DESA

1.0.0

Detecting Epidemics using School Absenteeism

0packages depend

6.4Kdownloads / year

–test coverage

13/13checks 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")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

pak::pak("vjoshy/DESA")

Development version from vjoshy/DESA. Requires the pak package.

Release

# one-time r2u setup for Ubuntu (noble)

curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash

# then install

sudo apt install r-cran-desa

Fast Ubuntu binaries via r2u (no compilation). Run the setup once per machine.

bspm (used by r2u) also needs make: sudo apt install make

sudo dnf copr enable iucar/cran

sudo dnf install R-CRAN-DESA

RPMs from the iucar/cran COPR, rebuilt from CRAN.

sudo zypper install R-DESA

RPMs auto-built from CRAN on openSUSE OBS.

Health

CRAN checks

13OK

Code health

Yes

Tests · ratio 0.14

not tracked

Coverage

100%

Documentation · exports

None

Vignettes

Yes

README

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

6.4K

CRAN downloads in the past year

Rank #6,848 · ~17/day · ~531/mo

52730 days

1.6K90 days

6.4K1 year

Also on100 r2u10 autocran

Source & community

GitHub ↗

Repository stars, issues, and contributor activity are not tracked yet.

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

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code

3,591Lines of code

13Exported functions

Code & tests

Open call graph →

Line coverage

–

Expression

–

Tests / Examples

–

Functions

30 13 exported

Complexity

5 avg / 42 max

Call network

30 nodes / 16 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (5)

Maintainer (1)

Vinay Joshy

Author, Maintainer, Copyright holder

Authors (4)

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

Release timeline

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

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

Package metadata

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