Package: mauricer 2.5.5

Richèl J.C. Bilderbeek

mauricer: Work with 'BEAST2' Packages

'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. 'BEAST2' is commonly accompanied by 'BEAUti 2' (<https://www.beast2.org>), which, among others, allows one to install 'BEAST2' package. This package allows to work with 'BEAST2' packages from 'R'.

Authors:Richèl J.C. Bilderbeek [aut, cre], Olivier Roy [ctb]

mauricer_2.5.5.tar.gz
mauricer_2.5.5.zip(r-4.5)mauricer_2.5.5.zip(r-4.4)mauricer_2.5.5.zip(r-4.3)
mauricer_2.5.5.tgz(r-4.5-any)mauricer_2.5.5.tgz(r-4.4-any)mauricer_2.5.5.tgz(r-4.3-any)
mauricer_2.5.5.tar.gz(r-4.5-noble)mauricer_2.5.5.tar.gz(r-4.4-noble)
mauricer_2.5.5.tgz(r-4.4-emscripten)mauricer_2.5.5.tgz(r-4.3-emscripten)
mauricer.pdf |mauricer.html✨
mauricer/json (API)
NEWS

# Install 'mauricer' in R:
install.packages('mauricer', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ropensci/mauricer/issues

Pkgdown site:https://docs.ropensci.org

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On CRAN:mauricer-2.5.4(2024-06-11)

Conda:

openjdk

5.56 score 3 stars 2 packages 10 scripts 734 downloads 7 exports 52 dependencies

Last updated 7 months agofrom:ee96fa2c97 (on main). Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 05 2025
R-4.5-winOKMar 05 2025
R-4.5-macOKMar 05 2025
R-4.5-linuxOKMar 05 2025
R-4.4-winOKMar 05 2025
R-4.4-macOKMar 05 2025
R-4.4-linuxOKMar 05 2025
R-4.3-winOKMar 05 2025
R-4.3-macOKMar 05 2025

Exports:get_beast2_pkg_namesget_mrc_pathget_mrc_pathsinstall_beast2_pkgis_beast2_ns_pkg_installedis_beast2_pkg_installeduninstall_beast2_pkg

Dependencies:ade4apebeastierbeautierbitbit64clicliprcpp11crayondigestfansifastmatchgenericsgluehmsigraphlatticelifecyclemagrittrMASSMatrixnlmephangornpillarpixmappkgconfigprettyunitsprogresspurrrquadprogR6rappdirsRcppRcppArmadilloreadrrJavarlangsegmentedseqinrsessioninfospstringistringrtibbletidyselecttzdbutf8vctrsvroomwithrxml2

mauricer demo

Richèl J.C. Bilderbeek

Rendered fromdemo.Rmdusingknitr::rmarkdownon Mar 05 2025.

Last update: 2021-05-22
Started: 2018-09-11

Citation

Bilderbeek RJ, Etienne RS (2018). “babette: BEAUti 2, BEAST 2 and Tracer for R.” Methods in Ecology and Evolution. doi:10.1111/2041-210X.13032.

Corresponding BibTeX entry: 

  @Article{,
    author = {Richèl JC Bilderbeek and Rampal S Etienne},
    title = {babette: BEAUti 2, BEAST 2 and Tracer for R},
    journal = {Methods in Ecology and Evolution},
    year = {2018},
    doi = {10.1111/2041-210X.13032},
  }

Readme and manuals

mauricer

Branch GitHub Actions logo Codecov logo
master R-CMD-check codecov.io
develop R-CMD-check codecov.io

Work with BEAST2 packages from R.

Related packages:

  • babette do a full BEAST2 workflow.
  • beautier creates BEAST2 input (.xml) files.
  • beastier runs BEAST2
  • lumier helps to create the babette function call needed
  • tracerer parses BEAST2 output (.log, .trees, etc) files.

Non-CRAN extensions:

Examples

To install the BEAST2 NS package:

remotes::install_github("richelbilderbeek/mauricerinstall")
mauricerinstall::install_beast2_pkg("NS")

An introduction video:

Package dependencies

Package Codecov logo
beastier codecov.io

Related packages

Package Codecov logo
babette codecov.io
beautier codecov.io
lumier codecov.io
tracerer codecov.io
Package Status
mauricer_on_windows Build status

ropensci_footer

Files used by continuous integration scripts

Filename Descriptions
mlc_config.json Configuration of the link checker, use markdown-link-check --config mlc_config.json --quiet docs/**/*.md to do link checking locally
.spellcheck.yml Configuration of the spell checker, use pyspelling -c .spellcheck.yml to do spellcheck locally
.wordlist.txt Whitelisted words for the spell checker, use pyspelling -c .spellcheck.yml to do spellcheck locally
.markdownlint.jsonc Configuration of the markdown linter, use markdownlint "**/*.md" to do markdown linting locally. The name of this file is a default name.
.markdownlintignore Files ignored by the markdown linter, use markdownlint "**/*.md" to do markdown linting locally. The name of this file is a default name.

Links