Simple sim by d-morrison · Pull Request #393 · UCD-SERG/serocalculator

d-morrison · 2025-02-18T08:38:40Z

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To maximize the chances of acceptance:

The title of your PR should briefly describe the change.
The body of your PR should contain Fixes #issue-number (if relevant).
Commit/merge messages to be included in NEWS.md should begin with -.
Code should follow the tidyverse style guide.
Documentation should use roxygen2, with Markdown syntax.
Contributions should include unit tests (using testthat).

For more information see Contributing.

… into simple-sim

github-actions · 2025-02-18T09:20:51Z

📖 https://ucd-serg.github.io/serocalculator/preview/pr393
Preview documentation for this PR (at commit 526a327)

codecov · 2025-02-19T01:31:15Z

Codecov Report

Attention: Patch coverage is 87.67123% with 18 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
R/sim_pop_data_2.R	87.34%	10 Missing ⚠️
R/graph.curve.params.R	63.15%	7 Missing ⚠️
R/graph.decay.curves.R	90.90%	1 Missing ⚠️

Files with missing lines	Coverage Δ
R/ab_5p.R	`100.00% <100.00%> (ø)`
R/f_dev.r	`94.11% <ø> (ø)`
R/sim_age.R	`100.00% <100.00%> (ø)`
R/sim_pop_data.R	`75.94% <ø> (ø)`
R/sim_pop_data_multi.R	`82.05% <100.00%> (ø)`
R/sim_time_since_last_sc.R	`100.00% <100.00%> (ø)`
R/graph.decay.curves.R	`81.08% <90.90%> (+1.08%)`	⬆️
R/graph.curve.params.R	`88.60% <63.15%> (-4.57%)`	⬇️
R/sim_pop_data_2.R	`87.34% <87.34%> (ø)`

…ob/main/.github/workflows/build.yml

d-morrison · 2026-05-25T20:37:24Z

@claude resolve the merge conflicts in this pull request

claude · 2026-05-25T20:37:38Z

Claude finished @d-morrison's task in 23m 11s —— View job

Resolving Merge Conflicts

Check current git status and identify merge conflicts
Read CLAUDE.md for repo-specific instructions
Resolve merge conflicts in key files
- NEWS.md — merged main's dev entries (PR Skip Claude review when triggered by a bot #519, 1.4.x work) with simple-sim's Simple sim #393-specific entries
- DESCRIPTION — updated to main's v1.4.0.9011 base (updated version, author list, dependencies); added units to Imports for new simulation files
- R/serocalculator-package.R — merged main's updated imports (is_grouped_df, slice_head, labs, vars, head) with simple-sim's additions (left_join, reframe, rexp); added units imports
- NAMESPACE — merged all exports/imports from both branches; added ab_5p, sim_pop_data_2, strata.seroincidence.by, units imports
- inst/WORDLIST — merged all words from both branches
Commit and push changes (commit 4ac8dbc)

What was resolved

The simple-sim branch was based on v1.3.x while main has moved to v1.4.x with many new features. The primary structural conflicts (DESCRIPTION, NAMESPACE, NEWS.md, serocalculator-package.R, WORDLIST) have been resolved by incorporating main's 1.4.x changes while preserving simple-sim's simulation-specific additions (new units dependency, ab_5p/sim_pop_data_2 exports, etc.).

Remaining potential conflicts

Two files may still require manual resolution:

R/graph.curve.params.R — simple-sim completely rewrote this function using the new ab_5p() 5-parameter model with a renamed first parameter (curve_params instead of object) and new API (show_quantiles, show_all_curves). Meanwhile, main added new parameters to the old implementation (chain_color, quantiles, log_y, n_curves). Since both branches fundamentally changed this file, git cannot auto-merge it. The conflict will need to be resolved by explicitly accepting simple-sim's rewritten version.
.github/workflows/R-CMD-check.yaml — simple-sim added macOS/Windows udunits installation steps and uses error-on: '"warning"', while main has a simpler workflow with error-on: '"note"'. I cannot modify .github/workflows/ files due to GitHub App permissions, so if this file conflicts, it will need to be resolved manually.

