R Observatory: Metrics for imuGAP version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

imuGAP

0.2.0Package record

Immunity: Geographic and Age-Based Projection

0packages depend

1.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Carl PearsonCRAN page ↗GitHub ↗Website ↗Issues ↗

Fits Bayesian hierarchical models of vaccine coverage by location, birth cohort, and age. Observations of vaccination status (which may span cohorts, ages, and doses) are used to fit a latent survival-style process model that decomposes coverage into a lifetime propensity to vaccinate and a time-varying force of vaccination. Hierarchical spatial structure (e.g., state, county, school) supports partial pooling via random effects. Models are implemented in 'Stan' and fit via 'rstan'. Provides helpers to validate user-supplied input data, and to predict coverage from fitted models.

Changes in 0.2.0

Major Features

**Arbitrary Hierarchy Layer Depth**:
sampling(), canonicalize_locations(), and underlying Stan models now support user-defined hierarchical location structures of arbitrary depth (e.g. 1-layer statewide, 2-layer state-county, 3-layer state-county-school, or deeper regional partitions).
Added assemble_layer_data() helper to construct and validate hierarchical metadata, bounds, and parent mappings.
Added dedicated single-layer model impute_school_coverage_process_v6_single_layer with automatic dispatch when single-layer inputs are supplied.
Added a new vignette (user_specified_layers) demonstrating 1-layer, 2-layer, and 3-layer model estimation and prediction workflows.
**Backend Abstraction via flexstanr**:
Integrated flexstanr (>= 0.2.0) to provide uniform backend abstraction across rstan and cmdstanr MCMC engines.
Re-exported flexstanr::stan_options() for seamless sampler configuration.
**Modular Stan Architecture**:
Refactored top-level Stan models into concise assembly skeletons utilizing modular #include directives (functions/, data/, transformed_data/, parameters/, model/).
Pruned legacy/vestigial Stan scripts to streamline code base maintenance.

Show all changes in 0.2.0Hide the rest of the changes in 0.2.0

**Data Pipeline & Target Generation**:
Split target generation into fit-free constructor create_target() and validation function canonicalize_target().
Added bundled example fitted datasets for single-layer and 2-layer models (fit_sim_1layer, fit_sim_2layer, predict_sim_1layer, predict_sim_2layer, target_sim_1layer, target_sim_2layer).

Enhancements & Bug Fixes

**Location Hierarchy Invariant**: Enforced structural validation ensuring location nodes have either 0 offspring (leaf) or $\ge 2$ offspring (preventing single-child degenerate chains).
**Error Handling & Assertions**: Standardized assertion messages across all functions using module-level ERR_* format string constants and helper assertion functions stop_fmt_if() and warn_fmt_if().
**Validation**: Added validation against NA weights in population and target specifications.
**Documentation Examples & Check Times**: Applied combined @examplesIf interactive() and \donttest{} idiom to computationally heavy examples, enabling fast pkgdown builds (~35 seconds) while remaining CRAN --as-cran compliant.
**Vignette Dark Mode Compatibility**: Enforced solid white backgrounds and high-contrast styling across all vignette plots for clean rendering in light/dark modes.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("imuGAP", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ACCIDDA/imuGAP")

Development version from ACCIDDA/imuGAP. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-imugap

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-imuGAP

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-imuGAP

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 14.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-29
ERROR12 OK, 1 ERROR2026-07-27
OK6 OK2026-06-23

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.0

READMEYes · 136 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.2.0Citation fileYes · software entry onlyWebsiteYes · pkgdown

Help pages: 30 (5 internal)includes a package overview page
Examples that run: 80%8 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 75%
Documented parameters: 100%
Return-value docs: 88%
Help pages citing references: 3%

Vignettes (2)

How these are measured

Downloads

1.6K

CRAN downloads in the past year

Rank #10,353 · ~4/day · ~131/mo

Releases R versions

Daily download trend is not available in this view yet.

29330 days

99790 days

1.6K1 year

Compare downloads with other packages →

Also on87 r2u1 autocran

How downloads are counted

Repository

accidda/imugap ↗Organization: ACCIDDA

2Stars

1Forks

14Open issues

2Open PRs

1Releases

282Commits

7Commit identities

282 commits · Last activity 2026-10-17 · Default branch at 0.3.0, ahead of CRAN 0.2.0 (checked 2026-10-22) · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 93%
Median days to close, 50 most recently updated closed issues: 5
Median days to close, 50 most recently updated closed PRs: 1

Issues over time

2026-07-14 · 92026-10-03 · 14

How these are measured

PracticesBeta

15 development-tooling and community-health practices detected across 8 families in the upstream repository

Checks run against github.com/accidda/imugap on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (2)

Contributing guideIssue templates

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-17 · The repository has a site deploy workflow

pkgdown site last built 2026-10-17

Coverage (2)

Coverage reporting (Codecov).covrignore

Show all practicesHide 4 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Research and citation (1)

CITATION.cff

Lint, format, editor (3)

lintrLint workflowAir

How this is detected·Detection ruleset v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-04-18
Named in .Rbuildignore: .claude
Commits: at least 1 crediting it in the message
Cursorfirst seen 2026-09-01
Named in .Rbuildignore: .cursor, .cursorrules

Shared conventions any agent may read, so they name no particular tool.

Seen in the repository: AGENTS.md

From outside contributors

Claude Code
Pull requests: 2 from outside contributors, first on 2026-03-01

Models named in its commits

Claude Opus 4.61 commit · Apr 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

25 external dependencies (excludes base and recommended)

Installing imuGAP adds 51 packages (24 with compiled code, 50 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.1.0

Imports (7)

data.table flexstanrmethodsRcpp RcppParallel rstan rstantools (>= 2.6.0)

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.32)

Suggests (13)

knitr rmarkdown testthat roxygen2 roxyglobals lintr spelling bayesplot ggplot2 withr pkgload thematic usethis

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (6)

Carl Pearson

Author, Maintainer since 0.1.0 (2026)

Author

Contributor

Contributor

Contributor

Contributor

Releases (2)

Pick two releases to compare their code metrics.

0.2.0Latest
record
2026-09-02 · current release · diff ↗ ·
added 2 exports
canonicalize_target, create_observation_populations
0.1.0
record
2026-06-22
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-22
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 2.4 MB / 13 files
Download size: 3.5 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("imuGAP")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.5281/zenodo.20562250.

The repository also keeps a CITATION.cff.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for imuGAP version 0.2.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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