R Observatory: Metrics for STraTUS version 1.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

STraTUS

1.1.2Package record

Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny

0packages depend

2.6Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Matthew HallCRAN page ↗GitHub ↗

For a single, known pathogen phylogeny, provides functions for enumeration of the set of compatible epidemic transmission trees, and for uniform sampling from that set. Optional arguments allow for incomplete sampling with a known number of missing individuals, multiple sampling, and known infection time limits. Always assumed are a complete transmission bottleneck and no superinfection or reinfection. See Hall and Colijn (2019) doi:10.1093/molbev/msz058 for methodology.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("STraTUS", 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("mdhall272/STraTUS")

Development version from mdhall272/STraTUS. 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-stratus

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

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) sample.partial.tt.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.partial.tt.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample.tt.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:38: Lost braces in \itemize; \
...[truncated]...
r.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:43-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tt.generator.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly

CRAN check page ↗

Slowest check: 2.9 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTE2026-06-18
ERROR12 NOTE, 1 ERROR2026-06-11
NOTE13 NOTE2026-06-09
ERROR12 NOTE, 1 ERROR2026-06-08
NOTE13 NOTE2026-05-10

Show 2 earlier changesHide 2 earlier changes

ERROR12 NOTE, 1 ERROR2026-05-03
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.2

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 8
Examples that run: 100%6 run in a plain check
Exported functions with examples: 100%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #18,195 · ~7/day · ~215/mo

Releases R versions

Daily download trend is not available in this view yet.

25030 days

70590 days

2.6K1 year

Compare downloads with other packages →

Also on66 r2u

How downloads are counted

Repository

mdhall272/stratus ↗Account: mdhall272

5Stars

2Forks

0Open issues

0Open PRs

1Releases

106Commits

4Commit identities

106 commits · Last activity 2024-10-23 · +25% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 469
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2026-07-11 · 42026-09-30 · 5

How these are measured

PracticesBeta

Checks run against github.com/mdhall272/stratus on 2026-10-11.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing STraTUS adds 29 packages (17 with compiled code, 26 MB of source tarballs). Heaviest: ggplot2 6.0 MB, igraph 4.8 MB, phangorn 1.9 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 3.4

Imports (8)

ape phangorn igraph gmp ggplot2 ggtree RcppAlgosstats

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 (2)

Matthew Hall

Author, Maintainer since 1.1 (2019)

Caroline Colijn

Contributor

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
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.1.2Latest
record
2020-04-04 · current release · diff ↗
1.1.1
record
2019-05-21 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.1
record
2019-03-18
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-03-18
Total releases: 3 / 7 yrs
License: GPL
Minimum R: ≥ 3.4
Bundled data: 0.7 KB / 2 files
Download size: 15 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("STraTUS")

Format

Hall, M., & Colijn, C. (2020). STraTUS: Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny (Version 1.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.STraTUS

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 STraTUS version 1.1.2 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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