CRAN requires the check problems on this package to be fixed before 2026-08-31 or it will be archived.

STraTUS

1.1.2

Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny

0packages depend

2.5Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Matthew HallFirst published 2019-03-183 releasesCRAN 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.

bspm (used by r2u) also needs make: sudo apt install make

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: 3.6 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

NOTE2026-06-18
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-11
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-06-09
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-05-10
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-05-03
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: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 0%

Downloads

2.5K

CRAN downloads in the past year

Rank #16,192 · ~7/day · ~206/mo

Releases R versions

Daily download trend is not available in this view yet.

21030 days

70590 days

2.5K1 year

Compare downloads with other packages →

Also on91 r2u

Repository

GitHub ↗ mdhall272/stratus

4Stars

2Forks

0Open issues

0Open PRs

1Releases

106Commits

4Contributors

106 commits · Last activity 2024-10-23

Repository practices

Upstream repositoryBeta

Checks run against github.com/mdhall272/stratus on 2026-07-19.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

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.

Code & Tests

Code Composition

R 1,197 (81%)Rd 288 (19%)

Code characteristics

Cyclomatic complexity: 3.0 median / 40 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

16 6 exported

Complexity

8.7 avg / 40 max

Call network

16 nodes / 20 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

Datasets

Bundled datasets · 1

Name	Class	Rows × Cols	Also ships in
grouping.map	vector	–	–

People & History

People (2)

Maintainer (1)

Matthew Hall

Author, Maintainer

Authors (1)

Matthew Hall

Author, Maintainer

Contributors (1)

Caroline Colijn

Contributor

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
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
2020-04-04 · current release · diff ↗
1.1.1
2019-05-21 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.1
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
Installed size: not tracked yet
With dependencies: not tracked yet

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