R Observatory: Metrics for serocalculator version 1.4.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

serocalculator

1.4.1

Estimating Infection Rates from Serological Data

1packages depend

17.3Kdownloads / year

83.8%test coverage

13/13checks pass

Overview

About

Maintained by Kristina LaiFirst published 2026-03-264 releasesCRAN page ↗GitHub ↗

Translates antibody levels measured in cross-sectional population samples into estimates of the frequency with which seroconversions (infections) occur in the sampled populations. Replaces the previous `seroincidence` package.

Install

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

install.packages("serocalculator", 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("UCD-SERG/serocalculator")

Development version from UCD-SERG/serocalculator. 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-serocalculator

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-serocalculator

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-serocalculator

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 6.2 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 4.20

83.8%

Coverage · measured lines

100%

Documentation · exports

23

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-03
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-05-30
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-26
8 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 644 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 69%
Documented parameters: 89%
Return-value docs: 79%
References docs: 0%

Downloads

17.3K

CRAN downloads in the past year

Rank #5,078 · ~48/day · ~1.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

33430 days

1.5K90 days

17.3K1 year

Compare downloads with other packages →

Also on420 r2u21 autocran

Repository

GitHub ↗ ucd-serg/serocalculator

7Stars

3Forks

125Open issues

27Open PRs

3Releases

3,374Commits

13Contributors

epidemiologyincidence-estimationrr-packagerstatsseroepidemiology

3,374 commits · Last activity 2026-08-10 · 0% stars, 30d

Stars over time

2025-03-05 · 62026-07-07 · 7

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/ucd-serg/serocalculator on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdrevdep/

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (3)

AirVS CodeRStudio project

Coverage (1)

Codecov

Governance and community (1)

Issue templates

Git structural (2)

.gitattributesSubmodules

How this is detected·Detection ruleset v1 (2026-07-18)

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: copilot on 2025-11-11

copilotclaudeagents-dirgemini

Most recent: gemini on 2026-07-20

Evidence

copilot: on 2025-11-11 · evidence A, D, PR · sole bot-author seen
claude: on 2026-05-08 · evidence A, B, D · sole bot-author seen
agents-dir: on 2026-07-20 · evidence D
agents-md: on 2026-07-20 · evidence D
gemini: on 2026-07-20 · evidence D

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

40 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (23)

cli doParallel dplyr foreach ggplot2 patchwork lifecycle magrittr Rcpp rlang rngtools scalesstatstibble tidyr tidyselectutilspurrr and glue stringrparallellabelled

LinkingTo (1)

Rcpp

Suggests (19)

bookdown DT fs ggbeeswarm knitr mixtools pak quarto rmarkdown spelling ssdtools testthat (>= 3.0.0)tidyverse qrcode vdiffr withr forcats rex readr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

serodynamics

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Kristina Lai

Author, Maintainer

Authors (5)

Kristina Lai

Author, Maintainer

Kristen Aiemjoy

Author

Douglas Ezra Morrison

Author

Chris Orwa

Author

Peter Teunis

Author, Copyright holder

Contributors (1)

Kwan Ho Lee

Contributor · added in 1.4.0

Copyright holders (1)

Peter Teunis

Author, Copyright holder

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.4.1Latest
2026-03-26 · current release · diff ↗
unarchivedReturned to CRAN
2026-03-25
archivedRemoved from CRAN
2026-01-16
issues were not addressed in time
1.4.0
2025-12-11 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.3.0
2025-01-25 · diff ↗
unarchivedReturned to CRAN
2025-01-25
archivedRemoved from CRAN
2024-11-26
policy violation On Internet access
1.0.3
2024-07-21
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2026-03-26
Total releases: 4 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 43 KB / 7 files
Download size: 3.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("serocalculator")

Format

Lai, K., Aiemjoy, K., Lee, K. H., Morrison, D. E., Orwa, C., & Teunis, P. (2026). serocalculator: Estimating Infection Rates from Serological Data (Version 1.4.1) [Computer software]. https://doi.org/10.32614/CRAN.package.serocalculator

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 serocalculator version 1.4.1 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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