beastier

R package to run BEAST2

https://github.com/ropensci/beastier

Science Score: 49.0%

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

○
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
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (10.3%) to scientific vocabulary

Keywords

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

Last synced: 6 months ago · JSON representation

Repository

R package to run BEAST2

Basic Info

Host: GitHub
Owner: ropensci
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://docs.ropensci.org/beastier
Size: 4.5 MB

Statistics

Stars: 11
Watchers: 2
Forks: 1
Open Issues: 7
Releases: 54

Topics

bayesian beast beast2 phylogenetic-inference 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

beastier

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

beastier is an R package to run BEAST2.

beastier logo

beastier is part of the babette package suite:

beautier creates BEAST2 input (.xml) files.
beastier runs BEAST2
mauricer: install BEAST2 packages
tracerer pastes BEAST2 output (.log, .trees, etc) files.

Related R packages:

beastierinstall: Install and uninstall BEAST2
beastier_on_windows: Verify that beastier works on the Windows operating system
lumier: Shiny app to help create the function call needed

Install BEAST2

Due to CRAN policy, beastier cannot install BEAST2. As a workaround, the non-CRAN beastierinstall can be used.

To install BEAST2:

r remotes::install_github("richelbilderbeek/beastierinstall") beastierinstall::install_beast2()

Example for `v2.1`

Run BEAST2:

```r outputstatefilename <- "out.state"

runbeast2( inputfilename = getbeastierpath("24.xml"), outputstatefilename = outputstate_filename ) ```

This will create the files as specified in the 2_4.xml BEAST2 input file.

Example for `v2.0.25`

```r outputlogfilename <- "out.log" outputtreesfilename <- "out.trees" outputstatefilename <- "out.state"

runbeast2( inputfilename = getbeastierpath("24.xml"), outputlogfilename = outputlogfilename, outputtreesfilenames = outputtreesfilename, outputstatefilename = outputstate_filename ) ```

Note that in this version, the filenames for the .log and .trees files could be specified. This is unneeded: the 2_4.xml BEAST2 input file specifies where these files will be stored:

```text <?xml [...]?>

[...]

[...]

<logger id="tracelog" fileName="test_output_0.log" [...]>
    [...]
</logger>

[...]

<logger id="treelog.t:[...]" fileName="$(tree).trees" [...]>
    [...]
</logger>

```

When using beautier, this can be specified in create_mcmc:

r create_mcmc( tracelog = create_tracelog( filename = "my_trace.log" ), treeslog = create_treeslog( filename = "my_trees.trees" ) )

Missing features/unsupported

beastier cannot do everything BEAST2 can.

Install BEAST2: this is removed from this package to follow CRAN rules. Use the non-CRAN package beastierinstall to do so.
Continue a BEAST2 run: this is an experimental feature.
Setup BEAGLE: this is an untested feature

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

Dependencies

Branch | | ---------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- beautier main | | beastierinstall main | |

Branch | -------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- beastier_on_windows main |

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.

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)

