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v1.0.0: transfer of functionalities for trait evolution from PhyloNetworks v0.16, with breaking changes and improvements #2

Merged
merged 52 commits into from
Jan 10, 2025
Merged

v1.0.0: transfer of functionalities for trait evolution from PhyloNetworks v0.16, with breaking changes and improvements #2

merged 52 commits into from
Jan 10, 2025

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cecileane
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cecileane and others added 30 commits July 25, 2024 15:01
@cecileane
src code and tests transferred from PhyloNetworks
89c7307
@cecileane
vcv and recursion routines moved back to PN
fe13c65
@cecileane
caudata tree, and much more
a214abf
@jjustison
moved some functions to PN and fixed some tests.
9951cbe 
Moved getHeights getGammas and setGammas! to PN.

All tests should work except test_traits_discrete. It uses some functions that are in PhyLiNC
@cecileane
tolerance / tuning params
0844e6a
@cecileane
start: update to new traversal routines
f536358
@cecileane
update to new traversal routines. pbm: tests use a time *in*consisten…
23b3f7f 
…t network
@jjustison
Low hanging fruit for fixing tests.
be15421 
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.
@jjustison
add StatsAPI to test project so it can be used and called
89403ca
@jjustison
Fix traversal function in substitution model.
f28fc9a 
Also brought back getGammas and setGammas.
@jjustison
change qualifier of SMatrix from PhyloTraits to StaticArrays.
1a74999
@cecileane
lambda model uses getnodeheights_majortree is net not time-consistent
787d396
@cecileane
type declaration first, default value after
1540d2b
@cecileane
fixed a log test
e3c0653
@cecileane
pagel's lambda tests now pass
42fa05b
@cecileane
tests for SSM and showdata
49d0248
@pbastide
Start moving man pages (website build passes locally)
08bfecc
@cecileane
man page to use fitdiscrete() on DNA data
c5ad627
@cecileane
main readme: title, refs
07c5911
@cecileane
doc index: started
cf741c5
@cecileane
Camel to smallcase name changes
f751943
@cecileane
discrete trait simulation: can use custom RNG. stable RNG in tests
0e546a6
@cecileane
CSV removed as dependency
54623f9
@cecileane
checkPreorder kwarg -> checkpreorder
f7a8330
@cecileane
rand to simulate; smallcase extractor names and default tipnames
d1a8603
@cecileane
start: separate trait_tree manual into 2 pages; StableRNGs in doc
834a050
@cecileane
rand for DNA models; separate doc page for discrete trait simulation
a6c7a4b
@cecileane
headers in doc
75f94fc
@cecileane
fixes to build doc
4fde2b9
@cecileane
v1.0.0, compat with PN 1.0.0
2423133
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@jjustison
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I just added a lightly modified version of the docs readme from the PN docs folder to note documentation practices and building things locally. There could potentially be an addition to this for the referencing external documentation and how the make.jl would be modified.

Otherwise I think this could be merged!

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I added a small blurb about external references. I haven't actually used them but wrote this with my understanding from what I gathered from previous discussions and changes in the code

@cecileane cecileane requested a review from jjustison January 9, 2025 22:09
@jjustison jjustison merged commit cc7659b into main Jan 10, 2025
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@cecileane
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fixes #1

@cecileane cecileane deleted the dev01 branch January 10, 2025 00:24
@cecileane cecileane mentioned this pull request Jan 10, 2025
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@cecileane @jjustison @pbastide