that serves as both a standalone R package and a jamovi module for descriptive analysis in clinicopathological research. It provides 11 analysis functions covering descriptive statistics, visualizations, and specialized medical research tools.

Architecture

Dual Architecture Pattern

Each analysis function follows a three-file pattern: - .b.R files: Business logic and implementation (e.g., tableone.b.R) - .h.R files: jamovi interface definitions (auto-generated, don't edit manually) - .a.yaml files: jamovi GUI configuration in jamovi/ directory

Key Directories

• R/: R source code with .b.R (implementation) and .h.R (interface) files
• jamovi/: YAML configurations for jamovi GUI (11 analysis modules)
• data/: Example datasets (histopathology.rda, treatmentResponse.rda)
• man/: Auto-generated documentation (via roxygen2)

Analysis Functions

• tableone: Generate "Table One" descriptive summaries
• summarydata: Continuous variable summaries
• reportcat: Categorical variable summaries
• crosstable: Cross-tabulations with statistical tests
• alluvial: Alluvial diagrams for categorical relationships
• agepyramid: Age pyramid visualizations
• benford: Benford's law analysis for data quality
• venn: Venn diagrams and UpSet plots
• vartree: Variable tree summaries
• waterfall: Treatment response analysis (RECIST criteria)
• swimmerplot: Patient timeline visualizations

Development Commands

Standard R Package Development

# Load package for testing
devtools::load_all()

# Generate documentation from roxygen2 comments
devtools::document()

# Run R CMD check
devtools::check()

# Build package
devtools::build()

# Build and install locally
devtools::install()

# Build vignettes
devtools::build_vignettes()

# Generate pkgdown website
pkgdown::build_site()

Dependencies

• Core: tidyverse packages (dplyr, ggplot2, tidyr)
• Clinical research: tableone, gtsummary, arsenal, finalfit
• jamovi integration: jmvcore
• Visualization: easyalluvial, ggvenn, DiagrammeR

Testing and Quality Assurance

No formal test suite exists. Testing is done through: - devtools::check() for R CMD check - Manual testing in jamovi GUI for module functionality - GitHub Actions CI/CD on multiple platforms

jamovi Development Notes

• jamovi YAML files in jamovi/ must be manually maintained
• Analysis options in YAML must match R function parameters exactly
• The 0000.yaml defines overall module structure and menu organization
• Test jamovi functionality requires jamovi installation and GUI testing

Website and Documentation

• pkgdown site: https://www.serdarbalci.com/ClinicoPathDescriptives/
• Main repository: https://github.com/sbalci/ClinicoPathDescriptives/
• Issue tracking: https://github.com/sbalci/ClinicoPathJamoviModule/issues/

sbalci/ClinicoPathDescriptives documentation built on July 4, 2025, 5:25 p.m.