mcbette

1.15.3

Model Comparison Using 'babette'

0packages depend

2.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Richèl J.C. BilderbeekFirst published 2020-11-166 releasesCRAN page ↗GitHub ↗

'BEAST2' (https://www.beast2.org) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'mcbette' allows to do a Bayesian model comparison over some site and clock models, using 'babette' (https://github.com/ropensci/babette/).

Install

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

install.packages("mcbette", 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("ropensci/mcbette")

Development version from ropensci/mcbette. 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-mcbette

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-mcbette

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

Slowest check: 1.4 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-06
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-04
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 95%
Return-value docs: 100%
References docs: 0%

Downloads

2.9K

CRAN downloads in the past year

Rank #13,656 · ~8/day · ~243/mo

Releases R versions

Daily download trend is not available in this view yet.

24530 days

79790 days

2.9K1 year

Compare downloads with other packages →

Also on114 r2u

Repository

GitHub ↗ ropensci/mcbette

7Stars

3Forks

3Open issues

0Open PRs

17Releases

732Commits

3Contributors

License GPL-3.0 · 732 commits · Last activity 2026-07-16

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/ropensci/mcbette on 2026-07-19.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Research and citation (3)

CITATION.cffcodemeta.jsonJOSS paper

Lint, format, editor (1)

RStudio project

Show all practices

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (9)

babette beautier beastier curl devtools mauricer Rmpfr testit txtplot

LinkingTo (0)

none

Suggests (14)

ape ggplot2 hunspell knitr lintr markdown nLTT phangorn rappdirs rmarkdown spelling stringr testthat (>= 2.1.0)tracerer

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 1,132 (50%)Rd 943 (42%)Vignettes 146 (6%)Other 34 (1%)Markdown 14 (1%)

Code characteristics

Cyclomatic complexity: 2.0 median / 9 max
System requirements: 1 external

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

17 15 exported

Complexity

3.1 avg / 9 max

Call network

17 nodes / 7 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

People & History

People (3)

Maintainer (1)

Richèl J.C. Bilderbeek

Author, Maintainer

Authors (1)

Richèl J.C. Bilderbeek

Author, Maintainer

Reviewers (2)

Vikram Baliga

Reviewer

Joëlle Barido-Sottani

Reviewer

Package Timeline

6 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
1.15.3Latest
2024-08-19 · current release · diff ↗
unarchivedReturned to CRAN
2024-08-19
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2023-10-24
requires archived package 'beastier'
1.15.2
2023-09-27 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.15.1
2022-12-15 · diff ↗
unarchivedReturned to CRAN
2022-12-15
archivedRemoved from CRAN
2022-12-11
issues were not corrected in time Did not allow for simultaneous use of 'beautier' and its cache directory
1.15
2022-08-27 · diff ↗
unarchivedReturned to CRAN
2022-08-27
R
R 4.2.0 released · 2022-04-22
archivedRemoved from CRAN
2021-07-13
requires archived package 'beastier'
R
R 4.1.0 released · 2021-05-18

Show 3 earlier events

1.13
2020-12-05 · diff ↗
1.12
2020-11-16
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-11-16
Total releases: 6 / 6 yrs
License: GPL-3 OSI
Download size: 2.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

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