serosv

1.3.0

Model Infectious Disease Parameters from Serosurveys

0packages depend

3.6Kdownloads / year

60.2%test coverage

13/13checks pass

Overview

About

Maintained by Anh Phan Truong QuynhFirst published 2024-10-074 releasesCRAN page ↗GitHub ↗

An easy-to-use and efficient tool to estimate infectious diseases parameters using serological data. Implemented models include SIR models (basic_sir_model(), static_sir_model(), mseir_model(), sir_subpops_model()), parametric models (polynomial_model(), fp_model()), nonparametric models (lp_model()), semiparametric models (penalized_splines_model()), hierarchical models (hierarchical_bayesian_model()). The package is based on the book "Modeling Infectious Disease Parameters Based on Serological and Social Contact Data: A Modern Statistical Perspective" (Hens, Niel & Shkedy, Ziv & Aerts, Marc & Faes, Christel & Damme, Pierre & Beutels, Philippe., 2013) doi:10.1007/978-1-4614-4072-7.

Install

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

install.packages("serosv", 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("OUCRU-Modelling/serosv")

Development version from OUCRU-Modelling/serosv. 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-serosv

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-serosv

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-serosv

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

Health

CRAN checks

13OK

Slowest check: 22.9 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.11

60.2%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-07-29
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-27
12 OK · 0 NOTE · 0 WARNING · 1 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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 5 earlier snapshots

NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-08
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-07
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 247 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 96%
Documented parameters: 98%
Return-value docs: 87%
References docs: 13%

Downloads

3.6K

CRAN downloads in the past year

Rank #7,079 · ~10/day · ~303/mo

Releases R versions

Daily download trend is not available in this view yet.

36530 days

1.4K90 days

3.6K1 year

Compare downloads with other packages →

Also on435 r2u2 autocran

Repository

GitHub ↗ oucru-modelling/serosv

0Stars

1Forks

7Open issues

0Open PRs

3Releases

165Commits

6Contributors

165 commits · Last activity 2026-07-28

Forks over time

2025-03-16 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

8 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/oucru-modelling/serosv on 2026-07-30.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (2)

renvdata-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (2)

Codecov.covrignore

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

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (23)

dplyr tidyr janitor ggplot2 locfit purrr stringr magrittrmethodsmgcvmixdist scam mvtnorm patchwork assertthat Rcpp RcppParallel rstan rstantoolsbootpROCstats4rlang

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.18.0)

Suggests (5)

covr knitr rmarkdown bookdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Anh Phan Truong Quynh

Author, Maintainer

Authors (6)

Anh Phan Truong Quynh

Author, Maintainer

Author

Author

Author

Author

Nguyen Pham Nguyen The

Author

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
1.3.0Latest
2026-04-07 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.0
2025-04-09 · diff ↗
1.0.1
2024-10-18 · diff ↗
1.0.0
2024-10-07
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-10-07
Total releases: 4 / 2 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 89 KB / 17 files
Download size: 2.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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