Merge pull request #27 from richardreeve/multiple

Updating phylogenetic diversity types, speed-up, Julia v1.0!

.travis.yml

@@ -14,26 +14,27 @@ os:
 julia:
  - 0.6
  - 0.7
+ - 1.0
  - nightly
 
 matrix:
  fast_finish: true
  allow_failures:
- - julia: 0.7
  - julia: nightly
 
 before_install:
  # linux
  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9; fi
  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo add-apt-repository -y "deb http://cran.rstudio.com/bin/linux/ubuntu $(lsb_release -s -c)/"; fi
  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-get update -qq -y; fi
- - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-get install git libxml2-dev r-base r-base-dev r-recommended -y; fi
+ - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-get install git libxml2-dev r-base r-base-dev r-recommended -y --allow-unauthenticated; fi
 
 script:
  - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
- - if [ "$TRAVIS_OS_NAME" == "linux" ]; then JULIA_MUST_CROSSVALIDATE=1 julia -e 'Pkg.init(); Pkg.clone(pwd()); Pkg.build("Diversity"); Pkg.test("Diversity", coverage=true)'; fi
- - if [ "$TRAVIS_OS_NAME" == "osx" ]; then julia -e 'Pkg.init(); Pkg.clone(pwd()); Pkg.build("Diversity"); Pkg.test("Diversity", coverage=true)'; fi
+ - if [ "$TRAVIS_OS_NAME" == "linux" ]; then JULIA_MUST_CROSSVALIDATE=1 julia -e '(try using Pkg; true catch; false end || Pkg.init()); Pkg.clone(pwd()); Pkg.build("Diversity"); Pkg.test("Diversity", coverage=true)'; fi
+ # (VERSION >= v"0.7.0-" && (ENV["JULIA_MUST_CROSSVALIDATE"] = "0")); 
+ - if [ "$TRAVIS_OS_NAME" == "osx" ]; then julia -e '(try using Pkg; true catch; false end || Pkg.init()); Pkg.clone(pwd()); Pkg.build("Diversity"); Pkg.test("Diversity", coverage=true)'; fi
 
 after_success:
- - julia -e 'cd(Pkg.dir("Diversity", "test")); include("coverage.jl")'
- - julia -e 'Pkg.add("Documenter"); cd(Pkg.dir("Diversity")); include(joinpath("docs", "make.jl"))'
+ - julia -e '(try using Pkg; catch end); using Diversity; cd(Diversity.path()); include("coverage.jl")'
+ - julia -e '(try using Pkg; catch end); Pkg.add("Documenter"); using Diversity; cd(Diversity.path(;dir=".")); include(joinpath("docs", "make.jl"))'

README.md

@@ -146,19 +146,19 @@ A complete list of these functions is shown below:
 * `norm_meta_beta()` : effective number of distinct subcommunities
 * `meta_gamma()` : metacommunity similarity-sensitive diversity
 
