Merge pull request #29 from JuliaPhylo/urls

links (cecileane and crsl4) updated to JuliaPhylo

CITATION.bib

@@ -1,15 +1,14 @@
 % reference for the package
-@misc{PhyloGaussianBeliefProp.jl,
-    author  = {Cécile Ané <cecileane@users.noreply.github.com> 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 <cecileane@users.noreply.github.com> 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},

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

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",
 )

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.
 

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:

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.
 

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.