Serocalculator Development

This skill helps you develop and maintain the serocalculator R package, which estimates infection rates from serological data. It follows UCD-SERG lab manual standards and automates common development workflows.

What This Skill Does

Prerequisites

The repository includes `.github/workflows/copilot-setup-steps.yml` which automatically configures your environment when you start working. If this workflow runs successfully, skip manual setup.

For manual setup: R >= 4.1.0 required with devtools, rcmdcheck, lintr, spelling, testthat packages.

Instructions

1. Initial Environment Setup

Before any development work:

```r

Install all package dependencies

devtools::install_dev_deps(dependencies = TRUE)

Verify environment

devtools::dev_sitrep()

Load package in development mode

devtools::load_all()

```

**CRITICAL**: Always run this step when starting work on a PR to avoid missing dependency issues.

2. Code Modification Workflow

When modifying R code:

1. **BEFORE changing any function**: Create value-based unit tests in `tests/testthat/` to lock in current behavior

- Use snapshot tests for complex outputs: `expect_snapshot_value()`

- Use direct comparisons for simple cases: `expect_equal()`

2. Make your code changes in `R/` directory

3. Update roxygen2 comments above functions (parameters, return values, examples)

4. **ALWAYS regenerate documentation** after changes:

```r

devtools::document()

```

5. If you modified README content, edit `README.Rmd` (never `README.md` directly), then:

```r

rmarkdown::render("README.Rmd")

```

3. Validation Checks

Run these checks in order before committing:

**Linting** (must pass before other checks):

```r

devtools::load_all() # REQUIRED before linting

lintr::lint_package()

```

Fix any issues. Key rules: use `|>` not `%>%`, snake_case naming, no trailing whitespace.

**Testing**:

```r

devtools::test()

```

All tests must pass. Add new tests for new functionality.

**Spelling**:

```r

spelling::spell_check_package()

```

Add legitimate terms to `inst/WORDLIST` if needed.

**Full Package Check**:

```r

devtools::check()

```

Must complete with 0 errors, 0 warnings, 0 notes (5-10 minutes).

4. Pre-PR Requirements

Before submitting a PR, ensure:

1. **Version increment**: Run `usethis::use_version()` to bump version in DESCRIPTION

2. **NEWS.md update**: Add bullet point under development version header describing your changes (or add `no-changelog` label if change doesn't warrant entry)

3. **Documentation sync**: Verify `man/` and `NAMESPACE` are up to date (should be if you ran `devtools::document()`)

4. All validation checks pass (see step 3)

5. CI Workflows

These workflows run automatically on PRs (all must pass for merge):

**PR Commands** (comment on PR to trigger):

6. Common Issues

**Documentation out of sync**: Run `devtools::document()` and commit changes

**Version not incremented**: Run `usethis::use_version()`

**Linting failures**: Check `.lintr` for custom rules. Common: wrong pipe operator, trailing whitespace

**Compilation errors**: Ensure C++ compiler installed (Rtools on Windows, Xcode tools on macOS, build-essential on Linux)

Key Principles

Package Details