R Observatory: Metrics for TransPhylo version 1.4.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2025-12-25. Its history is shown below.

Reason: issues were not addressed in time

Details below reflect version 1.4.5, its last release before removal.

TransPhylo

1.4.5Package record

Inference of Transmission Tree from a Dated Phylogeny

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Xavier DidelotCRAN page ↗

Inference of transmission tree from a dated phylogeny. Includes methods to simulate and analyse outbreaks. The methodology is described in Didelot et al. (2014) doi:10.1093/molbev/msu121, Didelot et al. (2017) doi:10.1093/molbev/msw275.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/TransPhylo/TransPhylo_1.4.5.tar.gz"
pkgFile <- "TransPhylo_1.4.5.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.4.5) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4.5

READMEYes · 315 wordsVignettesYes · 4 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 41includes a package overview page
Examples that run: 100%15 run in a plain check
Exported functions with examples: 30%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 2%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on336 r2u3 autocran2.4K conda_forge494 bioconda73 c2d4u

How downloads are counted

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.0

Imports (4)

Rcppstatsgraphicsape

LinkingTo (1)

Rcpp

Suggests (7)

knitr testthat purrr codagrDeviceslatticermarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Xavier Didelot

Author, Maintainer since 1.4.2 (2020)

Yuanwei Xu

Contributor

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2025-12-25
issues were not addressed in time
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
1.4.5
record
2021-04-20 · diff ↗
unarchivedReturned to CRAN
2020-06-08
1.4.4
record
2020-06-08 · diff ↗
archivedRemoved from CRAN
2020-05-28
check errors were not corrected in time ASAN and valgrind
1.4.2
record
2020-05-13
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-05-13
Total releases: 3 / 6 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.0.0

Cite

Cite this package

Run in R for the authors' entry:

citation("TransPhylo")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/molbev/msw275.

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 TransPhylo version 1.4.5 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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