R Observatory: Metrics for eSIR version 0.4.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

eSIR

0.4.2Package record

Extended State-Space SIR Models

0packages depend

3.4Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Michael KleinsasserCRAN page ↗

An implementation of extended state-space SIR models developed by Song Lab at UM school of Public Health. There are several functions available by 1) including a time-varying transmission modifier, 2) adding a time-dependent quarantine compartment, 3) adding a time-dependent antibody-immunization compartment. Wang L. (2020) doi:10.6339/JDS.202007_18(3).0003.

Install

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

install.packages("eSIR", repos = "https://cloud.r-project.org/")

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

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-esir

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-eSIR

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-eSIR

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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) USA_state_N.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) USA_state_N.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) confirmed.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) confirmed.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) death.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) death.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recovered.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recovered.Rd:11: Lost braces in \itemize; meant \describe ?

CRAN check page ↗

Slowest check: 2.4 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTENow
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.2

READMEYes · 1,349 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 8
Examples that run: 100%4 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #15,384 · ~9/day · ~282/mo

Releases R versions

Daily download trend is not available in this view yet.

31330 days

78190 days

3.4K1 year

Compare downloads with other packages →

Also on89 r2u10 autocran

How downloads are counted

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing eSIR adds 28 packages (16 with compiled code, 33 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.5.2

Imports (12)

coda chron data.table ggplot2grDevicesgraphicsgtools scalesstatsreshape2 rjagsutils

LinkingTo (0)

none

Suggests (1)

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 (4)

Michael Kleinsasser

Maintainer since 0.4.1 (2021)

Song Lab

Author

<http://websites.umich.edu/~songlab/>

Lili Wang

Author

Paul Egeler

Contributor

Spectrum Health Office of Research and Education

Releases (2)

Pick two releases to compare their code metrics.

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
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2021-12-10
0.4.2Latest
record
2021-12-10 · current release · diff ↗
archivedRemoved from CRAN
2021-11-26
check problems were not corrected in time
0.4.1
record
2021-11-11
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-11-11
Total releases: 2 / 5 yrs
License: CC BY 4.0
Minimum R: ≥ 3.5.2
Bundled data: 103 KB / 4 files
Download size: 2.6 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("eSIR")

Format

Kleinsasser, M., Song Lab, Egeler, P., & Wang, L. (2021). eSIR: Extended State-Space SIR Models (Version 0.4.2) [Computer software]. https://doi.org/10.32614/CRAN.package.eSIR

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 eSIR version 0.4.2 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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