R Observatory: Metrics for tbea version 1.7.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

tbea

1.7.0

Pre- And Post-Processing in Bayesian Evolutionary Analyses

0packages depend

5.4Kdownloads / year

22.4%test coverage

13/13checks pass

Overview

About

Maintained by Gustavo A. BallenFirst published 2024-06-044 releasesCRAN page ↗GitHub ↗

Functions are provided for prior specification in divergence time estimation using fossils as well as other kinds of data. It provides tools for interacting with the input and output of Bayesian platforms in evolutionary biology such as 'BEAST2', 'MrBayes', 'RevBayes', or 'MCMCTree'. It Implements a simple measure similarity between probability density functions for comparing prior and posterior Bayesian densities, as well as code for calculating the combination of distributions using conflation of Hill (2008). Functions for estimating the origination time in collections of distributions using the x-intercept (e.g., Draper and Smith, 1998) and stratigraphic intervals (Marshall 2010) are also available. Hill, T. 2008. "Conflations of probability distributions". Transactions of the American Mathematical Society, 363:3351-3372. doi:10.48550/arXiv.0808.1808, Draper, N. R. and Smith, H. 1998. "Applied Regression Analysis". 1--706. Wiley Interscience, New York. DOI:10.1002/9781118625590, Marshall, C. R. 2010. "Using confidence intervals to quantify the uncertainty in the end-points of stratigraphic ranges". Quantitative Methods in Paleobiology, 291--316. DOI:10.1017/S1089332600001911.

Install

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

install.packages("tbea", 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("gaballench/tbea")

Development version from gaballench/tbea. 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-tbea

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-tbea

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-tbea

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 7.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.13

22.4%

Coverage · measured lines

100%

Documentation · exports

7

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-16
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-09
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 334 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 56%
Documented parameters: 92%
Return-value docs: 100%
References docs: 18%

Downloads

5.4K

CRAN downloads in the past year

Rank #8,890 · ~15/day · ~454/mo

Releases R versions

Daily download trend is not available in this view yet.

22830 days

1K90 days

5.4K1 year

Compare downloads with other packages →

Also on106 r2u25 autocran

Repository

GitHub ↗ gaballench/tbea

3Stars

1Forks

11Open issues

0Open PRs

17Releases

115Commits

2Contributors

License GPL-3.0 · 115 commits · Last activity 2025-09-15 · 0% stars, 30d

Stars over time

2025-11-01 · 22026-07-07 · 3

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/gaballench/tbea on 2026-08-23.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (7)

ape Rfitbootgraphicsstatsutilscoda

LinkingTo (0)

none

Suggests (4)

testthat knitr rmarkdown Kendall

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Gustavo A. Ballen

Author, Maintainer

Authors (2)

Gustavo A. Ballen

Author, Maintainer

Sandra Reinales

Author

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.7.0Latest
2025-08-19 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.6.1
2025-04-10 · diff ↗
1.5.0
2024-07-01 · diff ↗
1.4.2
2024-06-04
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-06-04
Total releases: 4 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 72 KB / 4 files
Download size: 487 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("tbea")

Format

Ballen, G. A., & Reinales, S. (2025). tbea: Pre- And Post-Processing in Bayesian Evolutionary Analyses (Version 1.7.0) [Computer software]. https://doi.org/10.32614/CRAN.package.tbea

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 tbea version 1.7.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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