eSIR

0.4.2

Extended State-Space SIR Models

0packages depend

3.7Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Michael KleinsasserFirst published 2021-11-112 releasesCRAN 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.

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).

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 2.9 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,349 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

3.7K

CRAN downloads in the past year

Rank #14,225 · ~10/day · ~305/mo

Releases R versions

Daily download trend is not available in this view yet.

24830 days

77490 days

3.7K1 year

Compare downloads with other packages →

Also on133 r2u7 autocran

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

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.

Code & Tests

Code Composition

R 4,659 (84%)Rd 855 (16%)

Code characteristics

Cyclomatic complexity: 31.5 median / 33 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

6 4 exported

Complexity

21.7 avg / 33 max

Call network

6 nodes / 8 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

Datasets

Bundled datasets · 4

Name	Class	Rows × Cols	Also ships in
USA_state_N	tbl_df/tbl/data.frame	52 × 2	–
confirmed	spec_tbl_df/tbl_df/tbl/data.frame	41 × 362	–
death	spec_tbl_df/tbl_df/tbl/data.frame	41 × 362	–
recovered	tbl_df/tbl/data.frame	41 × 362	–

People & History

People (4)

Maintainer (1)

Michael Kleinsasser

Maintainer

Authors (2)

Song Lab

Author

Lili Wang

Author

Contributors (1)

Paul Egeler

Contributor

Package Timeline

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

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
0.4.2Latest
2021-12-10 · current release · diff ↗
unarchivedReturned to CRAN
2021-12-10
archivedRemoved from CRAN
2021-11-26
check problems were not corrected in time
0.4.1
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
Installed size: not tracked yet
With dependencies: not tracked yet

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