README.md

beautier

Peer Review Status CRAN_Status_Badge CRAN total downloads CRAN downloads per months DOI

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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:

Related R packages:

Examples

See examples.

Installation

beautier can be installed:

CRAN

For the latest CRAN version:

install.packages("beautier")

GitHub, master branch

For the latest stable version:

remotes::install_github("ropensci/beautier")

GitHub, develop branch

For the bleeding-edge version:

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

FAQ

See FAQ.

Supported

This works, and the interface is unlikely to change.

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 here for an example, of which the first rows are shown here:

KF767106_Indonesia_1976_VII 1976
KF767104_Indonesia_1988_VII 1988
KF767105_Indonesia_1988_VII 1988
AY288998_Indonesia_1990_VII 1990

In the future, there probably will be a ´to_tipdates_file´ function, to create a temporary tipdates file from a table.

Missing features/unsupported

beautier cannot do everything BEAUti can.

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

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

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:

FASTA files anthus_aco.fas and anthus_nd2.fas from:

FASTA file G_VII_pre2003_msa.fas from:

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ropensci/beautier documentation built on July 9, 2024, 6:14 a.m.