R Observatory: Metrics for DSAIDE version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DSAIDE

1.0.0

Dynamical Systems Approach to Infectious Disease Epidemiology (Ecology/Evolution)

0packages depend

4.4Kdownloads / year

90.5%test coverage

13/13flavors OK

Overview

About

Maintained by Andreas HandelCRAN page ↗GitHub ↗Website ↗Issues ↗

Exploration of simulation models (apps) of various infectious disease transmission dynamics scenarios. The purpose of the package is to help individuals learn about infectious disease epidemiology (ecology/evolution) from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models.

Changes in 1.0.0

Small bug fixes.
Other minor updates and improvements.

From NEWS.md in the release

Install

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

install.packages("DSAIDE", 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("andreashandel/DSAIDE")

Development version from andreashandel/DSAIDE. 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-dsaide

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-DSAIDE

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-DSAIDE

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 5.8 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 33 (1 internal)includes a package overview page
Examples that run: 96%22 run in a plain check · 1 never run
Exported functions with examples: 77%
Documented parameters: 100%
Return-value docs: 97%
Help pages citing references: 12%

Vignettes (1)

DSAIDE Package Tutorial

How these are measured

Downloads

4.4K

CRAN downloads in the past year

Rank #7,601 · ~12/day · ~370/mo

Releases R versions

Daily download trend is not available in this view yet.

50330 days

1.1K90 days

4.4K1 year

Compare downloads with other packages →

Also on114 r2u11 autocran67 c2d4u

How downloads are counted

Repository

andreashandel/dsaide ↗Account: andreashandel

2Stars

0Forks

0Open issues

0Open PRs

0Releases

5Commits

1Commit identities

5 commits · Last activity 2026-07-27 · +100% stars, 30d

Responsiveness

not measured

Stars over time

2025-01-31 · 262026-10-06 · 2

How these are measured

PracticesBeta

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

Checks run against github.com/andreashandel/dsaide on 2026-10-11.

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-07-27

pkgdown site last built 2026-07-27

Coverage (1)

Coverage reporting (Codecov)

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing DSAIDE adds 75 packages (43 with compiled code, 74 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (2)

R >= 4.0.0shiny

Imports (12)

adaptivetau deSolve dplyr ggplot2 gridExtra lhs nloptr plotly rlangstatsutilsXML

LinkingTo (0)

none

Suggests (8)

covr devtools emoji knitr pkgdown rmarkdown roxygen2 testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (12)

Andreas Handel

Author, Maintainer since 0.4.0 (2017)

Cody Dailey

Contributor · added in 0.9.0

Isaac Chun-Hai Fung

Contributor · added in 0.8.0

Ronald Galiwango

Contributor · added in 0.8.2

Salil Goyal

Contributor · added in 0.9.6

Spencer Hall

Contributor · added in 0.5.0

Ben Listyg

Contributor · added in 0.7.0

Brian McKay

Contributor · added in 0.5.0

John Rossow

Contributor · added in 0.5.0

Show 3 more contributorsHide 3 contributors

Sina Solaimanpour

Contributor

Alexis Vittengl

Contributor · added in 0.9.0

Henok Woldu

Contributor · added in 0.7.0

Listed in earlier versions (4)

Show 4 peopleHide 4 people

Isaac Fung

no longer listed · 0.7.0

Christine Casey

no longer listed · 0.8.2 to 0.8.3

Chase Golden

no longer listed · 0.8.2 to 0.8.3

Kevin Spiegel

no longer listed · 0.8.2 to 0.8.3

Releases (12)

Pick two releases to compare their code metrics.