-#### Diversity.Phylogenetics
+#### Phylogenetics
 
 Phylogenetic diversity (described [here][leinster-cobbold-url]) is
-included in the Diversity.Phylogenetics submodule. Documentation for
-these diversity measures can be found
+automatically included in the Diversity module when the `Phylo` package
+is loaded. Documentation for these diversity measures can be found
 [here](http://richardreeve.github.io/Diversity.jl/latest/phylogenetics/).
 The phylogenetics code relies on the [Phylo][phylo-url] package to
 generate trees to incorporate into the diversity code, and the
 `Diversity.Phylogenetics` sub-package will be created when both
 main packages are loaded:
 
 ```julia-repl
-julia> using Diversity, Phylo, Diversity.Phylogenetics
+julia> using Diversity, Phylo
 Creating Diversity to Phylo interface...
 
 julia> communities = [4 1; 3 2; 1 0; 0 1] / 12;
@@ -171,16 +171,11 @@ String["tip 1", "tip 2", "tip 3", "tip 4"]
 julia> metaphylo = Metacommunity(communities, PhyloTypes(nt));
 
 julia> raw_meta_rho(metaphylo, [1, 2])
-2×7 DataFrames.DataFrame
-│ Row │ measure │ q │ type_level │ type_name │ partition_level │
-├─────┼──────────┼───┼────────────┼───────────┼─────────────────┤
-│ 1 │ "RawRho" │ 1 │ "types" │ "" │ "metacommunity" │
-│ 2 │ "RawRho" │ 2 │ "types" │ "" │ "metacommunity" │
-
-│ Row │ partition_name │ diversity │
-├─────┼────────────────┼───────────┤
-│ 1 │ "" │ 1.66187 │
-│ 2 │ "" │ 1.51391 │
+2×8 DataFrames.DataFrame
+│ Row │ div_type │ measure │ q │ type_level │ type_name │ partition_level │ partition_name │ diversity │
+├─────┼──────────────┼─────────┼───┼────────────┼───────────┼─────────────────┼────────────────┼───────────┤
+│ 1 │ Phylogenetic │ RawRho │ 1 │ types │ │ metacommunity │ │ 1.75622 │
+│ 2 │ Phylogenetic │ RawRho │ 2 │ types │ │ metacommunity │ │ 1.61371 │
 ```
 
 The package also provides some other sub-modules for related measures:

appveyor.yml

@@ -1,8 +1,9 @@
 environment:
  matrix:
  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"
+ - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/1.0/julia-1.0-latest-win64.exe"
  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
- 
+
 branches:
  only:
  - master
@@ -40,8 +41,8 @@ install:
 build_script:
 # Need to convert from shallow to complete for Pkg.clone to work
  - IF EXIST .git\shallow (git fetch --unshallow)
- - C:\projects\julia\bin\julia -e "versioninfo();
+ - C:\projects\julia\bin\julia -e "(try using Pkg; true catch; false end || Pkg.init());
  Pkg.clone(pwd(), \"Diversity\"); Pkg.build(\"Diversity\")"
 
 test_script:
- - C:\projects\julia\bin\julia -e "Pkg.test(\"Diversity\")"
+ - C:\projects\julia\bin\julia -e "(try using Pkg; catch end); Pkg.test(\"Diversity\")"

docs/diversity.md

@@ -66,7 +66,7 @@ meta = Metacommunity(pop)
 ```
 
 #### Calculating diversity
-First we need to calculate the low-level diversity component seperately, by passing a `metacommunity` object to the appropriate function; `RawAlpha()`, `NormalisedAlpha()`, `RawBeta()`, `NormalisedBeta()`, `RawRho()`, `NormalisedRho()`, or `Gamma()`. 
+First we need to calculate the low-level diversity component seperately, by passing a `metacommunity` object to the appropriate function; `RawAlpha()`, `NormalisedAlpha()`, `RawBeta()`, `NormalisedBeta()`, `RawRho()`, `NormalisedRho()`, or `Gamma()`.
 
 ```julia
 # First, calculate the normalised alpha component
@@ -128,6 +128,7 @@ generate trees to incorporate into the diversity code:
 
 ```julia-repl
 julia> using Diversity, Phylo, Diversity.Phylogenetics
+Creating Diversity to Phylo interface...
 
 julia> communities = [4 1; 3 2; 1 0; 0 1] / 12;
 
@@ -139,16 +140,11 @@ String["tip 1", "tip 2", "tip 3", "tip 4"]
 julia> metaphylo = Metacommunity(communities, PhyloTypes(nt));
 
 julia> raw_meta_rho(metaphylo, [1, 2])
-2×7 DataFrames.DataFrame
-│ Row │ measure │ q │ type_level │ type_name │ partition_level │
-├─────┼──────────┼───┼────────────┼───────────┼─────────────────┤
-│ 1 │ "RawRho" │ 1 │ "types" │ "" │ "metacommunity" │
-│ 2 │ "RawRho" │ 2 │ "types" │ "" │ "metacommunity" │
-
-│ Row │ partition_name │ diversity │
-├─────┼────────────────┼───────────┤
-│ 1 │ "" │ 1.66187 │
-│ 2 │ "" │ 1.51391 │
+2×8 DataFrames.DataFrame
+│ Row │ div_type │ measure │ q │ type_level │ type_name │ partition_level │ partition_name │ diversity │
+├─────┼──────────────┼─────────┼───┼────────────┼───────────┼─────────────────┼────────────────┼───────────┤
+│ 1 │ Phylogenetic │ RawRho │ 1 │ types │ │ metacommunity │ │ 1.80666 │
+│ 2 │ Phylogenetic │ RawRho │ 2 │ types │ │ metacommunity │ │ 1.7056 │
 ```
 
