GitHub

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]'3×2 adjoint(::Matrix{Int64}) with eltype Int64:
 2  0
 2  2
 0  2
julia> ecosystem = ecosystem ./ sum(ecosystem)3×2 Matrix{Float64}:
 0.25  0.0
 0.25  0.25
 0.0   0.25
julia> jostbeta(ecosystem, [0, 1, 2])3×8 DataFrame
 Row │ div_type  measure   q      type_level  type_name  partition_level  part ⋯
     │ String    String    Int64  String      String     String           Stri ⋯
─────┼──────────────────────────────────────────────────────────────────────────
   1 │ Unique    JostBeta      0  types                  metacommunity         ⋯
   2 │ Unique    JostBeta      1  types                  metacommunity
   3 │ Unique    JostBeta      2  types                  metacommunity
                                                               2 columns omitted
julia> jostalpha(ecosystem, [0, 1, 2])3×8 DataFrame
 Row │ div_type  measure    q      type_level  type_name  partition_level  par ⋯
     │ String    String     Int64  String      String     String           Str ⋯
─────┼──────────────────────────────────────────────────────────────────────────
   1 │ Unique    JostAlpha      0  types                  metacommunity        ⋯
   2 │ Unique    JostAlpha      1  types                  metacommunity
   3 │ Unique    JostAlpha      2  types                  metacommunity
                                                               2 columns omitted

Jost's beta is the naive gamma diversity divided by Jost's alpha, and his alpha is in turn the raw alpha diversity divided by the naive-community beta. We believe our own NormalisedBeta has better properties — in particular it is invariant under shattering, which Jost's alpha and beta are not, as the framework explains — but these are provided for comparison.

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