1.0.0Latest
record
2026-07-27 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.9.6
record
2023-08-23 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.9.3
record
2021-07-23 · diff ↗ ·
added 1 export
simulate_idsurveillance_ode
R
R 4.1.0 released · 2021-05-18
0.9.1
record
2021-03-22 · diff ↗
0.9.0
record
2021-02-02 · diff ↗ ·
removed 20 exports
simulate_environmentaltransmission_ode, simulate_evolution_stochastic, simulate_fit_flu, simulate_fit_noro, simulate_heterogeneity_ode, simulate_idcharacteristics_ode, simulate_idcontrol_ode, simulate_idsurveillance_ode, simulate_maternalimmunity_ode, simulate_modelexploration_sir, simulate_parasites_ode, simulate_reproductivenumber1_ode, simulate_reproductivenumber2_ode, simulate_seir_stochastic, simulate_sir_discrete, simulate_sir_ode, simulate_sirdemographic_ode, simulate_sirdemographic_stochastic, simulate_usanalysis_sir, simulate_vectortransmission_ode

added 17 exports
simulate_Characteristics_of_ID_ode, simulate_Complex_ID_Control_ode, simulate_Drug_Resistance_Evolution_stochastic, simulate_Environmental_Transmission_model_ode, simulate_Host_Heterogeneity_Model_ode, simulate_SEIRSd_model_stochastic, simulate_SIRSd_model_ode, simulate_SIRSd_model_stochastic, simulate_SIR_model_discrete, simulate_SIR_model_ode, simulate_SIR_modelexploration, simulate_SIR_usanalysis, simulate_Vector_transmission_model_ode, simulate_flu_fit, simulate_idcontrolmultigroup_ode, simulate_idvaccine_ode, simulate_noro_fit
R
R 4.0.0 released · 2020-04-24
0.8.3
record
2020-01-09 · diff ↗
0.8.2
record
2019-07-04 · diff ↗ ·
removed 1 export
simulate_reproductivenumber_ode

added 8 exports
simulate_fit_flu, simulate_fit_noro, simulate_idcontrolmultioutbreak_ode, simulate_idsurveillance_ode, simulate_maternalimmunity_ode, simulate_parasites_ode, simulate_reproductivenumber1_ode, simulate_reproductivenumber2_ode
R
R 3.6.0 released · 2019-04-26
0.8.0
record
2019-03-30 · diff ↗ ·
removed 15 exports
dsaideapps, generate_plots, simulate_directtransmission, simulate_environmentaltransmission, simulate_evolution, simulate_heterogeneity, simulate_idcharacteristics, simulate_idcontrol, simulate_idpatterns, simulate_introduction, simulate_multipathogen, simulate_reproductivenumber, simulate_stochastic_SEIR, simulate_stochastic_SIR, simulate_vectortransmission

added 22 exports
generate_fctcall, generate_ggplot, generate_plotly, generate_shinyinput, run_model, simulate_directtransmission_ode, simulate_environmentaltransmission_ode, simulate_evolution_stochastic, simulate_heterogeneity_ode, simulate_idcharacteristics_ode, simulate_idcontrol_ode, simulate_idpatterns_ode, simulate_modelexploration_sir, simulate_multipathogen_ode, simulate_reproductivenumber_ode, simulate_seir_stochastic, simulate_sir_discrete, simulate_sir_ode, simulate_sirdemographic_ode, simulate_sirdemographic_stochastic, simulate_usanalysis_sir, simulate_vectortransmission_ode

Show 7 earlier eventsHide 7 earlier events

0.7.0
record
2018-08-07 · diff ↗ ·
removed 3 exports
generate_instruction_tabs, generate_simoutput, simulate_stochastic

added 6 exports
dsaideapps, generate_documentation, generate_plots, generate_text, simulate_stochastic_SEIR, simulate_stochastic_SIR
R
R 3.5.0 released · 2018-04-23
0.6.0
record
2017-09-30 · diff ↗
0.5.0
record
2017-08-07 · diff ↗ ·
added 1 export
simulate_multipathogen
R
R 3.4.0 released · 2017-04-21
0.4.0
record
2017-03-02
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-03-02
Total releases: 12 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 0.5 KB / 2 files
Download size: 3.2 MB

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' entry:

citation("DSAIDE")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1371/journal.pcbi.1005642.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for DSAIDE version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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