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Jost

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

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])
3×7 DataFrames.DataFrame
│ Row │ measure    │ q │ type_level │ type_name │ partition_level │
├─────┼────────────┼───┼────────────┼───────────┼─────────────────┤
│ 1   │ "JostBeta" │ 0 │ "types"    │ ""        │ "metacommunity" │
│ 2   │ "JostBeta" │ 1 │ "types"    │ ""        │ "metacommunity" │
│ 3   │ "JostBeta" │ 2 │ "types"    │ ""        │ "metacommunity" │

│ Row │ partition_name │ diversity │
├─────┼────────────────┼───────────┤
│ 1   │ ""             │ 1.5       │
│ 2   │ ""             │ 1.41421   │
│ 3   │ ""             │ 1.33333   │

Diversity.jl

# Diversity.Jost — Module.

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

source

# Diversity.Jost.jostalpha — Method.

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.jostbeta — Method.

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