beautier

R package to generate the same BEAST2 XML parameter files as generated by BEAUti 2

https://github.com/ropensci/beautier

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 2 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.8%) to scientific vocabulary

Keywords

bayesian beast beast2 beauti phylogenetic-inference phylogenetics r r-package rstats

Last synced: 4 months ago · JSON representation

Repository

R package to generate the same BEAST2 XML parameter files as generated by BEAUti 2

Basic Info

Host: GitHub
Owner: ropensci
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://docs.ropensci.org/beautier
Size: 11 MB

Statistics

Stars: 13
Watchers: 2
Forks: 2
Open Issues: 11
Releases: 54

Topics

bayesian beast beast2 beauti phylogenetic-inference phylogenetics r r-package rstats

Created almost 10 years ago · Last pushed 5 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Codemeta

beautier

Branch | | ---------|---------|--------- main | | develop||

beautier is BEAUti for R.

beautier logo

The purpose of beautier is to create a valid BEAST2 XML input file from a n inference model. In this way, a scientific pipeline using BEAST2 can be fully scripted, instead of using BEAUti's GUI.

beautier is part of the babette package suite:

beautier create a BEAST2 input (.xml) file from an inference model.
tiebeaur creates an inference model from a BEAST2 input (.xml) file :warning: experimental :warning:
beastier runs BEAST2
tracerer allows to works with BEAST2 output (.log, .trees, etc) files.
mauricer install BEAST2 packages

Related R packages:

beautier_on_windows: verifies beautier builds on Windows
lumier: Shiny app to help create the function call needed

Examples

See examples.

Installation

beautier can be installed:

Latest CRAN version: CRAN
Latest stable version: GitHub, main branch
Bleeding-edge version: GitHub, develop branch

CRAN

For the latest CRAN version:

r install.packages("beautier")

GitHub, `main` branch

For the latest stable version:

r remotes::install_github("ropensci/beautier")

GitHub, `develop` branch

For the bleeding-edge version:

r remotes::install_github("ropensci/beautier", ref = "develop")

FAQ

See FAQ.

Supported

This works, and the interface is unlikely to change.

1 DNA alignment
Site models:
- JC69
- HKY
- TN93
- GTR
Clock models:
- Strickt
- Relaxed log-normal
Tree models:
- Yule
- Birth-Death
- Coalescent Bayesian Skyline
- Coalescent Constant Population
- Coalescent Exponential Population
Handle missing data: simply use a dash (´-´) as a sequence in a FASTA file

Experimental

This works partially, and the interface may change as well.

Tip dating

The tip dates file is a file that needs to not have column, nor row names. The columns need to be tab separated.

See the example file G_VII_pre2003_dates_4.txt for an example, of which the first rows are shown here:

text KF767106_Indonesia_1976_VII 1976 KF767104_Indonesia_1988_VII 1988 KF767105_Indonesia_1988_VII 1988 AY288998_Indonesia_1990_VII 1990

Missing features/unsupported

beautier cannot do everything BEAUti can.

Here are some missing or (yet) unsupported features, some are linked to an Issue:

Add offset to a distribution
Two or more DNA alignments
Two or more site, clock or tree models
Two or more MRCA priors
Shared site, clock and/or tree models
Using an amino acid alignment
Support for hyper parameters
Clock models
- Relaxed exponential
- Random local
Tree priors
- Calibrated Yule model
- Coalescent Extended Bayesian Skyline
- Birth Death Skyline Serial
Initialization (this is a tab that is hidden by default in BEAUti)

There is a feature I miss

See CONTRIBUTING, at Submitting use cases

I want to collaborate

See CONTRIBUTING, at 'Submitting code'

I think I have found a bug

See CONTRIBUTING, at 'Submitting bugs'

There's something else I want to say

Sure, just add an Issue. Or send an email.

External links

BEAST2 GitHub

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.