 [docs-latest-img]: https://img.shields.io/badge/docs-latest-blue.svg

docs/make.jl

@@ -1,7 +1,7 @@
 using Documenter
 using Diversity
 
-makedocs(modules = [Diversity, Diversity.Phylogenetics,
+makedocs(modules = [Diversity,
  Diversity.Ecology, Diversity.Jost, Diversity.Hill],
  clean = false)
 

docs/mkdocs.yml

@@ -27,8 +27,8 @@ docs_dir: 'build'
 
 pages:
 - Introduction: index.md
+- Phylogenetics: phylogenetics.md
 - Submodules:
- - Phylogenetics: phylogenetics.md
  - API: api.md
 - Other related measures:
  - Ecology: ecology.md

docs/src/ecology.md

@@ -20,55 +20,34 @@ julia> community /= sum(community);
 
 julia> diversity = simpson(community)
 1×7 DataFrames.DataFrame
-│ Row │ measure │ q │ type_level │ type_name │ partition_level │
-├─────┼───────────┼───┼────────────┼───────────┼─────────────────┤
-│ 1 │ "Simpson" │ 2 │ "types" │ "" │ "subcommunity" │
-
-│ Row │ partition_name │ diversity │
-├─────┼────────────────┼───────────┤
-│ 1 │ "1" │ 0.36 │
-
+│ Row │ div_type │ measure │ type_level │ type_name │ partition_level │ partition_name │ diversity │
+├─────┼──────────┼─────────┼────────────┼───────────┼─────────────────┼────────────────┼───────────┤
+│ 1 │ Unique │ Simpson │ types │ │ subcommunity │ 1 │ 0.36 │
 julia> ecosystem = [2 2 0.; 0 2 2]';
 
 julia> ecosystem /= sum(ecosystem);
 
 julia> jaccard(ecosystem)
-1×7 DataFrames.DataFrame
-│ Row │ measure │ q │ type_level │ type_name │ partition_level │
-├─────┼───────────┼───┼────────────┼───────────┼─────────────────┤
-│ 1 │ "Jaccard" │ 0 │ "types" │ "" │ "metacommunity" │
-
-│ Row │ partition_name │ diversity │
-├─────┼────────────────┼───────────┤
-│ 1 │ "" │ 0.333333 │
+1×8 DataFrames.DataFrame
+│ Row │ div_type │ measure │ q │ type_level │ type_name │ partition_level │ partition_name │ diversity │
+├─────┼──────────┼─────────┼───┼────────────┼───────────┼─────────────────┼────────────────┼───────────┤
+│ 1 │ Unique │ Jaccard │ 0 │ types │ │ metacommunity │ │ 0.333333 │
 
 julia> generalisedjaccard(ecosystem, [0, 1, 2])
-3×7 DataFrames.DataFrame
-│ Row │ measure │ q │ type_level │ type_name │ partition_level │
-├─────┼───────────┼───┼────────────┼───────────┼─────────────────┤
-│ 1 │ "Jaccard" │ 0 │ "types" │ "" │ "metacommunity" │
-│ 2 │ "Jaccard" │ 1 │ "types" │ "" │ "metacommunity" │
-│ 3 │ "Jaccard" │ 2 │ "types" │ "" │ "metacommunity" │
-
-│ Row │ partition_name │ diversity │
-├─────┼────────────────┼───────────┤
-│ 1 │ "" │ 0.333333 │
-│ 2 │ "" │ 0.414214 │
-│ 3 │ "" │ 0.5 │
+3×8 DataFrames.DataFrame
+│ Row │ div_type │ measure │ q │ type_level │ type_name │ partition_level │ partition_name │ diversity │
+├─────┼─────────────┼─────────┼───┼────────────┼───────────┼─────────────────┼────────────────┼───────────┤
+│ 1 │ Arbitrary Z │ Jaccard │ 0 │ types │ │ metacommunity │ │ 0.333333 │
+│ 2 │ Arbitrary Z │ Jaccard │ 1 │ types │ │ metacommunity │ │ 0.414214 │
+│ 3 │ Arbitrary Z │ Jaccard │ 2 │ types │ │ metacommunity │ │ 0.5 │
 
