Diversity.Jost

Lou Jost's diversity measures are found in the Diversity.Jost submodule.

Usage

Accessing the main functionality in the package is simple:

julia> using Diversity.Jost

julia> ecosystem = [2 2 0; 0 2 2]';

julia> ecosystem /= sum(ecosystem);

julia> diversities = jostbeta(ecosystem, [0, 1, 2])
3×8 DataFrame
│ Row │ div_type │ measure  │ q     │ type_level │ type_name │ partition_level │ partition_name │ diversity │
│     │ String   │ String   │ Int64 │ String     │ String    │ String          │ String         │ Float64   │
├─────┼──────────┼──────────┼───────┼────────────┼───────────┼─────────────────┼────────────────┼───────────┤
│ 1   │ Unique   │ JostBeta │ 0     │ types      │           │ metacommunity   │                │ 1.5       │
│ 2   │ Unique   │ JostBeta │ 1     │ types      │           │ metacommunity   │                │ 1.41421   │
│ 3   │ Unique   │ JostBeta │ 2     │ types      │           │ metacommunity   │                │ 1.33333   │
Diversity.Jost.jostalphaMethod
jostalpha(proportions::AbstractMatrix, qs)

Calculates Jost's alpha diversity of a series of columns representing independent community counts, for a series of orders, repesented as a vector of qs. This is just the naive-community ecosystem diversity divided by the naive-community beta diversity.

Arguments:

  • proportions relative proportions of different individuals / species in population (vector, or matrix where columns are for individual sub-communities)

  • qs single number or vector of orders of diversity measurement

Returns:

  • DataFrame of diversities
source
Diversity.Jost.jostbetaMethod
jostbeta(proportions::AbstractMatrix, qs)

Calculates Jost's beta diversity of a series of columns representing independent community counts, for a series of orders, repesented as a vector of qs. This is just the naive gamma diversity divided by Jost's alpha diversity

Arguments:

  • proportions relative proportions of different individuals / species in population (vector, or matrix where columns are for individual sub-communities)

  • qs single number or vector of orders of diversity measurement

Returns:

  • DataFrame of diversities
source