links cecileane/crsl4 -> juliaphylo

README.md

@@ -1,25 +1,25 @@
 # PhyloPlots: to plot phylogenetic trees and networks
 
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://cecileane.github.io/PhyloPlots.jl/stable)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://cecileane.github.io/PhyloPlots.jl/dev)
-[![Build status](https://github.com/cecileane/PhyloPlots.jl/workflows/CI/badge.svg?branch=master)](https://github.com/cecileane/PhyloPlots.jl/actions/workflows/ci.yml)
-[![Coverage](https://codecov.io/gh/cecileane/PhyloPlots.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/cecileane/PhyloPlots.jl)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliaphylo.github.io/PhyloPlots.jl/stable)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliaphylo.github.io/PhyloPlots.jl/dev)
+[![Build status](https://github.com/juliaphylo/PhyloPlots.jl/workflows/CI/badge.svg?branch=master)](https://github.com/juliaphylo/PhyloPlots.jl/actions/workflows/ci.yml)
+[![Coverage](https://codecov.io/gh/juliaphylo/PhyloPlots.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/juliaphylo/PhyloPlots.jl)
 [![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)
 [![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/P/PhyloPlots.svg)](https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/report.html)
 
 ## overview
 
 PhyloPlots has utilities to plot tree and network objects
-from [PhyloNetworks](https://github.com/crsl4/PhyloNetworks.jl)
+from [PhyloNetworks](https://github.com/juliaphylo/PhyloNetworks.jl)
 through [R](https://www.r-project.org)
 via [RCall](https://github.com/JuliaInterop/RCall.jl).
 
 ## examples
 
-in PhyloPlots' documentation [manual](https://cecileane.github.io/PhyloPlots.jl/stable/man/getting_started/), and  
-in [PhyloNetworks](http://crsl4.github.io/PhyloNetworks.jl/latest/)'s documentation, see
+in PhyloPlots' documentation [manual](https://juliaphylo.github.io/PhyloPlots.jl/stable/man/getting_started/), and  
+in [PhyloNetworks](http://juliaphylo.github.io/PhyloNetworks.jl/latest/)'s documentation, see
 - basic examples
-  [here](http://crsl4.github.io/PhyloNetworks.jl/latest/man/snaq_plot/#Network-Visualization-1)
+  [here](http://juliaphylo.github.io/PhyloNetworks.jl/latest/man/snaq_plot/#Network-Visualization-1)
 - examples to annotate edges
-  [here](http://crsl4.github.io/PhyloNetworks.jl/latest/man/bootstrap/#support-for-tree-edges)
+  [here](http://juliaphylo.github.io/PhyloNetworks.jl/latest/man/bootstrap/#support-for-tree-edges)

docs/make.jl

@@ -29,6 +29,6 @@ makedocs(
 )
 
 deploydocs(
-    repo = "github.com/cecileane/PhyloPlots.jl.git",
+    repo = "github.com/JuliaPhylo/PhyloPlots.jl.git",
     push_preview = true,
 )

docs/readme.md

@@ -25,7 +25,7 @@ it will:
 - built with [Documenter](https://juliadocs.github.io/Documenter.jl), see
   its [doc](https://juliadocs.github.io/Documenter.jl/stable/man/syntax/)
   for more details on its md syntax.
-- deployed [here](https://cecileane.github.io/PhyloPlots.jl/)
+- deployed [here](https://juliaphylo.github.io/PhyloPlots.jl/)
   (go to `dev/` or `stable/`)
   using github and files committed to the `gh-pages` branch.
 

docs/src/index.md

@@ -1,10 +1,10 @@
 # PhyloPlots.jl
 
-[PhyloPlots](https://github.com/cecileane/PhyloPlots.jl) is a
+[PhyloPlots](https://github.com/juliaphylo/PhyloPlots.jl) is a
 [Julia](http://julialang.org) package to
 plot phylogenetic trees and networks.
 
-[PhyloNetworks](https://github.com/crsl4/PhyloNetworks.jl)
+[PhyloNetworks](https://github.com/juliaphylo/PhyloNetworks.jl)
 objects can be displayed
 through [R](https://www.r-project.org)
 via [RCall](https://github.com/JuliaInterop/RCall.jl).

docs/src/man/installation.md

@@ -2,7 +2,7 @@
 # Installation
 
 For information on how to install Julia and PhyloNetworks, see
-[here](https://crsl4.github.io/PhyloNetworks.jl/dev/man/installation/#Installation).
+[here](https://juliaphylo.github.io/PhyloNetworks.jl/dev/man/installation/#Installation).
 PhyloPlots depends on PhyloNetworks, and has further dependencies
 like
 [RCall](https://github.com/JuliaInterop/RCall.jl).

src/plotRCall.jl

@@ -103,7 +103,7 @@ as it calls `directEdges!` and `preorder!`.
 
 If hybrid edges cross tree and major edges, you may choose to rotate some tree
 edges to eliminate crossing edges, using `rotate!`
-(in [`PhyloNetworks`](http://crsl4.github.io/PhyloNetworks.jl/latest/lib/public/#PhyloNetworks.rotate!)).
+(in [`PhyloNetworks`](http://juliaphylo.github.io/PhyloNetworks.jl/latest/lib/public/#PhyloNetworks.rotate!)).
 
 **Alternative**: a tree or network can be exported with [`sexp`](@ref)
 and then displayed with R's "plot" and all its options.

src/rexport.jl

@@ -10,9 +10,6 @@ Used by the `$object` syntax and by `@rput` to use a Julia object in R:
 see the examples below. Makes it easy to plot a Julia tree or network
 using plotting facilities in R.
 
-
-code inspired from [Phylo.jl](https://github.com/richardreeve/Phylo.jl/blob/master/src/rcall.jl)
-
 # Examples
 
 ```julia-repl