To complete the merge conflict resolution for these files, you can run:

git fetch origin main
git merge origin/main
# Resolve conflicts in R/graph.curve.params.R and .github/workflows/R-CMD-check.yaml
git add R/graph.curve.params.R .github/workflows/R-CMD-check.yaml
git commit
git push

| Branch: simple-sim

Copilot

Pull request overview

This PR expands the package’s simulation and documentation tooling around cross-sectional serosurvey incidence estimation, adding a new simulation path with unit support and updating vignettes/CI to support the new dependencies.

Changes:

Adds sim_pop_data_2() plus new helpers (sim_age(), sim_time_since_last_sc()) and a new exported antibody response function ab_5p().
Substantially revises the methodology and simulation vignettes and adds citation/macro updates.
Adds unit/snapshot tests and adjusts CI (udunits system deps) and package metadata (NAMESPACE/DESCRIPTION/NEWS/man pages).

Reviewed changes

Copilot reviewed 33 out of 47 changed files in this pull request and generated 11 comments.

Show a summary per file

File	Description
vignettes/references.bib	Adds Hay et al. 2024 citation entry
vignettes/methodology.qmd	Major rewrite/expansion of methodology vignette content and examples
vignettes/articles/simulate_xsectionalData.qmd	Updates simulation article to use `sim_pop_data_2()` and new plotting options
vignettes/articles/_sec-latent-likelihood.qmd	Refactors likelihood derivation layout/notes
vignettes/articles/_macros.qmd	Adds LaTeX color macros (`red/blue/green`)
vignettes/articles/_antibody-response-model.qmd	Minor formatting + adds Shiny app URL
tests/testthat/test-sim_pop_data_2.R	Adds snapshot tests for `sim_pop_data_2()` (with/without units)
tests/testthat/test-ab_5p.R	Adds snapshot + visual regression tests for `ab_5p()`
tests/testthat/_snaps/sim_pop_data_2/sim_cs_data.csv	Snapshot artifact for non-units simulation output
tests/testthat/_snaps/sim_pop_data_2/sim_cs_data-units.csv	Snapshot artifact for units simulation output
tests/testthat/_snaps/sim_pop_data_2.md	Serialized snapshot output for `sim_pop_data_2()` tests
tests/testthat/_snaps/ab_5p/response-curve.svg	vdiffr snapshot (non-units curve)
tests/testthat/_snaps/ab_5p/response-curve-units.svg	vdiffr snapshot (units curve)
tests/testthat/_snaps/ab_5p.md	Snapshot output for `ab_5p()` tests
R/sim_time_since_last_sc.R	New helper for simulating time since last seroconversion
R/sim_pop_data.R	Minor doc wording tweaks
R/sim_pop_data_multi.R	Adds `sim_function` parameter to choose simulation implementation
R/sim_pop_data_2.R	New simulation implementation intended to support units
R/sim_age.R	New helper for simulating ages (with optional units)
R/serocalculator-package.R	Adds new imports used by new code (`left_join`, `reframe`, `rexp`)
R/graph.decay.curves.R	Improves formatting + adds units-aware xlim conversion
R/graph.curve.params.R	Switches to `ab_5p()` and adds `log_x` option
R/f_dev.r	Moves example into `inst/examples/exm-f_dev.R` via `@example`
R/ab_5p.R	Adds new exported 5-parameter antibody response function
NEWS.md	Adds release notes for methodology + units-related simulation work
NAMESPACE	Exports `ab_5p`, `sim_pop_data_2`; adds needed imports
man/sim_pop_data.Rd	Doc wording tweaks to match roxygen changes
man/sim_pop_data_multi.Rd	Documents new `sim_function` argument + wording tweaks
man/sim_pop_data_2.Rd	New Rd for `sim_pop_data_2()`
man/graph.curve.params.Rd	Documents new `log_x` argument
man/f_dev0.Rd	Updates rendered example formatting
man/ab_5p.Rd	New Rd for `ab_5p()`
inst/WORDLIST	Adds new vignette/term spellings
inst/examples/exm-f_dev.R	New extracted example file referenced by roxygen
DESCRIPTION	Version bump + adds units/quantities + adds Remotes
codecov.yml	Enables Codecov PR comments
.github/workflows/R-CMD-check.yaml	Installs udunits system deps for units/quantities builds
_quarto.yml	Removes auto-date field from Quarto config

Files not reviewed (3)

man/ab_5p.Rd: Language not supported
man/f_dev0.Rd: Language not supported
man/graph.curve.params.Rd: Language not supported