{
  "@context": [
    "https://doi.org/10.5063/schema/codemeta-2.0",
    "http://schema.org"
  ],
  "@type": "SoftwareSourceCode",
  "identifier": "beastier",
  "description": "'BEAST2' (<http://www.beast2.org>) is a widely used\n    Bayesian phylogenetic tool, that uses DNA/RNA/protein data\n    and many model priors to create a posterior of jointly estimated \n    phylogenies and parameters.\n    'BEAST2' is a command-line tool.\n    This package provides a way to call 'BEAST2' \n    from an 'R' function call.",
  "name": "beastier: Call 'BEAST2'",
  "codeRepository": "https://github.com/ropensci/beastier",
  "issueTracker": "https://github.com/ropensci/beastier",
  "license": "https://spdx.org/licenses/GPL-3.0",
  "version": "2.0.13",
  "programmingLanguage": {
    "@type": "ComputerLanguage",
    "name": "R",
    "version": "3.4.2",
    "url": "https://r-project.org"
  },
  "runtimePlatform": "R version 3.4.2 (2017-09-28)",
  "author": [
    {
      "@type": "Person",
      "givenName": "Richl J.C.",
      "familyName": "Bilderbeek",
      "email": "richel@richelbilderbeek.nl",
      "@id": "https://orcid.org/0000-0003-1107-7049"
    }
  ],
  "maintainer": [
    {
      "@type": "Person",
      "givenName": "Richl J.C.",
      "familyName": "Bilderbeek",
      "email": "richel@richelbilderbeek.nl",
      "@id": "https://orcid.org/0000-0003-1107-7049"
    }
  ],
  "softwareSuggestions": [
    {
      "@type": "SoftwareApplication",
      "identifier": "beautier",
      "name": "beautier",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=beautier"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "hunspell",
      "name": "hunspell",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=hunspell"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "knitr",
      "name": "knitr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=knitr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rmarkdown",
      "name": "rmarkdown",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rmarkdown"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "spelling",
      "name": "spelling",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=spelling"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "testit",
      "name": "testit",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=testit"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "testthat",
      "name": "testthat",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=testthat"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "tracerer",
      "name": "tracerer",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=tracerer"
    }
  ],
  "softwareRequirements": [
    {
      "@type": "SoftwareApplication",
      "identifier": "ape",
      "name": "ape",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=ape"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "phangorn",
      "name": "phangorn",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=phangorn"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rappdirs",
      "name": "rappdirs",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rappdirs"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rJava",
      "name": "rJava",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rJava"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "stringr",
      "name": "stringr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=stringr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "xml2",
      "name": "xml2",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=xml2"
    }
  ],
  "releaseNotes": "https://github.com/ropensci/beastier/blob/master/NEWS.md",
  "readme": "https://github.com/ropensci/beastier/blob/master/README.md",
  "fileSize": "109.901KB",
  "contIntegration": [
    "https://travis-ci.org",
    "https://www.appveyor.com",
    "https://www.codecov.io",
    "https://travis-ci.org/ropensci/beastier",
    "https://ci.appveyor.com/project/ropensci/beastier",
    "https://codecov.io/github/ropensci/beastier/branch/master",
    "https://travis-ci.org/ropensci/beastier",
    "https://ci.appveyor.com/project/ropensci/beastier",
    "https://codecov.io/github/ropensci/beastier/branch/develop"
  ],
  "citation": [
    {
      "@type": "ScholarlyArticle",
      "datePublished": "2018",
      "author": [
        {
          "@type": "Person",
          "givenName": [
            "Richl",
            "JC"
          ],
          "familyName": "Bilderbeek"
        },
        {
          "@type": "Person",
          "givenName": [
            "Rampal",
            "S"
          ],
          "familyName": "Etienne"
        }
      ],
      "name": "babette: BEAUti 2, BEAST 2 and Tracer for R",
      "url": "https://doi.org/10.1111/2041-210X.13032",
      "isPartOf": {
        "@type": "PublicationIssue",
        "datePublished": "2018",
        "isPartOf": {
          "@type": [
            "PublicationVolume",
            "Periodical"
          ],
          "name": "Methods in Ecology and Evolution"
        }
      }
    }
  ],
  "keywords": [
    "r",
    "r-package",
    "rstats"
  ],
  "developmentStatus": "https://www.repostatus.org/#active",
  "review": {
    "@type": "Review",
    "url": "https://github.com/ropensci/onboarding/issues/209",
    "provider": "http://ropensci.org"
  }
}

GitHub Events

Total

Issues event: 1
Watch event: 1
Delete event: 1
Issue comment event: 1
Push event: 29
Create event: 2

Last Year

Issues event: 1
Watch event: 1
Delete event: 1
Issue comment event: 1
Push event: 29
Create event: 2

Issues and Pull Requests

Last synced: 6 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

Dependencies

DESCRIPTION cran

ape * imports
assertive * imports
beautier >= 2.6.5 imports
devtools * imports
phangorn * imports
rJava * imports
rappdirs * imports
readr * imports
stringr * imports
tibble * imports
xml2 * imports
hunspell * suggests
knitr * suggests
markdown * suggests
rmarkdown * suggests
spelling * suggests
testit * suggests
testthat >= 2.1.0 suggests
tracerer * 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

beastier

Science Score: 49.0%

Keywords

Basic Info

Statistics

Topics

Metadata Files

beastier

Install BEAST2

Example for v2.1

Example for v2.0.25

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

Dependencies

Files used by continuous integration scripts

References

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies

Example for `v2.1`

Example for `v2.0.25`