Merge pull request #47 from EcoJulia/pielou

Add Pielou evenness

.github/workflows/CompatHelper.yaml

@@ -19,7 +19,7 @@ jobs:
         os:
           - ubuntu-latest
     steps:
-      - uses: julia-actions/setup-julia@latest
+      - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.julia-version }}
           arch: ${{ matrix.arch }}
@@ -28,7 +28,7 @@ jobs:
           import Pkg
           name = "CompatHelper"
           uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
-          version = "2"
+          version = "3"
           Pkg.add(; name, uuid, version)
         shell: julia --color=yes {0}
       - name: "Run CompatHelper"

.github/workflows/doc-cleanup.yaml

@@ -0,0 +1,26 @@
+name: Doc Preview Cleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v2
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+            if [ -d "previews/PR$PRNUM" ]; then
+              git config user.name "richardreeve"
+              git config user.email "[email protected]"
+              git rm -rf "previews/PR$PRNUM"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+            fi
+        env:
+            PRNUM: ${{ github.event.number }}

.github/workflows/docs.yaml

@@ -6,10 +6,13 @@ on:
       - dev
     tags:
       - 'v*'
+  pull_request:
   workflow_dispatch:
 
 jobs:
   build:
+    permissions:
+      contents: write
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code

.github/workflows/nightly.yaml

@@ -22,6 +22,6 @@ jobs:
           version: nightly
           arch: x64
       - name: Build package
-        uses: julia-actions/julia-buildpkg@latest
+        uses: julia-actions/julia-buildpkg@v1
       - name: Run tests
-        uses: julia-actions/julia-runtest@latest
+        uses: julia-actions/julia-runtest@v1

.github/workflows/testing.yaml

@@ -41,7 +41,7 @@ jobs:
       uses: r-lib/actions/setup-r@v2
       with:
         r-version: ${{ matrix.R-version }}
-    - name: Install R packages
+    - name: Install ape and rdiversity
       if: matrix.os == 'macOS-latest'
       run: |
         install.packages("ape", repos="http://cran.r-project.org")

NEWS.md

@@ -1,5 +1,8 @@
 # NEWS
 
+- v0.5.8
+  - Add in Pielou diversity measures
+  - Add docs for PRs
 - v0.5.7
   - Update compat and some doc fixes
 - v0.5.6

Project.toml

@@ -1,7 +1,7 @@
 name = "Diversity"
 uuid = "d3d5718d-52de-57ab-b67a-eca7fd6175a4"
 author = ["Richard Reeve <[email protected]>"]
-version = "0.5.7"
+version = "0.5.8"
 
 [deps]
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"

README.md

@@ -31,15 +31,16 @@ also recently revised, and may need further improvements.
 
 ## Installation
 
-The package is registered in the `General` registry on v1.x and so can be installed with `add`. For example on Julia v1.6:
+The package is registered in the `General` registry on v1.x and so can be
+installed with `add`. For example on Julia v1.8:
 
 ```julia
 (@v1.8) pkg> add Diversity
     Resolving package versions...
     Updating `~/.julia/environments/v1.8/Project.toml`
-  [d3d5718d] + Diversity v0.5.7
+  [d3d5718d] + Diversity v0.5.8
     Updating `~/.julia/environments/v1.8/Manifest.toml`
-  [d3d5718d] + Diversity v0.5.7
+  [d3d5718d] + Diversity v0.5.8
 
 (@v1.8) pkg>
 ```

docs/diversity.md

@@ -1,4 +1,4 @@
-## Diversity
+# Diversity package
 
 **Diversity** is a [Julia](http://www.julialang.org) package that
 provides functionality for measuring alpha, beta and gamma diversity
@@ -11,7 +11,7 @@ these are all ecological diversity measures, but this will be
 expanded, possibly through interfacing to BioJulia.
 
 This package is in beta now, but is cross-validated against our R
-package [boydorr/rdiversity][rdiversity-url], which is developed
+package [rdiversity][rdiversity-url], which is developed
 independently, so please [raise an issue][issues-url] if you find any
 problems. We now use a DataFrame as the common output format for all
 of the diversity calculations to provide consistency with our R
@@ -20,26 +20,21 @@ optimised for speed at the moment due to the substantial changes that
 have happened to it under the hood, and the Phylogenetics submodule is
 also new, and may need further improvements.
 
-Version 0.4, which has been recently released, has significant
-breaking changes to the underlying code, whuch mean it is no longer
-compatible with Julia v0.5. It is periodically working with Julia
-nightly and I aim to keep it that way (though other packages need to
-be updated too). Older interfaces from v0.2 have been removed in v0.4.
-
 ## Install
 
