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beautier

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Velocity0.0

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

github.com/ropensci/beautier ↗

A BEAST2 XML generator shipping releases CRAN can't accept because the CRAN team is on holiday.

phylogeneticsbeast2r-packagecraninput-validationbioinformatics
◆Current state
beautier turns R code into BEAST2 phylogenetics XML input files. The three most recent releases landed over four days in August 2025 and are all explicitly marked pre-CRAN, held back because the CRAN team was on summer holiday. The substance sits in 2.6.13, which added tip-date file handling; the two after it are lint and bug fixes.
◆Where it's heading
Development is fine-grained and test-driven — releases are small, numbered in tight sequence, and reported against a fixed NEW FEATURES / MINOR IMPROVEMENTS / BUG FIXES / DEPRECATED template with 100% code coverage tracked as a line item. The recent work concentrates on validating user-supplied input files rather than expanding BEAST2 model coverage, which suggests the model surface is considered largely done and the remaining friction is in what users feed it.
◆Prediction
The pre-CRAN backlog should be squashed into a single CRAN submission once the release window reopens; further work is most likely more input-file validation in the same check_/read_ family.

◆Recent moves

  1. 1y ago

    Infinity and NA handling fixed for s parameters

    s_parameter_to_xml() now copes with an upper value of infinity and create_s_parameter() defaults upper to NA, matching what the XML generator already assumed. Coverage is at 100%. Another release explicitly held back from CRAN.

    View source ↗
  2. 1y ago

    Lint-only release, held back from CRAN

    A clean-lint release with no features and no bug fixes, published a day after the previous one and equally unable to reach CRAN. It exists to keep the version history contiguous.

    View source ↗
  3. 1y ago

    Tip-date file reading and validation added

    Three new functions detect tip dates in a BEAST2 XML, validate a tip-date file, and read one, backed by clearer errors for the classic failure modes — a non-tab separator or a stray header row. This is the only feature work in the recent run and it targets input handling rather than model coverage.

    View source ↗