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Analysis and Metrics","monthly_downloads":25,"total_dependent_repos":4,"total_dependent_packages":1,"readme":"# Diversity\n\n## A package for measuring and partitioning diversity\n\n| **Documentation** | **Build Status** | **DOI** |\n|:-----------------:|:--------------------------:|:--------------------------:|\n| [![stable docs][docs-stable-img]][docs-stable-url] | [![build tests][actions-img]][actions-url] [![JuliaNightly][nightly-img]][nightly-url] | [![Zenodo][zenodo-badge]][zenodo-url] |\n| [![dev docs][docs-dev-img]][docs-dev-url] | [![codecov][codecov-img]][codecov-url] | |\n\n## Summary\n\n**Diversity** is a [Julia](http://www.julialang.org) package that\nprovides functionality for measuring alpha, beta and gamma diversity\nof metacommunities (e.g. ecosystems) and their constituent\nsubcommunities. It uses the diversity measures described in the arXiv\npaper [arXiv:1404.6520 (q-bio.QM)][paper-url],\n*How to partition diversity*. It also provides a series of other\nolder diversity measures through sub-modules. Currently\nthese are all ecological diversity measures, but this will be\nexpanded through interfacing to EcoJulia and BioJulia.\n\nThis package is in beta now, but is cross-validated against our R\npackage [boydorr/rdiversity][rdiversity-url], which is developed\nindependently, so please [raise an issue][issues-url] if you find any\nproblems. We now use a DataFrame as the common output format for all\nof the diversity calculations to provide consistency with our R\npackage [rdiversity][rdiversity-url]. The code is not\noptimised for speed at the moment due to the substantial changes that\nhave happened to it under the hood, and the Phylogenetics submodule is\nalso recently revised, and may need further improvements.\n\n## Installation\n\nThe package is registered in the `General` registry on v1.x and so can be\ninstalled with `add`. For example on Julia v1.10:\n\n```julia\n(@v1.10) pkg\u003e add Diversity\n    Resolving package versions...\n    Updating `~/.julia/environments/v1.10/Project.toml`\n  [d3d5718d] + Diversity v0.5.15\n    Updating `~/.julia/environments/v1.10/Manifest.toml`\n  [d3d5718d] + Diversity v0.5.15\n  \n(@v1.10) pkg\u003e\n```\n\n## Project Status\n\nThe package is confirmed to build and work against Julia v1.9 and the current\nrelease and the latest release on Linux, macOS, and Windows. It is also tested\nagainst nightly.\n\n## Contributing and Questions\n\nContributions are very welcome, as are feature requests and suggestions.\nPlease open an [issue][issues-url] if you encounter any problems or would\njust like to ask a question.\n\n## Usage\n\n### Diversity Measures\n\nThe main package provides basic numbers-equivalent diversity measures\n(described in [Hill, 1973](http://www.jstor.org/stable/1934352)),\nsimilarity-sensitive diversity measures (generalised from Hill, and\ndescribed in\n[Leinster and Cobbold, 2012][leinster-cobbold-url]),\nand related alpha, beta and gamma diversity measures at the level of\nthe metacommunity and its component subcommunities (generalised in\nturn from Leinster and Cobbold, and described in\n[arXiv:1404.6520 (q-bio.QM)][paper-url]). The diversity functions\nexist both with unicode names (e.g. ᾱ()), which are not automatically\nexported as we feel they are too short and with matching ascii names\n(e.g. NormalisedAlpha()), which are. We also provide a general\nfunction for extract any diversity measure for a series of\nsubcommunity relative abundances.\n\n#### Getting started\n\nBefore calculating diversity a `Metacommunity` object must be created. This object contains all the information needed to calculate diversity.\n\n```julia\n# Load the package into Julia\nusing Diversity\n\n# Example population\npop = [1 1 0; 2 0 0; 3 1 4]\npop = pop / sum(pop)\n\n# Create Metacommunity object\nmeta = Metacommunity(pop)\n```\n\n#### Calculating diversity\n\nFirst 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()`.\n\n```julia\n# First, calculate the normalised alpha component\ncomponent = NormalisedAlpha(meta)\n```\n\nAfterwhich, `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).\n\n```julia\n# Then, calculate species richness of the subcommunities\nsubdiv(component, 0)\n\n# or the average (alpha) species richness across the whole population\nmetadiv(component, 0)\n\n# We can also generate a diversity profile by calculating multiple q-values simultaneously\ndf = subdiv(component, 0:30)\n```\n\nIn 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()`:\n\n```julia\n# To calculate all subcommunity diversity measures\nsubdiv(meta, 0:2)\n\n# To calculate all metacommunity diversity measures\nmetadiv(meta, 0:2)\n```\n\nAlternatively, if computational efficiency is not an issue, a single measure of diversity may be calculated directly by calling a wrapper function:\n\n```julia\nnorm_sub_alpha(meta, 0:2)\n```\n\nA complete list of these functions is shown below:\n\n* `raw_sub_alpha()` : per-subcommunity estimate of naive-community metacommunity diversity\n* `norm_sub_alpha()` : similarity-sensitive diversity of each