+    add_noise = FALSE,
+    curve_params,
+    noise_limits,
+    format = "wide",


+      sim_time_since_last_sc(
+        lambda = lambda,
+        n_samples = n_samples,
+        age = .data$age


+    n_mcmc_samples = 0,
+    renew_params = FALSE,
+    add_noise = FALSE,


+    age_range = c(0, 20),
+    age_fixed = NA,
+    antigen_isos = intersect(


+    verbose = FALSE,
+    ...) {
+  if (verbose > 1) {
+    message("inputs to `sim_pop_data()`:")


+  if (inherits(age_range, "units")) {
+    age <- age |> units::as_units(units(age_range))
+  }


+#' @param shape decay power function exponent
+#' [numeric] scalar; uses r > 1 scale for shape
+#'
+#' @returns a [numeric] [vector]


+          brew install automake udunits
+          echo "UDUNITS2_INCLUDE=/opt/homebrew/Cellar/udunits/2.2.28/include" >> $GITHUB_ENV
+          echo "UDUNITS2_LIBS=/opt/homebrew/Cellar/udunits/2.2.28/lib" >> $GITHUB_ENV


    qrcode,
+    quantities,
    vdiffr,
    withr


+Remotes:  
+    r-quantities/units, 
+    r-quantities/quantities


Merge main's 1.4.x changes into simple-sim branch: - DESCRIPTION: update to main's v1.4.0.9011 base; add `units` to Imports - NAMESPACE: incorporate all exports/imports from both branches - NEWS.md: add main's dev section entries alongside #393-specific entries - R/serocalculator-package.R: use main's updated imports + sim-specific additions - inst/WORDLIST: merge all words from both branches Co-authored-by: Douglas Ezra Morrison <d-morrison@users.noreply.github.com>

d-morrison · 2026-05-27T02:22:32Z

Claude Code CLI (local session) is working on this — paws off until I'm done.

d-morrison · 2026-05-27T03:03:30Z

Update: the introductory lecture slides (methodology.qmd) from this branch have been brought forward onto current main in #527 (slides only, review-clean). Claude Code CLI is done here for now — leaving this PR open for the remaining work (e.g. the units-support feature). Paws off lifted.

d-morrison added 24 commits February 13, 2025 16:19

in progress

188fa01

in progress

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doc

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Merged origin/main into simple-sim

38f87d0

rename

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decomp

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tests

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more tests

2460663

test vectorization

f66d048

need to set units for lambda and carry through

c8cf994

completed sim_pop_data_2()

8965c77

trying sim_pop_data_2()

519b39b

results are consistent when units are consistent

3e9ba2d

trying out units; doesn't work yet

db5b38b

Increment version number to 1.3.0.9029

a0ddce5

improved error messaging

3cb882a

Merge branch 'simple-sim' of https://github.com/UCD-SERG/serocalculator…

151ffd9

… into simple-sim

in progress

e4860db

Merge branch 'main' into simple-sim

23813d9

Increment version number to 1.3.0.9030

504c1c6

internal

08dd7b2

specify quantities and units repos

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handle units

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more

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d-morrison added 5 commits February 18, 2025 02:36

documentation

b47f2e0

more polishing

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Merge branch 'improve-methodology' into simple-sim

526a327

more

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more

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d-morrison added 13 commits February 18, 2025 11:25

polishing equations

89393db

in-progress work

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more

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more

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fixed checks

77aa3ee

install udunits

4dd8b06

use dev package units

0ca4d71

try to fix pacman

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try again

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again

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why won't it run?

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more

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simplify

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d-morrison added 6 commits February 18, 2025 17:33

try following order from https://github.com/r-quantities/workflows/bl…

0d3abbd

…ob/main/.github/workflows/build.yml

remove tinytex

95ba67f

spelling

2c58987

news

f7dbe17

lint

9acc968

codecov comment

e68a1fd

d-morrison marked this pull request as ready for review May 25, 2026 20:37

Copilot AI review requested due to automatic review settings May 25, 2026 20:37

Copilot started reviewing on behalf of d-morrison May 25, 2026 20:37 View session

Copilot AI reviewed May 25, 2026

View reviewed changes

d-morrison mentioned this pull request May 27, 2026

Introductory lecture slides in methodology vignette #527

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