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links (cecileane and crsl4) updated to JuliaPhylo #29

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18 changes: 9 additions & 9 deletions CITATION.bib
Original file line number Diff line number Diff line change
@@ -1,15 +1,14 @@
% reference for the package
@misc{PhyloGaussianBeliefProp.jl,
author = {Cécile Ané <[email protected]> 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 <[email protected]> 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},
Expand All @@ -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},
Expand Down
10 changes: 5 additions & 5 deletions README.md
Original file line number Diff line number Diff line change
@@ -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)

Expand All @@ -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
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4 changes: 2 additions & 2 deletions docs/make.jl
Original file line number Diff line number Diff line change
Expand Up @@ -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[]
),
Expand All @@ -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",
)
2 changes: 1 addition & 1 deletion docs/readme.md
Original file line number Diff line number Diff line change
@@ -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.

Expand Down
4 changes: 2 additions & 2 deletions docs/src/index.md
Original file line number Diff line number Diff line change
@@ -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:
Expand Down
2 changes: 1 addition & 1 deletion docs/src/man/simulate.md
Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand Down
6 changes: 3 additions & 3 deletions src/quarnetGoF.jl
Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand All @@ -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).
Expand Down Expand Up @@ -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.
Expand Down
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