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Diversity

Julia package for diversity measurement

Readme

Diversity

Package for measuring and partitioning diversity

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Diversity is a Julia package that provides functionality for measuring alpha, beta and gamma diversity of metacommunities (e.g. ecosystems) and their constituent subcommunities. It uses the diversity measures described in the arXiv paper arXiv:1404.6520 (q-bio.QM), How to partition diversity. It also provides a series of other related and older diversity measures through sub-modules. Currently these are all ecological diversity measures, but this will be expanded, possibly through interfacing to BioJulia.

This package is in beta now, but is cross-validated against our R package boydorr/rdiversity, which is developed independently, so please raise an issue if you find any problems. The phylogenetics submodule in particular is currently under heavy development.

Version 0.3, which has been recently released, has significant breaking changes to the standard interface for calculating diversity and especially to the output format to provide consistency with our R package rdiversity. In particular, we now use a DataFrame as the common output format for all of the diversity calculations. The code is certainly not optimised for speed at the moment due to the substantial changes that have happened to it under the hood.

Older interfaces have been deprecated, and will be removed in v0.4.

Install

Diversity is in METADATA and can be installed via Pkg.add("Diversity").

Usage

Diversity

The main 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 arXiv:1404.6520 (q-bio.QM)). 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 ascii names (e.g. NormalisedAlpha()), which are. We also provide a general function for extract any diversity measure for a series of subcommunity relative abundances.

Getting started

Before calculating diversity a Metacommunity object must be created. This object contains all the information needed to calculate diversity.

# Load the package into R
using Diversity

# Example population
pop = [1 1 0; 2 0 0; 3 1 4]
pop = pop / sum(pop)

# Create Metacommunity object
meta = Metacommunity(pop)

Calculating diversity

First we need to calculate the low-level diversity component seperately, by passing a metacommunity object to the appropriate function; RawAlpha(), NormalisedAlpha(), RawBeta(), NormalisedBeta(), RawRho(), NormalisedRho(), or Gamma().

# First, calculate the normalised alpha component
component = NormalisedAlpha(meta)

Afterwhich, subdiv() or metadiv() are used to calculate subcommunity or metacommunity diversity, respectively (since both subcommunity and metacommunity diversity measures are transformations of the same low-level components, this is computationally more efficient).

# Then, calculate species richness of the subcommunities
subdiv(component, 0)

# or the average (alpha) species richness across the whole population
metadiv(component, 0)

# We can also generate a diversity profile by calculating multiple q-values simultaneously
df = subdiv(component, 0:30)

In some instances, it may be useful to calculate all subcommunity (or metacommunity) measures. In which case, a Metacommunity object may be passed directly to subdiv() or metadiv():

# To calculate all subcommunity diversity measures
subdiv(meta, 0:2)

# To calculate all metacommunity diversity measures
metadiv(meta, 0:2)

Alternatively, if computational efficiency is not an issue, a single measure of diversity may be calculated directly by calling a wrapper function:

norm_sub_alpha(meta, 0:2)

A complete list of these functions is shown below:

  • raw_sub_alpha() : per-subcommunity estimate of naive-community metacommunity diversity
  • norm_sub_alpha() : similarity-sensitive diversity of each subcommunity in isolation
  • raw_sub_rho() : redundancy of individual subcommunities
  • norm_sub_rho() : representativeness of individual subcommunities
  • raw_sub_beta() : distinctiveness of individual subcommunities
  • norm_sub_beta() : per-subcommunity estimate of effective number of distinct subcommunities
  • sub_gamma() : contribution per individual in a subcommunity toward metacommunity diversity
  • raw_meta_alpha() : naive-community metacommunity diversity
  • norm_meta_alpha() : average similarity-sensitive diversity of subcommunities
  • raw_meta_rho() : average redundancy of subcommunities
  • norm_meta_rho() : average representativeness of subcommunities
  • raw_meta_beta() : average distinctiveness of subcommunities
  • norm_meta_beta() : effective number of distinct subcommunities
  • meta_gamma() : metacommunity similarity-sensitive diversity

Diversity.Phylogenetics

Phylogenetic diversity (described here) is included in the Diversity.Phylogenetics submodule. Documentation for these diversity measures can be found here. The phylogenetics code relies on the Phylo package to generate trees to incorporate into the diversity code:

julia> using Diversity, Phylo, Diversity.Phylogenetics

julia> communities = [4 1; 3 2; 1 0; 0 1] / 12;

julia> nt = rand(Nonultrametric(4))
NamedTree phylogenetic tree with 7 nodes and 6 branches
Leaf names:
String["tip 1", "tip 2", "tip 3", "tip 4"]

julia> metaphylo = Metacommunity(communities, PhyloTypes(nt));

julia> raw_meta_rho(metaphylo, [1, 2])
2×7 DataFrames.DataFrame
│ Row │ measure  │ q │ type_level │ type_name │ partition_level │
├─────┼──────────┼───┼────────────┼───────────┼─────────────────┤
│ 1   │ "RawRho" │ 1 │ "types"    │ ""        │ "metacommunity" │
│ 2   │ "RawRho" │ 2 │ "types"    │ ""        │ "metacommunity" │

│ Row │ partition_name │ diversity │
├─────┼────────────────┼───────────┤
│ 1   │ ""             │ 1.66187   │
│ 2   │ ""             │ 1.51391   │

The package also provides some other sub-modules for related measures:

Diversity.Ecology

Many existing ecological diversity measures can be derived from our diversity measures, and so we provide them in the Diversity.Ecology submodule along with generalised versions of them that relate to our general measures of alpha, beta and gamma diversity at subcommunity and metacommunity levels. The generalisations of species richness, Shannon entropy and Simpson's index are the only standard measures we are aware of whose subcommunity components sum directly to the corresponding metacommunity measure (although note that Simpson's index decreases for increased diversity, so small components are more diverse). Documentation for these diversity measures can be found here.

Diversity.Hill

Hill numbers are found in the Diversity.Hill sub-module. Documentation for these diversity measures can be found here.

Diversity.Jost

Lou Jost's diversity measures are found in the Diversity.Jost sub-module. Documentation for these diversity measures is here.

Documentation

Documentation is generated by the Base documentation in Julia and online via the Documenter package.

Usage

Accessing the documentation in Julia is easy:

using Diversity

# Returns any documentation for the subdiv() function
?subdiv

The documentation is also available online.

Stable branch

The online documentation for the current stable branch is here.

Master branch

The online documentation for the latest master (unreleased) branch is here.

First Commit

08/31/2014

Last Touched

8 days ago

Commits

538 commits

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