R Observatory: Metrics for beautier version 2.6.12

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

beautier

2.6.12Package record

'BEAUti' from R

4packages dependsuggested by 2

7.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Richèl J.C. BilderbeekCRAN page ↗GitHub ↗Website ↗Issues ↗rOpenSci review: issue 209 ↗

'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. 'BEAUti 2' (which is part of 'BEAST2') is a GUI tool that allows users to specify the many possible setups and generates the XML file 'BEAST2' needs to run. This package provides a way to create 'BEAST2' input files without active user input, but using R function calls instead.

Install

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

install.packages("beautier", 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/beautier")

Development version from ropensci/beautier. 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-beautier

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-beautier

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-beautier

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 4.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.6.12

READMENoVignettesYes · 3 · dynamicNEWSNoCitation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 494 (1 internal)includes a package overview page
Examples that run: 100%300 run in a plain check
Exported functions with examples: 61%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

7.3K

CRAN downloads in the past year

Rank #5,218 · ~20/day · ~608/mo

Releases R versions

Daily download trend is not available in this view yet.

58230 days

1.6K90 days

7.3K1 year

Compare downloads with other packages →

Also on152 r2u32 autocran120 c2d4u

How downloads are counted

Repository

ropensci/beautier ↗Organization: ropensci

15Stars

4Forks

11Open issues

0Open PRs

54Releases

3,025Commits

4Commit identities

rr-packagerstatsbayesianbeastbeast2phylogenetic-inferencephylogenetics

License file reads as GPL-3.0 · 3,025 commits · Last activity 2025-12-08 · 0% stars, 30d · Default branch at 2.6.16, ahead of CRAN 2.6.12 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2023-11-02 · 132026-09-08 · 15

How these are measured

PracticesBeta

13 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/ropensci/beautier on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (4)

Code of conductContributing guideIssue templatesPR template

Coverage (1)

Coverage reporting (Codecov)

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 2 practices

Research and citation (2)

CITATION.cffcodemeta.json

Lint, format, editor (2)

Lint workflowRStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing beautier adds 19 packages (15 with compiled code, 30 MB of source tarballs). Heaviest: stringi 11 MB, sp 4.3 MB, seqinr 3.4 MB.

Depends (0)

none

Imports (6)

ape rappdirs purrr rlang seqinr stringr

LinkingTo (0)

none

Suggests (5)

knitr markdown readr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

1indirect

Depends 1 · Imports 3

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

beastier babette nodeSub mcbette

Suggests, most downloaded first

mauricer mhcnuggetsr

How these are counted

Code & Tests

Datasets

People & History

People (13)

Richèl J.C. Bilderbeek

Author, Maintainer · added in 2.2.1

Yacine B. Chehida

Contributor · added in 2.2.1

Jason Griffiths

Contributor · added in 2.5.2

Thijs Janzen

Contributor · added in 2.5.2

Gary Napier

Contributor · added in 2.5.2

Jana Riederer

Contributor · added in 2.2.1

Olivier Roy

Contributor · added in 2.6.11

Raphael Scherrer

Contributor · added in 2.2.1

Pedro Taucce

Contributor · added in 2.6.9

Show 2 more contributorsHide 2 contributors

Paul Van Els

Contributor · added in 2.2.1

Katharine S. Walter

Contributor · added in 2.3.6

Joëlle Barido-Sottani

Reviewer · added in 2.2.1

Joëlle reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209

David Winter

Reviewer · added in 2.2.1

David reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209

Maintainer since 1.13 (2018)

Listed in earlier versions (1)

Richel J.C. Bilderbeek

no longer listed · 1.13

Releases (15)

Pick two releases to compare their code metrics.

