R Observatory: Metrics for modelSSE version 0.1-3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

modelSSE

0.1-3

Modelling Infectious Disease Superspreading from Contact Tracing Data

0packages depend

2.1Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Shi ZhaoFirst published 2023-06-303 releasesCRAN page ↗

Comprehensive analytical tools are provided to characterize infectious disease superspreading from contact tracing surveillance data. The underlying theoretical frameworks of this toolkit include branching process with transmission heterogeneity (Lloyd-Smith et al. (2005) doi:10.1038/nature04153), case cluster size distribution (Nishiura et al. (2012) doi:10.1016/j.jtbi.2011.10.039, Blumberg et al. (2014) doi:10.1371/journal.ppat.1004452, and Kucharski and Althaus (2015) doi:10.2807/1560-7917.ES2015.20.25.21167), and decomposition of reproduction number (Zhao et al. (2022) doi:10.1371/journal.pcbi.1010281).

Install

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

install.packages("modelSSE", 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-modelsse

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-modelSSE

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-modelSSE

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: 58 s · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

1

Dependencies · direct

Check history

NOTE2026-06-08
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 85%
Documented parameters: 54%
Return-value docs: 100%
References docs: 100%

Downloads

2.1K

CRAN downloads in the past year

Rank #21,012 · ~6/day · ~173/mo

Releases R versions

Daily download trend is not available in this view yet.

14230 days

54490 days

2.1K1 year

Compare downloads with other packages →

Also on123 r2u20 autocran

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Depends (1)

R >= 3.0.0

Imports (1)

Delaporte

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Shi Zhao

Author, Maintainer

Authors (1)

Shi Zhao

Author, Maintainer

Package Timeline

3 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
0.1-3Latest
2023-09-07 · current release · diff ↗
0.1-2
2023-08-28 · diff ↗
0.1-1
2023-06-30
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-06-30
Total releases: 3 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.0.0
Bundled data: 1.1 KB / 4 files
Download size: 29 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("modelSSE")

Format

Zhao, S. (2023). modelSSE: Modelling Infectious Disease Superspreading from Contact Tracing Data (Version 0.1-3) [Computer software]. https://doi.org/10.32614/CRAN.package.modelSSE

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 modelSSE version 0.1-3 [Data set]. HJJB, LLC. Data release v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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