serocalculator

1.4.1

Estimating Infection Rates from Serological Data

1packages depend

17Kdownloads / 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)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

# 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: 6.9 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 4.20

83.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

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
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

Show 2 earlier snapshots

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

17K

CRAN downloads in the past year

Rank #5,395 · ~47/day · ~1.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

41730 days

1.7K90 days

17K1 year

Compare downloads with other packages →

Also on442 r2u34 autocran

Repository

GitHub ↗ ucd-serg/serocalculator

7Stars

4Forks

117Open issues

27Open PRs

3Releases

3,255Commits

12Contributors

epidemiologyincidence-estimationrr-packagerstatsseroepidemiology

3,255 commits · Last activity 2026-07-28 · 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 2026-07-26.

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)

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

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: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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