R Observatory: Metrics for DSAIRM version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DSAIRM

1.0.0Package record

Dynamical Systems Approach to Immune Response Modeling

0packages depend

3.6Kdownloads / year

83.4%test coverage

13/13flavors OK

Overview

About

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

Simulation models (apps) of various within-host immune response scenarios. The purpose of the package is to help individuals learn about within-host infection and immune response modeling 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("DSAIRM", 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("ahgroup/DSAIRM")

Development version from ahgroup/DSAIRM. 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-dsairm

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-DSAIRM

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-DSAIRM

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: 5.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMENoVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.0Citation fileYes · cites a publicationWebsiteYes · Quarto

Help pages: 33 (1 internal)includes a package overview page
Examples that run: 95%20 run in a plain check · 1 never run
Exported functions with examples: 70%
Documented parameters: 100%
Return-value docs: 97%
Help pages citing references: 3%

Vignettes (1)

DSAIRM Package Tutorial

How these are measured

Downloads

3.6K

CRAN downloads in the past year

Rank #7,910 · ~10/day · ~304/mo

Releases R versions

Daily download trend is not available in this view yet.

44030 days

1.1K90 days

3.6K1 year

Compare downloads with other packages →

Also on96 r2u4 autocran

How downloads are counted

Repository

ahgroup/dsairm ↗Organization: ahgroup

34Stars

14Forks

0Open issues

0Open PRs

2Releases

575Commits

6Commit identities

575 commits · Last activity 2026-07-27

Responsiveness

How these are sampled

PRs merged (all time): 65%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-01-06 · 342026-07-07 · 34

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/ahgroup/dsairm on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (2)

Quarto project

GitHub Pages site last deployed 2026-07-27

Coverage (1)

Coverage reporting

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing DSAIRM 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 (13)

adaptivetaubootdeSolve 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 (8)

Andreas Handel

Author, Maintainer since 0.4.0 (2018)

Cody Dailey

Contributor · added in 0.9.3

Yang Ge

Contributor · added in 0.8.0

Spencer Hall

Contributor

Brian McKay

Contributor · added in 0.9.3

Sina Solaimanpour

Contributor

Alexis Vittengl

Contributor · added in 0.8.7

Henok Woldu

Contributor

Releases (11)

Pick two releases to compare their code metrics.

1.0.0Latest
record
2026-07-09 · 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
0.9.5
record
2022-07-01 · diff ↗ ·
removed 2 exports
simulate_Basic_Virus_Model_ode, simulate_Basic_Virus_Model_stochastic

added 8 exports
check_simresults, generate_modelsettings, simulate_acutevirusir_ode, simulate_bacteria_fit, simulate_basicvirus_ode, simulate_basicvirus_stochastic, simulate_chronicvirusir_ode, simulate_extendedbacteria_ode
R
R 4.2.0 released · 2022-04-22
0.9.3
record
2021-07-29 · diff ↗ ·
removed 3 exports
generate_equations, simulate_basicvirus_ode, simulate_basicvirus_stochastic

added 2 exports
simulate_Basic_Virus_Model_ode, simulate_Basic_Virus_Model_stochastic
R
R 4.1.0 released · 2021-05-18
0.8.7
record
2021-03-20 · diff ↗
0.8.6
record
2020-07-14 · diff ↗ ·
removed 4 exports
simulate_fit_basicmodel, simulate_fit_confint, simulate_fit_modelcomparison, simulate_modelexploration

added 7 exports
generate_equations, simulate_basicbacteria_modelexploration, simulate_basicvirus_fit, simulate_basicvirus_modelexploration, simulate_confint_fit, simulate_fludrug_fit, simulate_modelcomparison_fit
R
R 4.0.0 released · 2020-04-24
0.8.2
record
2019-07-08 · diff ↗ ·
removed 3 exports
simulate_basicmodel_fit, simulate_confint_fit, simulate_modelcomparison_fit

added 3 exports
simulate_fit_basicmodel, simulate_fit_confint, simulate_fit_modelcomparison
R
R 3.6.0 released · 2019-04-26
0.8.0
record
2019-04-04 · diff ↗ ·
removed 1 export
generate_plots

added 3 exports
generate_fctcall, generate_ggplot, generate_plotly

Show 4 earlier eventsHide 4 earlier events

0.5.5
record
2019-02-11 · diff ↗
0.5.0
record
2019-01-17 · diff ↗ ·
removed 12 exports
dsairmapps, simulate_basicbacteria, simulate_basicvirus, simulate_drugresistance, simulate_fitbasicmodel, simulate_fitconfint, simulate_fitmodelcomparison, simulate_modelvariants, simulate_pkpdmodel, simulate_stochasticvirus, simulate_virus_tx, simulate_virusandir

added 13 exports
generate_shinyinput, run_model, simulate_basicbacteria_ode, simulate_basicmodel_fit, simulate_basicvirus_ode, simulate_basicvirus_stochastic, simulate_confint_fit, simulate_drugresistance_stochastic, simulate_modelcomparison_fit, simulate_modelvariants_ode, simulate_pkpdmodel_ode, simulate_virusandir_ode, simulate_virusandtx_ode
0.4.0
record
2018-08-13
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-08-13
Total releases: 11 / 8 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 1.0 KB / 2 files
Download size: 3.2 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("DSAIRM")

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

It points to 10.1186/s12865-019-0321-0.

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 DSAIRM version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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