R Observatory: Metrics for modelSSE version 0.1-3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

modelSSE

0.1-3Package record

Modelling Infectious Disease Superspreading from Contact Tracing Data

0packages depend

2.2Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Shi ZhaoCRAN 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. 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-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). 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

r-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-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) convert.epipara.to.delappara.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.epipara.to.delappara.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.epipara.to.delappara.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.epipara.to.delappara.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.epipara.to.delappara.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.epipara.to.delappara.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.epipara.to.delappara.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.epipara.to.delappara.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) d_nextgenclusterdistn.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) d_nextgenclusterdistn.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) d_nextgenclusterdistn.Rd:60: Lost braces in \itemize; meant \describe 
...[truncated]...
Rd: (-1) overalllikelihood.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) paraest.MCMC.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) paraest.MCMC.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) paraest.MCMC.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) paraest.MCMC.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) paraest.ML.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) paraest.ML.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) paraest.ML.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) paraest.ML.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tailoffspringQ.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tailoffspringQ.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tailoffspringQ.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tailoffspringQ.Rd:36: Lost braces in \itemize; meant \describe ?

r-oldrel-macos-arm64, r-oldrel-macos-x86_64

checkRd: (-1) convert.epipara.to.delappara.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.epipara.to.delappara.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.epipara.to.delappara.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.epipara.to.delappara.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.epipara.to.delappara.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.epipara.to.delappara.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.epipara.to.delappara.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.epipara.to.delappara.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) d_nextgenclusterdistn.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) d_nextgenclusterdistn.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) d_nextgenclusterdistn.Rd:60: Lost braces in \itemize; meant \describe 
...[truncated]...
\item{}{} directly
checkRd: (-1) paraest.MCMC.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paraest.ML.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) paraest.ML.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) paraest.ML.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) paraest.ML.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) paraest.ML.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paraest.ML.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paraest.ML.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tailoffspringQ.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tailoffspringQ.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tailoffspringQ.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tailoffspringQ.Rd:36: Lost braces in \itemize; meant \describe ?

CRAN check page ↗

Slowest check: 58 s · r-devel-windows-x86_64

Status changes

NOTE13 NOTE2026-06-08
ERROR12 NOTE, 1 ERROR2026-06-07
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1-3

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 13 (1 internal)
Examples that run: 77%10 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran) · 1 hold no code
Exported functions with examples: 100%
Documented parameters: 54%
Return-value docs: 100%
Help pages citing references: 100%

How these are measured

Downloads

2.2K

CRAN downloads in the past year

Rank #22,081 · ~6/day · ~181/mo

Releases R versions

Daily download trend is not available in this view yet.

25030 days

58890 days

2.2K1 year

Compare downloads with other packages →

Also on89 r2u10 autocran

How downloads are counted

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Installing modelSSE adds 1 package (1 with compiled code, 79 KB of source tarballs). Heaviest: Delaporte 79 KB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Shi Zhao

Author, Maintainer since 0.1-1 (2023)

Releases (3)

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
0.1-3Latest
record
2023-09-07 · current release · diff ↗
0.1-2
record
2023-08-28 · diff ↗
0.1-1
record
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

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 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 modelSSE version 0.1-3 [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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