In the Diversity.Ecology package, 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 and Simpson are the only standard measures we are aware of whose subcommunity components sum directly to the corresponding ecosystem measure (although note that Simpson's index decreases for increased diversity, so small components are more diverse).

Usage

Accessing the functionality in the package is simple:

julia> using Diversity.Ecology, LinearAlgebra

julia> community = [10, 20, 20];

julia> community /= sum(community);

julia> diversity = simpson(community)
1×7 DataFrames.DataFrame
│ 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)
1×8 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])
3×8 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], Matrix(1.0I, 3, 3))
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

```@autodocs
Modules = [Diversity.Ecology]
Private = false

@index