 julia> generalisedjaccard(ecosystem, [0, 1, 2], eye(3))
-3×7 DataFrames.DataFrame
-│ Row │ measure │ q │ type_level │ type_name │ partition_level │
-├─────┼───────────┼───┼────────────┼───────────┼─────────────────┤
-│ 1 │ "Jaccard" │ 0 │ "types" │ "" │ "metacommunity" │
-│ 2 │ "Jaccard" │ 1 │ "types" │ "" │ "metacommunity" │
-│ 3 │ "Jaccard" │ 2 │ "types" │ "" │ "metacommunity" │
-
-│ Row │ partition_name │ diversity │
-├─────┼────────────────┼───────────┤
-│ 1 │ "" │ 0.333333 │
-│ 2 │ "" │ 0.414214 │
-│ 3 │ "" │ 0.5 │
+3×8 DataFrames.DataFrame
+│ Row │ div_type │ measure │ q │ type_level │ type_name │ partition_level │ partition_name │ diversity │
+├─────┼─────────────┼─────────┼───┼────────────┼───────────┼─────────────────┼────────────────┼───────────┤
+│ 1 │ Arbitrary Z │ Jaccard │ 0 │ types │ │ metacommunity │ │ 0.333333 │
+│ 2 │ Arbitrary Z │ Jaccard │ 1 │ types │ │ metacommunity │ │ 0.414214 │
+│ 3 │ Arbitrary Z │ Jaccard │ 2 │ types │ │ metacommunity │ │ 0.5 │
 ```
 
 ```@contents

docs/src/hill.md

@@ -6,25 +6,19 @@
 Accessing the main functionality in the package is simple:
 
 ```jldoctest
-julia> using Diversity.Hill
+ulia> using Diversity.Hill
 
 julia> community = [10, 20, 20, 0, 3];
 
 julia> community /= sum(community);
 
 julia> diversities = hillnumber(community, [0, 1, 2])
-3×7 DataFrames.DataFrame
-│ Row │ measure │ q │ type_level │ type_name │ partition_level │
-├─────┼──────────────┼───┼────────────┼───────────┼─────────────────┤
-│ 1 │ "HillNumber" │ 0 │ "types" │ "" │ "subcommunity" │
-│ 2 │ "HillNumber" │ 1 │ "types" │ "" │ "subcommunity" │
-│ 3 │ "HillNumber" │ 2 │ "types" │ "" │ "subcommunity" │
-
-│ Row │ partition_name │ diversity │
-├─────┼────────────────┼───────────┤
-│ 1 │ "1" │ 4.0 │
-│ 2 │ "1" │ 3.36264 │
-│ 3 │ "1" │ 3.09021 │
+3×8 DataFrames.DataFrame
+│ Row │ div_type │ measure │ q │ type_level │ type_name │ partition_level │ partition_name │ diversity │
+├─────┼──────────┼────────────┼───┼────────────┼───────────┼─────────────────┼────────────────┼───────────┤
+│ 1 │ Unique │ HillNumber │ 0 │ types │ │ subcommunity │ 1 │ 4.0 │
+│ 2 │ Unique │ HillNumber │ 1 │ types │ │ subcommunity │ 1 │ 3.36264 │
+│ 3 │ Unique │ HillNumber │ 2 │ types │ │ subcommunity │ 1 │ 3.09021 │
 ```
 
 ```@contents