Multiple 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