New package: PhyloTraits v1.0.0 #122724
Open
New package: PhyloTraits v1.0.0 #122724
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Contributor
JuliaRegistrator
commented
Jan 10, 2025
- Registering package: PhyloTraits
- Repository: https://github.com/JuliaPhylo/PhyloTraits.jl
- Created by: @cecileane
- Version: v1.0.0
- Commit: cc7659be0097aae50f500faba44f4d7033a6f6c4
- Reviewed by: @cecileane
- Reference: JuliaPhylo/PhyloTraits.jl@cc7659b#commitcomment-151158139
- Description: Julia package for the analysis of trait evolution along a phylogeny, including phylogenetic networks.
- Release notes:
UUID: bce24f4f-6725-4ba4-a77f-2b043c8e33c5 Repo: https://github.com/JuliaPhylo/PhyloTraits.jl.git Tree: 6fecc51cd4c397d40f7389b05d94c48ecc504ea7 Registrator tree SHA: 17aec322677d9b81cdd6b9b9236b09a3f1374c6a
JuliaRegistrator
referenced
this pull request
in JuliaPhylo/PhyloTraits.jl
Jan 10, 2025
…works v0.16, with breaking changes and improvements (#2) * src code and tests transferred from PhyloNetworks * vcv and recursion routines moved back to PN * caudata tree, and much more * moved some functions to PN and fixed some tests. Moved getHeights getGammas and setGammas! to PN. All tests should work except test_traits_discrete. It uses some functions that are in PhyLiNC * tolerance / tuning params * start: update to new traversal routines * update to new traversal routines. pbm: tests use a time *in*consistent network * Low hanging fruit for fixing tests. Since setLength! was removed from PN, places where edge lengths are changed are directly changed as opposed to using the function call. Also made updateHybridRandomTrait! return true, making it work with the updated traversal functions. * add StatsAPI to test project so it can be used and called * Fix traversal function in substitution model. Also brought back getGammas and setGammas. * change qualifier of SMatrix from PhyloTraits to StaticArrays. * lambda model uses getnodeheights_majortree is net not time-consistent * type declaration first, default value after * fixed a log test * pagel's lambda tests now pass * tests for SSM and showdata * Start moving man pages (website build passes locally) * man page to use fitdiscrete() on DNA data * main readme: title, refs * doc index: started * Camel to smallcase name changes * discrete trait simulation: can use custom RNG. stable RNG in tests * CSV removed as dependency * checkPreorder kwarg -> checkpreorder * rand to simulate; smallcase extractor names and default tipnames * start: separate trait_tree manual into 2 pages; StableRNGs in doc * rand for DNA models; separate doc page for discrete trait simulation * headers in doc * fixes to build doc * v1.0.0, compat with PN 1.0.0 * format convention; withExp -> withexpectation * adding CSV to docs * new function predict to replace expectations, expectationsPlots, predint, predintPlot * Typo in docs * new function descendencedataframe to replace regressorShift and regressorHybrid * docstrings * allhybrids as keyword arg, not tested yet * renamed: models_*.jl * start: move type defs from traits_continuous to models_continuous * moved more * documentation: separate pages for library, for public + internal methods * remove deprecated.jl * move and rename continuous * move and rename discrete * Change argument order in descendencedataframe * rand() for discrete traits moved to separate file * set docmeta in CI.yml too * push doc preview * added very lightly modifed docs readme from PN. Gives doc info and tells how to build PhyloTraits documentation locally. * added documentation for external references * further documentation for external references * install R in doc workflow. updated readme to fit PhyloTraits workflow --------- Co-authored-by: jjustison <justisnojo@gmail.com> Co-authored-by: Paul Bastide <paul.bastide@m4x.org>
|
Hello, I am an automated registration bot. I help manage the registration process by checking your registration against a set of AutoMerge guidelines. If all these guidelines are met, this pull request will be merged automatically, completing your registration. It is strongly recommended to follow the guidelines, since otherwise the pull request needs to be manually reviewed and merged by a human. 1. New package registrationPlease make sure that you have read the package naming guidelines. 2. AutoMerge Guidelines are all met! ✅Your new package registration met all of the guidelines for auto-merging and is scheduled to be merged when the mandatory waiting period (3 days) has elapsed. 3. To pause or stop registrationIf you want to prevent this pull request from being auto-merged, simply leave a comment. If you want to post a comment without blocking auto-merging, you must include the text Tip: You can edit blocking comments to add |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.