-The package is registered in the `General` registry on v1.x and so can be installed with `add`. For example on Julia v1.6:
+The package is registered in the `General` registry on v1.x and so can be installed with `add`. For example on Julia v1.8:
 
 ```julia
-(@v1.6) pkg> add Diversity
+(@v1.8) pkg> add Diversity
     Resolving package versions...
-    Updating `~/.julia/environments/v1.6/Project.toml`
-  [d3d5718d] + Diversity v0.5.5
-    Updating `~/.julia/environments/v1.6/Manifest.toml`
-  [d3d5718d] + Diversity v0.5.5
+    Updating `~/.julia/environments/v1.8/Project.toml`
+  [d3d5718d] + Diversity v0.5.8
+    Updating `~/.julia/environments/v1.8/Manifest.toml`
+  [d3d5718d] + Diversity v0.5.8
 
-(@v1.6) pkg>
+(@v1.8) pkg>
 ```
+
 ## Usage
 
 ### Diversity
@@ -69,13 +64,14 @@ using Diversity
 
 # Example population
 pop = [1 1 0; 2 0 0; 3 1 4]
-pop = pop / sum(pop)
+pop ./= sum(pop)
 
 # Create Metacommunity object
 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()`.
 
 ```julia
@@ -107,9 +103,11 @@ metadiv(meta, 0:2)
 ```
 
 Alternatively, if computational efficiency is not an issue, a single measure of diversity may be calculated directly by calling a wrapper function:
+
 ```julia
 norm_sub_alpha(meta, 0:2)
 ```
+
 A complete list of these functions is shown below:
 
 * `raw_sub_alpha()` : per-subcommunity estimate of naive-community metacommunity diversity
@@ -139,7 +137,7 @@ generate trees to incorporate into the diversity code:
 ```julia-repl
 julia> using Diversity, Phylo
 
-julia> communities = [4 1; 3 2; 1 0; 0 1] / 12;
+julia> communities = [4 1; 3 2; 1 0; 0 1] ./ 12;
 
 julia> nt = rand(Nonultrametric(4))
 RootedTree with 4 tips, 7 nodes and 6 branches.
@@ -156,31 +154,8 @@ julia> raw_meta_rho(metaphylo, [1, 2])
 │ 2   │ Phylogenetic Branch │ RawRho  │ 2     │ types      │           │ metacommunity   │                │ 1.52575   │
 ```
 
-[docs-latest-img]: https://img.shields.io/badge/docs-latest-blue.svg
-[docs-latest-url]: https://richardreeve.github.io/Diversity.jl/latest
-
-[docs-stable-img]: https://img.shields.io/badge/docs-stable-blue.svg
-[docs-stable-url]: https://richardreeve.github.io/Diversity.jl/stable
-
-[travis-img]: https://travis-ci.org/richardreeve/Diversity.jl.svg?branch=master
-[travis-url]: https://travis-ci.org/richardreeve/Diversity.jl?branch=master
-
-[appveyor-img]: https://ci.appveyor.com/api/projects/status/github/richardreeve/Diversity.jl?svg=true&branch=master
-[appveyor-url]: https://ci.appveyor.com/project/richardreeve/diversity-jl/branch/master
-
-[coveralls-img]: https://img.shields.io/coveralls/richardreeve/Diversity.jl.svg
-[coveralls-url]: https://coveralls.io/r/richardreeve/Diversity.jl?branch=master
-
-[codecov-img]: https://codecov.io/gh/richardreeve/Diversity.jl/branch/master/graph/badge.svg
-[codecov-url]: https://codecov.io/gh/richardreeve/Diversity.jl
-
 [issues-url]: https://github.com/richardreeve/Diversity.jl/issues
 
-[pkg-0.5-img]: http://pkg.julialang.org/badges/Diversity_0.5.svg
-[pkg-0.5-url]: http://pkg.julialang.org/?pkg=Diversity&ver=0.5
-[pkg-0.6-img]: http://pkg.julialang.org/badges/Diversity_0.6.svg
-[pkg-0.6-url]: http://pkg.julialang.org/?pkg=Diversity&ver=0.6
-
 [paper-url]: http://arxiv.org/abs/1404.6520
 
 [rdiversity-url]: https://github.com/boydorr/rdiversity

docs/src/ecology.md

@@ -1,6 +1,6 @@
 # Diversity.Ecology
 
-n the **Diversity.Ecology** submodule, we replicate old ecological
+In the **Diversity.Ecology** submodule, we replicate old ecological
 diversity measures and generalised versions of them that relate to our
 general measures of alpha, beta and gamma diversity at subcommunity
 and ecosystem measures. The generalisations of the richness, Shannon
@@ -18,7 +18,7 @@ julia> using Diversity.Ecology, LinearAlgebra
 
 julia> community = [10, 20, 20];
 
-julia> community /= sum(community);
+julia> community = community ./ sum(community); # Convert counts to proportions
 
 julia> diversity = simpson(community)
 1×7 DataFrame
@@ -27,6 +27,10 @@ julia> diversity = simpson(community)
 ─────┼──────────────────────────────────────────────────────────────────────────────────────
    1 │ Unique    Simpson  types                  subcommunity     1                    0.36
 
