phylogenetics.md

Phylogenetic diversity

When both Diversity and Phylo are loaded, we generate Phylogenetic diversity measures, based on Faith PD and extended by Chao.

Usage

Using the functionality in the package is simple:

• Create a tree (using our Phylo package)
• Create a PhyloBranches (AbstractTypes subtype) object from it
• Create a Metacommunity from that
• Calculate diversity!

julia> using Diversity, Phylo

julia> species = ["Dog", "Cat", "Human", "Potato"];

julia> community = [4, 1, 3, 2] ./ 10;

julia> nt = rand(Nonultrametric(species))
RootedTree with 4 tips, 7 nodes and 6 branches.
Leaf names are Dog, Human, Potato and Cat

julia> collect(getbranches(nt))
6-element Vector{LinkBranch{OneRoot, String, Dict{String, Any}, Float64}}:
 LinkBranch 7, from node Node 5 to node Human (length 0.48129057007442144).

 LinkBranch 8, from node Node 5 to node Potato (length 0.04547304399403693).

 LinkBranch 9, from node Node 6 to node Node 5 (length 0.5257296693452039).

 LinkBranch 10, from node Node 6 to node Cat (length 1.2058770065006985).

 LinkBranch 11, from node Node 7 to node Dog (length 1.0055430448967724).

 LinkBranch 12, from node Node 7 to node Node 6 (length 0.07011899861455448).


julia> ph = PhyloBranches(nt);

julia> metaphylo = Metacommunity(community, ph);

julia> leafnames = gettypenames(metaphylo, true)
4-element Vector{String}:
 "Dog"
 "Human"
 "Potato"
 "Cat"

julia> meta_gamma(metaphylo, 0)
1×8 DataFrame
│ Row │ div_type            │ measure │ q     │ type_level │ type_name │ partition_level │ partition_name │ diversity │
│     │ String              │ String  │ Int64 │ String     │ String    │ String          │ String         │ Float64   │
├─────┼─────────────────────┼─────────┼───────┼────────────┼───────────┼─────────────────┼────────────────┼───────────┤
│ 1   │ Phylogenetic Branch │ Gamma   │ 0     │ types      │           │ metacommunity   │                │ 3.48192   │