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Pull request overview
Adds a CLAUDE.md guide intended for Claude Code usage in this repository, documenting PKPDmap’s purpose, key entry points, common dev commands, and high-level architecture.
Changes:
- Introduces a repository guidance document (
CLAUDE.md) with devtools-based workflows for local development. - Documents the estimation methods supported by
get_map_estimates()and the main estimation pipeline components. - Summarizes key functions, parameter conventions, test layout, and CI behavior.
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| devtools::document() | ||
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| # Full R CMD check (as done in CI) | ||
| devtools::check("--no-manual --as-cran") |
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devtools::check("--no-manual --as-cran") passes both flags as a single argument string; R CMD check expects them as separate args, and this doesn’t match the CI workflow (which passes --no-manual and --as-cran separately). Update the example to pass a character vector of args so local checks behave like CI.
| devtools::check("--no-manual --as-cran") | |
| devtools::check(args = c("--no-manual", "--as-cran")) |
| # Full R CMD check (as done in CI) | ||
| devtools::check("--no-manual --as-cran") | ||
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| # Install PKPDsim dependency from GitHub (requires PAT_TOKEN) |
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The comment says installing from GitHub “requires PAT_TOKEN”, but remotes::install_github() uses the GITHUB_PAT environment variable (and in CI this is populated from the PAT_TOKEN secret). Reword this to avoid confusion for local dev (e.g., mention GITHUB_PAT for local installs and that CI maps it from secrets.PAT_TOKEN).
| # Install PKPDsim dependency from GitHub (requires PAT_TOKEN) | |
| # Install PKPDsim dependency from GitHub (requires GITHUB_PAT locally; in CI this comes from secrets.PAT_TOKEN) |
| ``` | ||
| get_map_estimates() | ||
| ├── check_inputs() # validate all inputs upfront | ||
| ├── parse_*()/ # ~10 parse_ functions normalize inputs |
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In the pipeline diagram, parse_*()/ includes a trailing /, which reads like a typo and is inconsistent with the other entries. Consider removing the slash to keep the diagram clean.
| ├── parse_*()/ # ~10 parse_ functions normalize inputs | |
| ├── parse_*() # ~10 parse_ functions normalize inputs |
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