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
2.6.12Latest
record
2024-04-01 · current release · diff ↗
unarchivedReturned to CRAN
2023-11-02
2.6.11
record
2023-11-02 · diff ↗
archivedRemoved from CRAN
2023-10-24
requires archived package 'assertive'
2.6.9
record
2023-09-24 · diff ↗ ·
removed 4 exports
create_branch_rate_model_rln_xml, create_branch_rate_model_sc_xml, create_branch_rate_model_stuff_xml, parameter_to_xml_s

added 36 exports
b_pop_sizes_param_to_xml, b_pop_sizes_parameter_to_xml, create_b_pop_sizes_param, create_freq_param, create_kappa_param, create_param_b_pop_sizes, create_param_freq, create_param_kappa, create_rln_clock_branch_rate_model_xml, create_strict_clock_branch_rate_model_xml, freq_param_to_xml, get_default_beast_namespace, get_default_beast_namespace_v2_4, get_default_beast_namespace_v2_6, gtr_site_model_to_xml_prior_distr, gtr_site_model_to_xml_state, hky_site_model_to_xml_prior_distr, hky_site_model_to_xml_state, is_b_pop_sizes_param, is_freq_param, is_kappa_param, is_one_empty_string, is_one_string, is_one_string_that_is_a_number, jc69_site_model_to_xml_state, kappa_param_to_xml, rln_clock_model_to_xml_operators, rln_clock_model_to_xml_state, rln_clock_model_to_xml_tracelog, s_parameter_to_xml and 6 more
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-08-11
2.6.5
record
2022-08-11 · diff ↗ ·
removed 7 exports
clock_models_to_xml_operators, clock_models_to_xml_prior_distr, clock_models_to_xml_state, clock_models_to_xml_tracelog, mrca_priors_to_xml_tracelog, tree_models_to_xml_tracelog, tree_priors_to_xml_operators

added 4 exports
is_on_appveyor, is_on_ci, is_on_github_actions, is_on_travis
archivedRemoved from CRAN
2022-08-08
issues were not corrected in time
2.6.4
record
2022-06-05 · diff ↗ ·
added 3 exports
check_filename, create_beautier_tempfolder, remove_beautier_folder
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2021-07-25
2.6.2
record
2021-07-25 · diff ↗ ·
removed 13 exports
clock_model_to_xml_lh_distr, clock_models_to_xml_state_check_deprecated, distr_to_xml_gamma, mrca_prior_to_xml_lh_distr, mrca_priors_to_xml_state, parameter_to_xml_alpha, parameter_to_xml_beta, parameter_to_xml_clock_rate, parameter_to_xml_m, site_model_to_xml_lh_distr, site_model_to_xml_subst_model, site_models_to_xml_state, tree_priors_to_xml_state

added 22 exports
alpha_parameter_to_xml, are_equivalent_xml_lines_section, beta_parameter_to_xml, check_empty_beautier_folder, clock_rate_param_to_xml, create_clock_rate_state_node_parameter_xml, create_rate_categories_state_node_xml, create_strict_clock_rate_scaler_operator_xml, create_ucld_mean_state_node_param_xml, create_ucld_stdev_state_node_param_xml, gamma_distr_to_xml, get_beautier_folder, has_mrca_prior_with_distr, has_rln_clock_model, has_strict_clock_model, has_tip_dating, m_param_to_xml, rln_clock_model_to_xml_prior_distr, tipdate_taxa_to_xml_trait, tree_model_to_tracelog_xml, unindent, yule_tree_prior_to_xml_operators

Show 19 earlier eventsHide 19 earlier events

archivedRemoved from CRAN
2021-07-13
requires archived package 'beastier'
2.6
record
2021-05-23 · diff ↗ ·
added 1 export
get_beautier_tempfilename
2.5.2
record
2021-05-22 · diff ↗ ·
removed 1 export
phylo_to_xml_state

added 1 export
ccp_tree_prior_to_xml_state
R
R 4.1.0 released · 2021-05-18
2.4
record
2020-10-16 · diff ↗ ·
added 1 export
create_ns_inference_model
unarchivedReturned to CRAN
2020-08-05
2.3.7
record
2020-08-05 · diff ↗ ·
removed 4 exports
gtr_site_model_to_xml_subst_model, hky_site_model_to_xml_subst_model, jc69_site_model_to_xml_subst_model, tn93_site_model_to_xml_subst_model