References

Article about babette:

Bilderbeek, Richèl JC, and Rampal S. Etienne. "babette: BEAUti 2, BEAST 2 and Tracer for R." Methods in Ecology and Evolution (2018). https://doi.org/10.1111/2041-210X.13032

FASTA files anthus_aco.fas and anthus_nd2.fas from:

Van Els, Paul, and Heraldo V. Norambuena. "A revision of species limits in Neotropical pipits Anthus based on multilocus genetic and vocal data." Ibis.

FASTA file G_VII_pre2003_msa.fas from:

Durr, PA; Wibowo, MH; Tabbu, CR; Asmara, W; Selleck, P; Wang, J; Broz, I; Graham, K.; Dimitrov, K and Afonso, C. (in preparation). Phylodynamics of Genotype VII Newcastle disease virus in Indonesia.

Owner

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

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GitHub Events

Total

Create event: 3
Release event: 2
Issues event: 1
Delete event: 1
Issue comment event: 4
Push event: 51

Last Year

Create event: 3
Release event: 2
Issues event: 1
Delete event: 1
Issue comment event: 4
Push event: 51

Committers

Last synced: about 2 years ago

All Time

Total Commits: 2,832
Total Committers: 4
Avg Commits per committer: 708.0
Development Distribution Score (DDS): 0.006

Past Year

Commits: 169
Committers: 2
Avg Commits per committer: 84.5
Development Distribution Score (DDS): 0.071

Top Committers

Name	Email	Commits
richelbilderbeek	r**l@r**l	2,815
olivroy	o**1@h**m	12
Richel Bilderbeek	r****k	4
ropenscibot	m**t@g**m	1

Committer Domains (Top 20 + Academic)

richelbilderbeek.nl: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 1
Total pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Total issue authors: 1
Total pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

richelbilderbeek (2)

Pull Request Authors

olivroy (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 494 last-month
Total docker downloads: 21,661

Total dependent packages: 6
Total dependent repositories: 10
Total versions: 15
Total maintainers: 1

cran.r-project.org: beautier

'BEAUti' from R

Homepage: https://docs.ropensci.org/beautier/
Documentation: http://cran.r-project.org/web/packages/beautier/beautier.pdf
License: GPL-3
Latest release: 2.6.12
published almost 2 years ago

Versions: 15
Dependent Packages: 6
Dependent Repositories: 10
Downloads: 494 Last month
Docker Downloads: 21,661

Rankings

Docker downloads count: 0.6%

Dependent packages count: 7.3%

Dependent repos count: 9.2%

Average: 12.0%

Stargazers count: 15.1%

Downloads: 18.8%

Forks count: 21.0%

Maintainers (1)

rjcbilderbeek@gmail.com

Last synced: 5 months ago

Dependencies

DESCRIPTION cran

ape * imports
assertive * imports
pryr * imports
rappdirs * imports
seqinr * imports
stringr * imports
testit * imports
devtools * suggests
ggplot2 * suggests
hunspell * suggests
knitr * suggests
lintr * suggests
markdown * suggests
readr * suggests
rmarkdown * suggests
spelling * suggests
testthat >= 2.1.0 suggests

.github/workflows/R-CMD-check.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite

.github/workflows/build_singularity.yaml actions

actions/checkout v2 composite

.github/workflows/check_bash_style.yaml actions

actions/checkout v2 composite

.github/workflows/check_links.yaml actions

actions/checkout v2 composite
gaurav-nelson/github-action-markdown-link-check v1 composite

beautier

Science Score: 49.0%

Keywords

Basic Info

Statistics

Topics

Metadata Files

beautier

Examples

Installation

CRAN

GitHub, main branch

GitHub, develop branch

Supported

Experimental

Tip dating

Missing features/unsupported

There is a feature I miss

I want to collaborate

I think I have found a bug

There's something else I want to say

External links

Files used by continuous integration scripts

References

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: beautier

Rankings

Maintainers (1)

Dependencies

GitHub, `main` branch

GitHub, `develop` branch