serodynamics

0.1.0

Modeling Longitudinal Antibody Responses to Infection

0packages depend

659downloads / year

40.1%test coverage

12/13checks pass

Overview

About

Maintained by Samuel SchildhauerFirst published 2026-06-021 releasesCRAN page ↗GitHub ↗

Implements Bayesian hierarchical models for estimating antibody kinetic parameters from longitudinal serological data. Fits two-phase within-host models capturing antibody rise, peak, and decay following pathogen infection, using 'JAGS' for posterior inference. Designed as the upstream companion to the 'serocalculator' package for end-to-end seroepidemiological analysis. Methods are described in Teunis and colleagues (2016) doi:10.1016/j.epidem.2016.04.001 and Teunis and van Eijkeren (2020) doi:10.1002/sim.8578.

Install

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

install.packages("serodynamics", 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/serodynamics")

Development version from UCD-SERG/serodynamics. 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-serodynamics

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-serodynamics

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-serodynamics

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

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 3.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 16.64

40.1%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

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
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 57 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 86%
Return-value docs: 94%
References docs: 0%

Downloads

659

CRAN downloads in the past year

Rank #16,191 · ~2/day · ~55/mo

Releases R versions

Daily download trend is not available in this view yet.

21030 days

65990 days

6591 year

Compare downloads with other packages →

Also on14 r2u

Repository

GitHub ↗ ucd-serg/serodynamics

3Stars

0Forks

58Open issues

23Open PRs

1Releases

2,200Commits

8Contributors

2,200 commits · Last activity 2026-08-02 · 0% stars, 30d

Stars over time

2025-02-08 · 12026-07-07 · 3

Repository practices

Upstream repositoryBeta

11 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/ucd-serg/serodynamics on 2026-07-31.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (2)

data-raw/Dev Container

CRAN release process (2)

cran-comments.mdrevdep/

Docs source (2)

README.RmdQuarto project

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

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 2025-10-02

copilotclaude

Most recent: claude on 2026-05-14

Evidence

copilot: on 2025-10-02 · evidence A, D · sole bot-author seen
claude: on or before 2026-05-14 · evidence A, B, D · sole bot-author seen

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

Dependencies

Declared dependencies

31 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (15)

cli coda dplyr ggmcmc ggplot2 purrr rlang runjags scales serocalculatorstatstibble tidyr tidyselectutils

LinkingTo (0)

none

Suggests (18)

Hmisc knitr readr rlist sessioninfo spelling stringr testthat tidyverse withr vdiffr fs here rjags rmarkdown magrittr rex quarto

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (5)

Maintainer (1)

Samuel Schildhauer

Author, Maintainer

Authors (5)

Samuel Schildhauer

Author, Maintainer

Kristen Aiemjoy

Author

Kwan Ho Lee

Author

Douglas Ezra Morrison

Author

Peter Teunis

Author, Copyright holder

Peter Teunis

Author, Copyright holder

Package Timeline

1 release. R releases are shown for context.

0.1.0Latest
2026-06-02 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-02
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 233 KB / 2 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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