diff --git a/CITATION.bib b/CITATION.bib index 33badab..e3ceed7 100644 --- a/CITATION.bib +++ b/CITATION.bib @@ -1,15 +1,14 @@ % reference for the package -@misc{PhyloGaussianBeliefProp.jl, - author = {Cécile Ané and - contributors}, - title = {QuartetNetworkGoodnessFit.jl: Julia package for phylogenetic networks analyses using four-taxon subsets}, - url = {https://github.com/cecileane/QuartetNetworkGoodnessFit.jl}, - version = {v0.0.1}, - year = {2023}, +@misc{QuartetNetworkGoodnessFit.jl, + author = {Cécile Ané and contributors}, + title = {QuartetNetworkGoodnessFit.jl: Julia package for phylogenetic networks analyses using four-taxon subsets}, + url = {https://github.com/JuliaPhylo/QuartetNetworkGoodnessFit.jl}, + version = {v0.5.1}, + year = {2023}, } % reference for the goodness-of-fit test @article{2021CaiAne, - author = {Ruoyi Cai & Cécile Ané}, + author = {Ruoyi Cai & C{\'e}cile An{\'e}}, title = {Assessing the fit of the multi-species network coalescent to multi-locus data}, year = {2021}, journal = {Bioinformatics}, @@ -20,7 +19,8 @@ @article{2021CaiAne } % reference for the algorithm to calculate expected quartet concordance factors @article{2024AFABR-anomalous, - author = {Cécile Ané and John Fogg and Elizabeth S. Allman and Hector Baños and John A. Rhodes}, + author = {C{\'e}cile An{\'e} and John Fogg and Elizabeth S. Allman and + Hector Ba{\~n}os and John A. Rhodes}, title = {Anomalous networks under the multispecies coalescent: theory and prevalence}, year = {2024}, journal = {Journal of Mathematical Biology}, diff --git a/README.md b/README.md index a951a70..29adf14 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ -[![doc: stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://cecileane.github.io/QuartetNetworkGoodnessFit.jl/stable) -[![doc: dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://cecileane.github.io/QuartetNetworkGoodnessFit.jl/dev) -[![Build status](https://github.com/cecileane/QuartetNetworkGoodnessFit.jl/workflows/CI/badge.svg?branch=master)](https://github.com/cecileane/QuartetNetworkGoodnessFit.jl/actions) -[![Coverage](https://codecov.io/gh/cecileane/QuartetNetworkGoodnessFit.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/cecileane/QuartetNetworkGoodnessFit.jl) +[![doc: stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://JuliaPhylo.github.io/QuartetNetworkGoodnessFit.jl/stable) +[![doc: dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://JuliaPhylo.github.io/QuartetNetworkGoodnessFit.jl/dev) +[![Build status](https://github.com/JuliaPhylo/QuartetNetworkGoodnessFit.jl/workflows/CI/badge.svg?branch=master)](https://github.com/JuliaPhylo/QuartetNetworkGoodnessFit.jl/actions) +[![Coverage](https://codecov.io/gh/JuliaPhylo/QuartetNetworkGoodnessFit.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/JuliaPhylo/QuartetNetworkGoodnessFit.jl) [![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac) [![PkgEval](https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/Q/QuartetNetworkGoodnessFit.svg)](https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/report.html) @@ -11,7 +11,7 @@ is a Julia package for phylogenetic networks analyses using four-taxon subsets. It includes tools to measure the goodness of fit of a phylogenetic network to data on subsets of 4 tips. -It depends on the [PhyloNetworks](https://github.com/crsl4/PhyloNetworks.jl) +It depends on the [PhyloNetworks](https://github.com/JuliaPhylo/PhyloNetworks.jl) package. ## citing diff --git a/docs/make.jl b/docs/make.jl index 507cef5..325ed90 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -9,7 +9,7 @@ makedocs( authors = "Cécile Ané and Ruoyi Cai", format = Documenter.HTML(; prettyurls = get(ENV, "CI", nothing) == "true", # easier local build - canonical="https://cecileane.github.io/QuartetNetworkGoodnessFit.jl/stable/", + canonical="https://JuliaPhylo.github.io/QuartetNetworkGoodnessFit.jl/stable/", edit_link="master", assets=String[] ), @@ -28,7 +28,7 @@ makedocs( ) deploydocs( - repo = "github.com/cecileane/QuartetNetworkGoodnessFit.jl.git", + repo = "github.com/JuliaPhylo/QuartetNetworkGoodnessFit.jl.git", push_preview = true, devbranch="master", ) diff --git a/docs/readme.md b/docs/readme.md index 0fd4f4e..d5ef6d0 100644 --- a/docs/readme.md +++ b/docs/readme.md @@ -1,7 +1,7 @@ # notes to maintain documentation - built with [Documenter](https://juliadocs.github.io/Documenter.jl) -- deployed [here](https://cecileane.github.io/QuartetNetworkGoodnessFit.jl/dev/) +- deployed [here](https://JuliaPhylo.github.io/QuartetNetworkGoodnessFit.jl/dev/) (go to `dev/` or `stable/`) using github and files committed to the `gh-pages` branch. diff --git a/docs/src/index.md b/docs/src/index.md index 867cf9b..c06663a 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -1,12 +1,12 @@ # Quarnet GoF --or simply QGoF QuartetNetworkGoodnessFit.jl is a Julia -[package](https://github.com/cecileane/QuartetNetworkGoodnessFit.jl) +[package](https://github.com/JuliaPhylo/QuartetNetworkGoodnessFit.jl) for phylogenetic networks analyses using four-taxon subsets. It includes tools to measure the goodness of fit of a candidate network to data on subsets of 4 tips. -It depends on the [PhyloNetworks](https://github.com/crsl4/PhyloNetworks.jl) +It depends on the [PhyloNetworks](https://github.com/JuliaPhylo/PhyloNetworks.jl) package. For a tutorial, see the manual: diff --git a/docs/src/man/simulate.md b/docs/src/man/simulate.md index 53c4fcd..eba42ec 100644 --- a/docs/src/man/simulate.md +++ b/docs/src/man/simulate.md @@ -6,7 +6,7 @@ The correction for dependence across 4-taxon uses a simulation approach. We provide more examples here to simulate gene trees and extract the quartet concordance factors observed in these simulated gene trees. -We use [PhyloCoalSimulations](https://cecileane.github.io/PhyloCoalSimulations.jl/stable/) +We use [PhyloCoalSimulations](https://JuliaPhylo.github.io/PhyloCoalSimulations.jl/stable/) for the simulation of trees under the network multispecies coalescent, assuming that the network edges lengths are in coalescent units. diff --git a/src/quarnetGoF.jl b/src/quarnetGoF.jl index cb2cc52..66c55b8 100644 --- a/src/quarnetGoF.jl +++ b/src/quarnetGoF.jl @@ -32,7 +32,7 @@ across 4-taxon sets: it makes no correction for dependence. To correct for dependence with `correction=:simulation`, the distribution of z-values is obtained by simulating gene trees under the coalescent along the network (after branch length optimization if `optbl=true`) -using [PhyloCoalSimulations](https://github.com/cecileane/PhyloCoalSimulations.jl). +using [PhyloCoalSimulations](https://github.com/JuliaPhylo/PhyloCoalSimulations.jl). The z-score is calculated on each simulated data set. Under independence, these z-scores have mean 0 and variance 1. Under dependence, these z-scores still have mean 0, but an inflated variance. @@ -54,7 +54,7 @@ Note that `net` is **not** modified. in coalescent units. When `optbl=true`, branch lengths in `net` are optimized, to optimize the pseudo log likelihood score as in SNaQ (see - [here](https://crsl4.github.io/PhyloNetworks.jl/stable/lib/public/#PhyloNetworks.topologyMaxQPseudolik!)). + [here](https://JuliaPhylo.github.io/PhyloNetworks.jl/stable/lib/public/#PhyloNetworks.topologyMaxQPseudolik!)). In both cases, any missing branch length is assigned a value with [`ultrametrize!`](@ref), which attempts to make the major tree ultrametric (but never modifies an existing edge length). @@ -194,7 +194,7 @@ end seed::Int, nsim::Int, verbose::Bool, keepfiles::Bool) Simulate gene trees under the multispecies coalescent model along network `net` -using [PhyloCoalSimulations](https://github.com/cecileane/PhyloCoalSimulations.jl). +using [PhyloCoalSimulations](https://github.com/JuliaPhylo/PhyloCoalSimulations.jl). The quartet concordance factors (CFs) from these simulated gene trees are used as input to `outlierp_fun!` to categorize each 4-taxon set as an outlier (p-value < 0.05) or not.