add claude.md#58
Conversation
There was a problem hiding this comment.
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.
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
| devtools::document() | ||
|
|
||
| # Full R CMD check (as done in CI) | ||
| devtools::check("--no-manual --as-cran") |
There was a problem hiding this comment.
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") | ||
|
|
||
| # Install PKPDsim dependency from GitHub (requires PAT_TOKEN) |
There was a problem hiding this comment.
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 |
There was a problem hiding this comment.
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 |
jasmineirx
left a comment
jasmineirx
left a comment
There was a problem hiding this comment.
automated codereview brought up a valid point, otherwise lgtm
…2007) Replace the incorrect ad-hoc CWRES normalization with proper FOCE-based conditional weighted residuals. The Jacobian F = df/deta is computed via central finite differences and used to derive both CWRES and the FOCE variance-covariance matrix, replacing the more expensive numDeriv::hessian computation when residuals=TRUE. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
No description provided.