Diversity.jl
The main Diversity package provides basic numbers-equivalent
diversity measures (described in
Hill, 1973),
similarity-sensitive diversity measures (generalised from Hill, and
described in
Leinster and Cobbold, 2012),
and related alpha, beta and gamma diversity measures at the level of
the metacommunity and its component subcommunities (generalised in
turn from Leinster and Cobbold, and described in
Reeve et al, 2014). The diversity
functions exist both with unicode names (e.g. ᾱ()
), which are
not automatically exported (as we feel they are too short) and with
matching longer ASCII names (e.g. NormalisedAlpha()
), which are.
We also provide functions to calculate appropriate
subdiv()
and metadiv()
values for each measure, a general diversity()
function for
extract any diversity measure at a series of scales.
Accessing the main functionality in the package is simple:
julia> # Load the package into R
using Diversity
julia> # Example population
pop = [1 1 0; 2 0 0; 3 1 4];
julia> pop = pop / sum(pop);
julia> # Create Metacommunity object
meta = Metacommunity(pop);
julia> diversities = norm_meta_alpha(meta, [0, 1, 2, Inf])
4×8 DataFrames.DataFrame
│ Row │ div_type │ measure │ q │ type_level │ type_name │ partition_level │ partition_name │ diversity │
├─────┼──────────┼─────────────────┼─────┼────────────┼───────────┼─────────────────┼────────────────┼───────────┤
│ 1 │ Unique │ NormalisedAlpha │ 0.0 │ types │ │ metacommunity │ │ 2.16667 │
│ 2 │ Unique │ NormalisedAlpha │ 1.0 │ types │ │ metacommunity │ │ 1.86121 │
│ 3 │ Unique │ NormalisedAlpha │ 2.0 │ types │ │ metacommunity │ │ 1.63636 │
│ 4 │ Unique │ NormalisedAlpha │ Inf │ types │ │ metacommunity │ │ 1.0 │
julia> Z = [1.0 0 0; 0 1 1; 1 1 1];
julia> meta_z = Metacommunity(pop, Z);
julia> rho = RawRho(meta_z);
julia> redundancies = subdiv(rho, 2)
3×8 DataFrames.DataFrame
│ Row │ div_type │ measure │ q │ type_level │ type_name │ partition_level │ partition_name │ diversity │
├─────┼─────────────┼─────────┼───┼────────────┼───────────┼─────────────────┼────────────────┼───────────┤
│ 1 │ Arbitrary Z │ RawRho │ 2 │ types │ │ subcommunity │ 1 │ 2.0 │
│ 2 │ Arbitrary Z │ RawRho │ 2 │ types │ │ subcommunity │ 2 │ 3.0 │
│ 3 │ Arbitrary Z │ RawRho │ 2 │ types │ │ subcommunity │ 3 │ 3.0 │
```@contents
```@autodocs
Modules = [Diversity]
Private = false
@index