added 16 exports
are_equivalent_xml_lines, clock_models_to_xml_state_check_deprecated, create_beauti_options_v2_4, create_beauti_options_v2_6, create_branch_rate_model_rln_xml, create_branch_rate_model_sc_xml, create_branch_rate_model_stuff_xml, create_branch_rate_model_xml, create_gtr_subst_model_xml, create_hky_subst_model_xml, create_jc69_subst_model_xml, create_site_model_parameters_xml, create_site_model_xml, create_subst_model_xml, create_tn93_subst_model_xml, create_tree_likelihood_distr_xml
archivedRemoved from CRAN
2020-07-31
required archived package 'assertive'
2.3.6
record
2020-05-06 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.3.5
record
2020-02-25 · diff ↗ ·
removed 2 exports
fasta_to_phylo, fastas_to_phylos

added 161 exports
are_equal_xml_files, are_equal_xml_lines, are_equivalent_xml_files, are_equivalent_xml_lines_loggers, are_equivalent_xml_lines_operators, are_rln_clock_models, bd_tree_prior_to_xml_prior_distr, cbs_tree_prior_to_xml_prior_distr, ccp_tree_prior_to_xml_prior_distr, cep_tree_prior_to_xml_prior_distr, check_gtr_site_model, check_gtr_site_model_names, check_mcmc_list_element_names, check_mcmc_values, check_param, check_param_names, check_param_types, check_rename_fun, check_screenlog_names, check_screenlog_values, check_site_model_names, check_site_model_types, check_tn93_site_model, check_tn93_site_model_names, check_tracelog_names, check_tracelog_values, check_treelog_names, check_treelog_values, clock_model_to_xml_lh_distr, clock_model_to_xml_operators and 131 more
2.3.2
record
2019-12-01 · diff ↗ ·
removed 3 exports
create_nested_sampling_mcmc, create_tree_prior_from_name, create_tree_priors_from_names

added 179 exports
are_equal_screenlogs, are_equal_tracelogs, are_equal_treelogs, are_equivalent_xml_lines_all, are_fasta_filenames, are_ids, are_init_clock_models, are_init_mrca_priors, are_init_site_models, are_init_tree_priors, are_mrca_align_ids_in_fasta, are_mrca_priors, are_mrca_taxon_names_in_fasta, check_alignment_id, check_file_and_model_agree, check_file_exists, check_gamma_site_model, check_gamma_site_model_names, check_is_monophyletic, check_log_mode, check_log_sort, check_mcmc_nested_sampling, check_mrca_prior_name, check_mrca_prior_names, check_mrca_prior_taxa_names, check_nested_sampling_mcmc, check_ns_mcmc, check_screenlog, check_store_every, check_tracelog and 149 more
R
R 3.6.0 released · 2019-04-26
unarchivedReturned to CRAN
2019-03-01
2.2.1
record
2019-03-01 · diff ↗ ·
removed 9 exports
create_beast2_input_1_12, create_beast2_input_file_1_12, create_jc69_site_models, create_misc_options, create_strict_clock_models, create_yule_tree_priors, get_id, get_ids, is_mrca_prior

added 52 exports
are_clock_models, are_equal_mcmcs, are_site_models, are_tree_priors, check_beauti_options, check_clock_model, check_clock_models, check_inference_model, check_inference_models, check_mcmc, check_mrca_prior, check_phylogeny, check_rln_clock_model, check_site_model, check_site_models, check_strict_clock_model, check_tree_prior, check_tree_priors, create_beast2_input_file_from_model, create_beauti_options, create_clock_model_from_name, create_clock_models, create_clock_models_from_names, create_inference_model, create_mcmc_nested_sampling, create_nested_sampling_mcmc, create_site_model_from_name, create_site_models, create_site_models_from_names, create_tree_prior_from_name and 22 more
R
R 3.5.0 released · 2018-04-23
archivedRemoved from CRAN
2018-03-28
policy violation Checking creates '{created,expected}.xml' in home
1.13
record
2018-03-27
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-03-27
Total releases: 15 / 8 yrs
License: GPL-3 OSI
Download size: 1.5 MB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' entry:

citation("beautier")

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

It points to 10.1111/2041-210x.13032.

The repository also keeps a CITATION.cff.

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 beautier version 2.6.12 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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