+julia> ecosystem = [2 2 0; 0 2 2]';
+
+julia> ecosystem = ecosystem ./ sum(ecosystem);
+
 julia> jaccard(ecosystem)
 1×8 DataFrame
  Row │ div_type  measure  q      type_level  type_name  partition_level  partition_name  diversity 
@@ -51,6 +55,40 @@ julia> generalisedjaccard(ecosystem, [0, 1, 2], Matrix(1.0I, 3, 3))
    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> community = [0.7, 0.2, 0.1];
+
+julia> pielou(community)
+1×7 DataFrame
+ Row │ div_type  measure  type_level  type_name  partition_level  partition_name  diversity 
+     │ String    String   String      String     String           String          Float64   
+─────┼──────────────────────────────────────────────────────────────────────────────────────
+   1 │ Unique    Pielou   types                  subcommunity     1                0.729847
+
+julia> communitymat = [10 20 30 20 0; #5 sites/subcommunities (columns) and 6 species (rows)
+                       10 0 50 80 10;
+                       60 10 90 0 0; 
+                       10 10 10 10 10;
+                       70 70 70 70 70;
+                       10 0 0 90 0];
+
+julia> generalisedpielou(subcommunityDiversity, communitymat)
+5×7 DataFrame
+ Row │ div_type     measure  type_level  type_name  partition_level  partition_name  diversity 
+     │ String       String   String      String     String           String          Float64   
+─────┼─────────────────────────────────────────────────────────────────────────────────────────
+   1 │ Arbitrary Z  Pielou   types                  subcommunity     1                0.781115
+   2 │ Arbitrary Z  Pielou   types                  subcommunity     2                0.745557
+   3 │ Arbitrary Z  Pielou   types                  subcommunity     3                0.888073
+   4 │ Arbitrary Z  Pielou   types                  subcommunity     4                0.864562
+   5 │ Arbitrary Z  Pielou   types                  subcommunity     5                0.622366
+
+julia> generalisedpielou(metacommunityDiversity, communitymat)
+1×7 DataFrame
+ Row │ div_type     measure  type_level  type_name  partition_level  partition_name  diversity 
+     │ String       String   String      String     String           String          Float64   
+─────┼─────────────────────────────────────────────────────────────────────────────────────────
+   1 │ Arbitrary Z  Pielou   types                  metacommunity                     0.510146
 ```
 
 ```@contents

docs/src/hill.md

@@ -12,7 +12,7 @@ julia> using Diversity.Hill
 
 julia> community = [10, 20, 20, 0, 3];
 
-julia> community /= sum(community);
+julia> community ./= sum(community);
 
 julia> diversities = hillnumber(community, [0, 1, 2])
 3×7 DataFrame

docs/src/index.md

@@ -29,7 +29,7 @@ julia> # Load the package into R
 julia> # Example population
        pop = [1 1 0; 2 0 0; 3 1 4];
 
-julia> pop = pop / sum(pop);
+julia> pop = pop ./ sum(pop);
 
 julia> # Create Metacommunity object
        meta = Metacommunity(pop);

docs/src/jost.md

@@ -14,7 +14,7 @@ julia> using Diversity.Jost
 
 julia> ecosystem = [2 2 0; 0 2 2]';
 
-julia> ecosystem /= sum(ecosystem);
+julia> ecosystem = ecosystem ./ sum(ecosystem);
 
 julia> diversities = jostbeta(ecosystem, [0, 1, 2])
 3×8 DataFrame

docs/src/phylogenetics.md

@@ -18,7 +18,7 @@ julia> using Diversity, Phylo
 
 julia> species = ["Dog", "Cat", "Human", "Potato"];
 
-julia> community = [4, 1, 3, 2] / 10;
+julia> community = [4, 1, 3, 2] ./ 10;
 
 julia> nt = rand(Nonultrametric(species))
 RootedTree with 4 tips, 7 nodes and 6 branches.

src/Diversity.jl

@@ -157,7 +157,7 @@ export generalisedrichness, richness
 export generalisedshannon, shannon
 export generalisedsimpson, simpson
 export generalisedjaccard, jaccard
-
+export generalisedpielou, pielou
 end # sub-module Ecology
 
 """

src/DiversityMeasure.jl

@@ -193,10 +193,9 @@ function inddiv end
     df = reduce(append!, dfs)
     cols = addedoutputcols(_getmeta(measure))
     if length(cols) > 0
-        len = length(df)
         data = getaddedoutput(_getmeta(measure))
         for col in keys(cols)
-            insert!(df, length(df) + 1, data[col], col)
+            insertcols!(df, ncol(df) + 1, col => data[col])
         end
     end
     return df
@@ -249,10 +248,9 @@ function subdiv end
     df = reduce(append!, dfs)
     cols = addedoutputcols(_getmeta(measure))
     if length(cols) > 0
-        len = length(df)
         data = getaddedoutput(_getmeta(measure))
         for col in keys(cols)
-            insert!(df, length(df) + 1, data[col], col)
+            insertcols!(df, ncol(df) + 1, col => data[col])
         end
     end
     return df
@@ -307,10 +305,9 @@ function metadiv end
                    diversity=raw)
    cols = addedoutputcols(_getmeta(measure))
    if length(cols) > 0
-       len = length(df)
        data = getaddedoutput(_getmeta(measure))
        for col in keys(cols)
-           insert!(df, length(df) + 1, data[col], col)
+           insertcols!(df, ncol(df) + 1, col => data[col])
        end
    end
    return df