initial: quarnetGoFtest

.gitignore

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+docs/build/
+docs/site/
+*Manifest.toml

.travis.yml

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+## Documentation: http://docs.travis-ci.com/user/languages/julia/
+language: julia
+os:
+  - linux
+  - osx
+julia:
+  - 1.2
+
+notifications:
+  email: false
+git:
+  depth: 99999999
+
+## uncomment and modify the following lines to manually install system packages
+#addons:
+#  apt: # apt-get for linux
+#    packages:
+#    - gfortran
+
+# before_install:
+
+codecov: true
+coveralls: true
+
+jobs:
+  include:
+    - stage: "Documentation"
+      julia: 1.2
+      os: linux
+      script:
+        - julia --project=docs/ -e 'using Pkg; Pkg.instantiate();
+                                    Pkg.develop(PackageSpec(path=pwd()))'
+        - julia --project=docs/ docs/make.jl
+      after_success: skip

LICENSE.md

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+The QuartetNetworkGoodnessFit.jl package is licensed under the MIT "Expat" License:
+
+> Copyright (c) 2019: Ruoyi Cai & Cecile Ane.
+>
+> Permission is hereby granted, free of charge, to any person obtaining a copy
+> of this software and associated documentation files (the "Software"), to deal
+> in the Software without restriction, including without limitation the rights
+> to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+> copies of the Software, and to permit persons to whom the Software is
+> furnished to do so, subject to the following conditions:
+>
+> The above copyright notice and this permission notice shall be included in all
+> copies or substantial portions of the Software.
+>
+> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+> SOFTWARE.
+>

Project.toml

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+name = "QuartetNetworkGoodnessFit"
+uuid = "1382f7fc-2744-4d9d-8ec6-1e3efdec0746"
+authors = ["Cecile Ane <[email protected]>"]
+version = "0.1.0"
+
+[deps]
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+NLopt = "76087f3c-5699-56af-9a33-bf431cd00edd"
+PhyloNetworks = "33ad39ac-ed31-50eb-9b15-43d0656eaa72"
+SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
+
+[compat]
+PhyloNetworks = "≥ 0.10.0"
+SpecialFunctions = "≥ 0.8.0"
+julia = "≥ 1.2"

README.md

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+[![Build Status](https://travis-ci.org/cecileane/QuartetNetworkGoodnessFit.jl.svg?branch=master)](https://travis-ci.org/cecileane/QuartetNetworkGoodnessFit.jl)
+[![Coverage Status](https://coveralls.io/repos/cecileane/QuartetNetworkGoodnessFit.jl/badge.svg?branch=master&service=github)](https://coveralls.io/github/cecileane/QuartetNetworkGoodnessFit.jl?branch=master)
+[![codecov.io](http://codecov.io/github/cecileane/QuartetNetworkGoodnessFit.jl/coverage.svg?branch=master)](http://codecov.io/github/cecileane/QuartetNetworkGoodnessFit.jl?branch=master)
+
+## overview
+
+`QuartetNetworkGoodnessFit` is a Julia package, providing 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)
+package.
+
+[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://cecileane.github.io/QuartetNetworkGoodnessFit.jl/stable)
+[![](https://img.shields.io/badge/docs-dev-blue.svg)](https://cecileane.github.io/QuartetNetworkGoodnessFit.jl/dev)

docs/Project.toml

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+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterMarkdown = "997ab1e6-3595-5248-9280-8efb232c3433"
+
+[compat]
+Documenter = "~0.23"

docs/make.jl

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+using Documenter
+using QuartetNetworkGoodnessFit
+DocMeta.setdocmeta!(QuartetNetworkGoodnessFit, :DocTestSetup, :(using QuartetNetworkGoodnessFit); recursive=true)
+
+makedocs(
+    sitename = "QuartetNetwork GoF.jl",
+    format = Documenter.HTML(prettyurls = get(ENV, "CI", nothing) == "true"), # easier local build
+    modules = [QuartetNetworkGoodnessFit],
+    pages = [
+        "home" => "index.md",
+        "library" => [
+            "public" => "lib/public.md",
+            "internal" => "lib/internal.md",
+        ]
+    ],
+)
+
+deploydocs(
+    repo = "github.com/cecileane/QuartetNetworkGoodnessFit.jl.git"
+)

docs/src/index.md

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+# QuartetNetworkGoodnessFit.jl
+
+
+Julia
+[package](https://github.com/cecileane/QuartetNetworkGoodnessFit.jl)
+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)
+package.
+
+```@contents
+Pages = ["lib/public.md", "lib/internals.md"]
+Depth = 1
+```
+
+## functions
+
+```@index
+Pages = ["lib/public.md", "lib/internals.md"]
+Order = [:function]
+```

docs/src/lib/internal.md

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+# internal documentation
+
+Documentation for `QuartetNetworkGoodnessFit`'s internal functions.
+Those functions are not exported, but can still be used
+(like: `QuartetNetworkGoodnessFit.foo()` for a function named `foo()`).
+
+## index
+
+```@index
+Pages = ["internals.md"]
+```
+
+## functions
+
+```@autodocs
+Modules = [QuartetNetworkGoodnessFit]
+Public  = false
+Order   = [:function]
+```

docs/src/lib/public.md

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+# public documentation
+
+Documentation for `QuartetNetworkGoodnessFit`'s public (exported) functions.
+
+## index
+
+```@index
+Pages = ["public.md"]
+```
+
+## functions
+
+```@autodocs
+Modules = [QuartetNetworkGoodnessFit]
+Private = false
+Order   = [:function]
+```

src/QuartetNetworkGoodnessFit.jl

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+module QuartetNetworkGoodnessFit
+
+using CategoricalArrays: cut
+using DataFrames
+using NLopt
+using PhyloNetworks
+using SpecialFunctions: loggamma
+using Statistics: mean
+using StatsFuns: normccdf, chisqccdf, betacdf, betaccdf
+using StatsBase: countmap
+
+import PhyloNetworks: ticr
+import PhyloNetworks: ticr!
+# fixit: delete from PhyloNetworks:
+# - the ticr and ticr! functions: src/ticr.jl
+# - mention of ticr in PhyloNetwork.jl and in docs/src/lib/public.md
+# - test_ticr.jl
+# - dependencies? like: "using SpecialFunctions: loggamma, gamma"
+# then delete "import PhyloNetworks: ticr, ticr!" from this package
+
+export
+quarnetGoFtest!,
+quarnetGoFtest,
+ticr,
+ticr!
+
+include("ticr.jl")
+include("quarnetGoF.jl")
+
+end # module