subcommunity in isolation\n* `raw_sub_rho()` : redundancy of individual subcommunities\n* `norm_sub_rho()` : representativeness of individual subcommunities\n* `raw_sub_beta()` : distinctiveness of individual subcommunities\n* `norm_sub_beta()` : per-subcommunity estimate of effective number of distinct subcommunities\n* `sub_gamma()` : contribution per individual in a subcommunity toward metacommunity diversity\n* `raw_meta_alpha()` : naive-community metacommunity diversity\n* `norm_meta_alpha()` : average similarity-sensitive diversity of subcommunities\n* `raw_meta_rho()` : average redundancy of subcommunities\n* `norm_meta_rho()` : average representativeness of subcommunities\n* `raw_meta_beta()` : average distinctiveness of subcommunities\n* `norm_meta_beta()` : effective number of distinct subcommunities\n* `meta_gamma()` : metacommunity similarity-sensitive diversity\n\n#### Phylogenetic diversity\n\nPhylogenetic diversity (described [here][leinster-cobbold-url]) is\nautomatically included in the Diversity module when the `Phylo` package\nis loaded. Documentation for these diversity measures can be found\n[here](http://docs.ecojulia.org/Diversity.jl/latest/phylogenetics/).\nThe phylogenetics code relies on the [Phylo][phylo-url] package to\ngenerate trees to incorporate into the diversity code, and the\nppropriate code will be created when both main packages are loaded:\n\n```julia-repl\njulia\u003e using Diversity, Phylo\n\njulia\u003e communities = [4 1; 3 2; 1 0; 0 1] / 12;\n\njulia\u003e nt = rand(Nonultrametric(4))\nRootedTree with 4 tips, 7 nodes and 6 branches.\nLeaf names are tip 1, tip 2, tip 4 and tip 3\n\n\njulia\u003e metaphylo = Metacommunity(communities, PhyloBranches(nt));\n\njulia\u003e raw_meta_rho(metaphylo, [1, 2])\n2×8 DataFrame\n│ Row │ div_type            │ measure │ q     │ type_level │ type_name │ partition_level │ partition_name │ diversity │\n│     │ String              │ String  │ Int64 │ String     │ String    │ String          │ String         │ Float64   │\n├─────┼─────────────────────┼─────────┼───────┼────────────┼───────────┼─────────────────┼────────────────┼───────────┤\n│ 1   │ Phylogenetic Branch │ RawRho  │ 1     │ types      │           │ metacommunity   │                │ 1.7787    │\n│ 2   │ Phylogenetic Branch │ RawRho  │ 2     │ types      │           │ metacommunity   │                │ 1.66749   │\n```\n\nThe package also provides some other sub-modules for related measures:\n\n#### Diversity.Ecology\n\nMany existing ecological diversity measures can be derived from our\ndiversity measures, and so we provide them in the Diversity.Ecology\nsubmodule along with generalised versions of them that relate to our\ngeneral measures of alpha, beta and gamma diversity at subcommunity\nand metacommunity levels. The generalisations of species richness,\nShannon entropy and Simpson's index are the only standard measures we\nare aware of whose subcommunity components sum directly to the\ncorresponding metacommunity measure (although note that Simpson's\nindex decreases for increased diversity, so small components are more\ndiverse). Documentation for these diversity measures can be found\n[here](http://docs.ecojulia.org/Diversity.jl/stable/ecology/).\n\n#### Diversity.Hill\n\n[Hill numbers](http://www.jstor.org/stable/1934352) are found in the\nDiversity.Hill sub-module.\nDocumentation for these diversity measures can be found\n[here](http://docs.ecojulia.org/Diversity.jl/stable/hill/).\n\n#### Diversity.Jost\n\nLou Jost's\n[diversity](http://dx.doi.org/10.1111/j.2006.0030-1299.14714.x)\n[measures](http://www.esajournals.org/doi/abs/10.1890/06-1736.1) are\nfound in the Diversity.Jost sub-module.\nDocumentation for these diversity measures is\n[here](http://docs.ecojulia.org/Diversity.jl/stable/jost/).\n\n## Documentation\n\nDocumentation is generated by the Base documentation in Julia and\nonline via the\n[Documenter](https://github.com/JuliaDocs/Documenter.jl) package.\n\n### Using the docs\n\nAccessing the documentation in Julia is easy:\n\n```julia\nusing Diversity\n\n# Returns any documentation for the subdiv() function\n?subdiv\n```\n\nThe documentation is also available online.\n\n### Latest release\n\nThe online documentation for the current stable release is\n[here][docs-stable-url].\n\n### Development branch\n\nThe online documentation for the latest dev (unreleased) branch is\n[here][docs-dev-url].\n\n[docs-dev-img]: https://img.shields.io/badge/docs-dev-blue.svg\n[docs-dev-url]: https://docs.ecojulia.org/Diversity.jl/dev\n\n[docs-stable-img]: https://img.shields.io/badge/docs-stable-blue.svg\n[docs-stable-url]: https://docs.ecojulia.org/Diversity.jl/stable\n\n[actions-img]: https://github.com/EcoJulia/Diversity.jl/actions/workflows/testing.yaml/badge.svg\n[actions-url]: https://github.com/EcoJulia/Diversity.jl/actions/workflows/testing.yaml\n\n[nightly-img]: https://github.com/EcoJulia/Diversity.jl/actions/workflows/nightly.yaml/badge.svg\n[nightly-url]: https://github.com/EcoJulia/Diversity.jl/actions/workflows/nightly.yaml\n\n[codecov-img]: 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