v0.15.0

PhyloNetworks v0.15.0

Diff since v0.14.3

new features in newick network parsing:

• faster reading of multiple phylogenies
• negative edge lengths are now read, but set to 0
• nexus-style comments are allowed (and ignored)

breaking change:

• nulldeviance considers the null model without an intercept if the input model doesn't have one.

bug fixes in:

• reading of fasta files, with ambiguous sites
• deleteleaf! for highly non-tree-child networks
• hybridlambdaformat with existing original internal node names, e.g. when read as bootstrap values, that caused Hybrid-Lambda to fail silently.

Closed issues:

• deleteleaf method bug (#153)
• Minor doc typo (#166)
• PhyloNetworks prevents BioSequences package upgrade (#168)
• Speed of readMultiTopology compared to map and fmap with large amount of trees (#170)
• readTopology with negative edge lengths (#176)

Merged pull requests:

• Fast read multi topology (#173) (@gaballench)
• CompatHelper: bump compat for StatsFuns to 1, (keep existing compat) (#174) (@github-actions[bot])
• Update nulldeviance for models with no intercept (#175) (@pbastide)
• newick parsing: handle negative edge lengths, comments (#177) (@cecileane)

v0.14.3

PhyloNetworks v0.14.3

Diff since v0.14.2

• plot fix in doc
• compat: julia v1.7, BioSequences v3, CSV 0.10

Merged pull requests:

• CompatHelper: bump compat for BioSequences to 3, (keep existing compat) (#167) (@github-actions[bot])
• added contributing file (#171) (@crsl4)
• Project.toml, not REQUIRE (#172) (@dmbates)

v0.14.2

PhyloNetworks v0.14.2

Diff since v0.14.1

Merged pull requests:

• bug fix, for v0.14.2 (#165) (@cecileane)

v0.14.1

PhyloNetworks v0.14.1

Diff since v0.14.0

Closed issues:

• using phylolm() with multiple records / individuals (#101)
• Cannot precompile PhyloPlots (#141)

Merged pull requests:

• migrate tests+doc from travis-ci to github actions (#160) (@cecileane)
• CompatHelper: bump compat for "Distributions" to "0.25" (#161) (@github-actions[bot])
• CompatHelper: bump compat for "BioSymbols" to "5" (#163) (@github-actions[bot])
• CompatHelper: bump compat for CSV to 0.9, (keep existing compat) (#164) (@github-actions[bot])

v0.14.0

PhyloNetworks v0.14.0

Diff since v0.13.0

new features:

• continuous trait evolution:
  • model for within-species variation
  • REML option (now default: breaking change)
• support for julia 1.6, DataFrames 1.0

v0.13.0

PhyloNetworks v0.13.0

Diff since v0.12.0

new features:

• support for julia 1.5, DataFrames 0.22 etc
• move to flip a hybrid edge
• check that a graph is a valid semi-directed network

Closed issues:

• equal rates model fitdiscrete bug (#147)
• hybridBootstrapSupport error (#154)

Merged pull requests:

• Minor fixes: added 2 spaces and QuartetNetwork docstring (#135) (@crsl4)
• CompatHelper: bump compat for "DataStructures" to "0.18" (#137) (@github-actions[bot])
• Flip Hybrid Edge Move (#139) (@coraallensavietta)
• Fix bug in backward likelihood calculation (#142) (@coraallensavietta)
• Tree component functions (#145) (@jingchengx)
• CompatHelper: bump compat for "Distributions" to "0.24" (#146) (@github-actions[bot])
• CompatHelper: bump compat for "CSV" to "0.8" (#149) (@github-actions[bot])
• CompatHelper: bump compat for "DataFrames" to "0.22" (#150) (@github-actions[bot])
• CompatHelper: bump compat for "StaticArrays" to "1.0" (#151) (@github-actions[bot])
• prep for v0.13.0; travis-ci.com migration; rm test broken by GLM v1.4 (#156) (@cecileane)

v0.12.0

PhyloNetworks v0.12.0

Diff since v0.11.0

new features:

• simulation of multivariate BM process
• NNI moves on semi-directed networks

bug fixes in:

• hybridlambdaformat
• neighbor-joining
• likelihood of discrete traits: the bug affected data with >1 trait on non-tree networks

Closed issues:

• hardwiredCluster does not accept Int taxa (#39)
• strange behavior of plot/writeTopology after deleteLeaf! (#84)
• Problem when analyzing choice of h (#111)
• Reroot conflicts (#112)
• error in hybridlambdaformat (#113)
• readTrees2CF does not work (#118)
• wrong warning readTableCF (#120)
• minor typo in documentation (#125)

Merged pull requests:

• Bug fix: wrong net.node in nj! function (#105) (@jokeitei)
• Nearest Neighbor Interchange Moves in PhyloNetworks (#106) (@coraallensavietta)
• major bug fix for likelihood of discrete traits (#107) (@cecileane)
• Moves (#109) (@coraallensavietta)
• Optimize Network Wrappers (#114) (@coraallensavietta)
• Install TagBot as a GitHub Action (#115) (@JuliaTagBot)
• phyLiNC Bug Fixes (#117) (@coraallensavietta)
• gradient-based optimization of branch lengths (#119) (@cecileane)
• AddHybridEdgeLiNC Bug Fix (#121) (@coraallensavietta)
• bug fixes: root and gamma NaN (#123) (@coraallensavietta)
• implementing multivariate BM process (#124) (@gabehassler)
• hardwiredClusterDistance fix (#127) (@coraallensavietta)
• models for rate variation across sites: +I and +G+I (#128) (@cecileane)
• update to DataFrames v0.21, CSV v0.7 (#131) (@cecileane)
• update to BioSymbols 4.0, BioSequences 2.0, add FASTX (#132) (@cecileane)
• prep for v0.12.0 (#133) (@cecileane)

v0.11.0

new features:

• neighbor-joining
• faster function to extract quartets from gene trees
• format for HybridLambda simulator

breaking changes:

• TICR functions migrated to QuartetNetworkGoodnessFit

v0.10.0

• StatsModels v0.6 compatibility
• indexing rules from DataFrames v0.19
• REQUIRE -> Project.toml
• better phylogeny read/write (e.g. internal node names)
• fitdiscrete: better wrapper; tools for DNA substitution models & rate variation
• clean-up: test folder, getIndex -> findfirst

v0.9.1

bug fix for bootstrap