babette

babette is an R package to work with BEAST2

https://github.com/ropensci/babette

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
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 5 DOI reference(s) in README
✓
Academic publication links
Links to: wiley.com, zenodo.org
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Academic email domains
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (9.5%) to scientific vocabulary

Keywords

bayesian-inference beast2 phylogenetics r r-package rstats

Last synced: 6 months ago · JSON representation

Repository

babette is an R package to work with BEAST2

Basic Info

Host: GitHub
Owner: ropensci
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://docs.ropensci.org/babette
Size: 10.2 MB

Statistics

Stars: 46
Watchers: 6
Forks: 6
Open Issues: 8
Releases: 17

Topics

bayesian-inference beast2 phylogenetics r r-package rstats

Created about 8 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Codemeta

babette

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

babette is an R package that combines:

beautier creates 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
mauricer install BEAST2 packages
tracerer parses BEAST2 output (.log, .trees, etc) files.

babette logo

Non-CRAN extensions:

beastierinstall Install and uninstall BEAST2
mauricerinstall Install and uninstall BEAST2 packages

Related R packages:

lumier: Shiny app to help create the function call needed

Related R functions:

Related function |babette function ----------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------- [ips::rbeauti](https://github.com/heibl/ips/blob/main/R/rbeauti.R) |[beautier::create_beast2_input_from_model](https://github.com/ropensci/beautier/blob/main/R/create_beast2_input_from_model.R)

Related software:

BEASTifier: command-line tool to generate BEAST2 XML input files

Examples

See:

lumier: R Shiny app to help create the R function call needed
examples: examples tested by Travis CI and AppVeyor
article, in 'Methods in Ecology and Evolution'
Methods.blog post: The babette R Package: How to Sooth the Phylogenetic BEAST2
rOpenSci blog post: Call BEAST2 for Bayesian evolutionary analysis from R
pre-print article, in bioRxiv
'babette' YouTube channel

Installation

See doc/install.md (or just click here)

FAQ

See FAQ.

Missing features/unsupported

babette cannot do everything BEAUti and BEAST2 and Tracer can.

See beautier for missing features in creating a BEAST2 input (.xml) file.

See beastier for missing features in running BEAST2

See mauricer for missing features in installing BEAST2 packages.

See tracerer for missing features in parsing BEAST2 output (.log, .trees, etc) files.

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

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

@article{bilderbeek2018babette, title={babette: BEAUti 2, BEAST 2 and Tracer for R}, author={Bilderbeek, Richèl JC and Etienne, Rampal S}, journal={Methods in Ecology and Evolution}, year={2018}, publisher={Wiley Online Library} }

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.

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

CodeMeta (codemeta.json)

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GitHub Events

Total

Issues event: 4
Watch event: 1
Delete event: 1
Issue comment event: 34
Push event: 14
Create event: 1

Last Year

Issues event: 4
Watch event: 1
Delete event: 1
Issue comment event: 34
Push event: 14
Create event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 3
Total pull requests: 0
Average time to close issues: 16 days
Average time to close pull requests: N/A
Total issue authors: 3
Total pull request authors: 0
Average comments per issue: 14.67
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 0
Average time to close issues: 16 days
Average time to close pull requests: N/A
Issue authors: 3
Pull request authors: 0
Average comments per issue: 14.67
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

richelbilderbeek (3)
thijsjanzen (1)
WJH58 (1)
ngoc-xb-nguyen (1)
AJFeng (1)
rscherrer (1)

Pull Request Authors

NailouZhang (1)

Top Labels

Issue Labels

waiting_for_user (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 393 last-month
Total docker downloads: 48

Total dependent packages: 3
Total dependent repositories: 4
Total versions: 9
Total maintainers: 1

cran.r-project.org: babette

Control 'BEAST2'

Homepage: https://docs.ropensci.org/babette/ (website)
Documentation: http://cran.r-project.org/web/packages/babette/babette.pdf
License: GPL-3
Latest release: 2.3.4
published over 1 year ago

Versions: 9
Dependent Packages: 3
Dependent Repositories: 4
Downloads: 393 Last month
Docker Downloads: 48

Rankings

Dependent packages count: 10.9%

Dependent repos count: 14.7%

Average: 15.2%

Downloads: 20.0%

Maintainers (1)

rjcbilderbeek@gmail.com

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 3.5.0 depends
beastier >= 2.4.10 depends
beautier >= 2.6.5 depends
mauricer >= 2.5 depends
tracerer * depends
phangorn * imports
remotes * imports
stringr * imports
xml2 * imports
ape * suggests
curl * suggests
ggplot2 * suggests
hunspell * suggests
knitr * suggests
lintr * suggests
markdown * suggests
nLTT * suggests
rappdirs * suggests
rmarkdown * suggests
spelling * suggests
testthat >= 2.1.0 suggests