DESA

1.0.0

Detecting Epidemics using School Absenteeism

0packages depend

6.1Kdownloads / year

43.8%test coverage

12/13checks pass

Overview

About

Maintained by Vinay JoshyFirst published 2025-05-071 releasesCRAN page ↗GitHub ↗

Provides a comprehensive framework for early epidemic detection through school absenteeism surveillance. The package offers three core functionalities: (1) simulation of population structures, epidemic spread, and resulting school absenteeism patterns; (2) implementation of surveillance models that generate alerts for impending epidemics based on absenteeism data and (3) evaluation of alert timeliness and accuracy through alert time quality metrics to optimize model parameters. These tools enable public health officials and researchers to develop and assess early warning systems before implementation. Methods are based on research published in Vanderkruk et al. (2023) doi:10.1186/s12889-023-15747-z and Ward et al. (2019) doi:10.1186/s12889-019-7521-7.

Install

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

install.packages("DESA", 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("vjoshy/DESA")

Development version from vjoshy/DESA. 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-desa

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-DESA

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-DESA

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-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.14

43.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 565 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 0%

Downloads

6.1K

CRAN downloads in the past year

Rank #7,677 · ~17/day · ~510/mo

Releases R versions

Daily download trend is not available in this view yet.

19830 days

1.3K90 days

6.1K1 year

Compare downloads with other packages →

Also on103 r2u3 autocran

Repository

GitHub ↗ vjoshy/desa

2Stars

0Forks

1Open issues

0Open PRs

2Releases

129Commits

1Contributors

License GPL-3.0 · 129 commits · Last activity 2025-12-18 · 0% stars, 30d

Stars over time

2024-07-27 · 12026-07-07 · 2

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/vjoshy/desa on 2026-08-02.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (7)

dplyr purrr zoo ggplot2 gridExtra rlang scales

LinkingTo (0)

none

Suggests (8)

knitr rmarkdown cli fansi farver utf8 devtools testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Vinay Joshy

Author, Maintainer, Copyright holder

Authors (5)

Vinay Joshy

Author, Maintainer, Copyright holder

Lorna Deeth

Author, Copyright holder, Thesis advisor

Zeny Feng

Author, Copyright holder, Thesis advisor

Justin Slater

Author, Copyright holder, Thesis advisor

Kayla Vanderkruk

Author, Compiler, Contributor

Contributors (1)

Kayla Vanderkruk

Author, Compiler, Contributor

Vinay Joshy

Author, Maintainer, Copyright holder

Lorna Deeth

Author, Copyright holder, Thesis advisor

Zeny Feng

Author, Copyright holder, Thesis advisor

Justin Slater

Author, Copyright holder, Thesis advisor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-05-07
Total releases: 1 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Download size: 220 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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