CLAUDE.md

In sbalci/jsurvival: Survival Module of ClinicoPath for jamovi

CLAUDE.md

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

Project Overview

This is jsurvival, a jamovi module for survival analysis that is part of the ClinicoPath statistical analysis suite. It provides survival analysis functions with natural language summaries, Kaplan-Meier plots, Cox regression, and various survival-related calculations for medical research.

Development Commands

Package Development Workflow

# Documentation and building
devtools::document()          # Generate documentation from roxygen comments
devtools::check()            # Run R CMD check 
devtools::build()            # Build package
devtools::install()          # Install package locally

# Website documentation
pkgdown::build_site()        # Build documentation website locally

Testing

• No formal test suite currently exists
• To add testing: usethis::use_testthat() and usethis::use_test("function-name")

Architecture

jamovi Module Structure

• R functions: Located in /R/ with paired .h.R (header/options) and .b.R (body/implementation) files
• jamovi configuration: YAML files in /jamovi/ define module interface and menu structure
• Analysis types:
• singlearm: Single arm survival analysis
• survival: Univariate survival analysis with Cox regression
• survivalcont: Survival analysis for continuous variables with cut-offs
• multisurvival: Multivariable Cox regression
• oddsratio: Odds ratio calculations for binary outcomes
• timeinterval: Time interval calculations

Key Dependencies

• Core: jmvcore (jamovi framework), R6 (class system)
• Survival analysis: survival, survminer, finalfit, rms, KMunicate
• Data manipulation: dplyr, tidyr, purrr, janitor
• Visualization: ggplot2, scales

File Patterns

• Analysis functions: {name}.h.R (options/header) + {name}.b.R (implementation)
• jamovi config: {name}.a.yaml (analysis), {name}.r.yaml (results), {name}.u.yaml (UI)
• Documentation: Roxygen2 comments with markdown support

CI/CD and Automation

• GitHub Actions: Runs R CMD check on multiple platforms, skips "WIP" commits
• Documentation: Auto-deployed to https://www.serdarbalci.com/jsurvival/ via pkgdown
• Package checking: Multi-platform testing (macOS, Windows, Ubuntu)

Development Notes

• Uses devtools workflow with roxygen2 documentation
• No formal testing framework - consider adding testthat
• All exported functions should have proper roxygen documentation
• Follow existing code patterns for new analyses (header + body structure)
• Version managed in DESCRIPTION file (currently 0.0.3.21)

sbalci/jsurvival documentation built on July 4, 2025, 5:26 p.m.