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Analysis and Metrics","monthly_downloads":735,"total_dependent_repos":1,"total_dependent_packages":0,"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n collapse = TRUE,\n comment = \"#\u003e\",\n fig.path = \"man/figures/README-\",\n out.width = \"100%\"\n)\n\ntemp_dir = tempdir(check = TRUE)\n\npkg_has_vignettes_and_test = function(pkg_name, pkg_dir = temp_dir) {\n pkg_archive = download.packages(pkg_name, destdir = pkg_dir,\n repos = \"https://cran.r-project.org\")\n \n files_list = untar(pkg_archive[1, 2], list = TRUE)\n \n has_vignette = paste0(pkg_archive[1, 1], \"/vignettes/\") %in% files_list\n\n has_tests = paste0(pkg_archive[1, 1], \"/tests/\") %in% files_list\n\n c(ifelse(has_vignette, \"βœ…\", \"❌\"), ifelse(has_tests, \"βœ…\", \"❌\"))\n}\n```\n\n# fundiversity \u003cimg src=\"man/figures/logo.png\" align=\"right\" alt=\"fundiversity logo\" width=\"120\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)\n[![R build status](https://github.com/funecology/fundiversity/workflows/R-CMD-check/badge.svg)](https://github.com/funecology/fundiversity/actions)\n[![Coverage Status](https://codecov.io/gh/funecology/fundiversity/branch/main/graph/badge.svg?token=HR4YH118VT)](https://app.codecov.io/gh/funecology/fundiversity)\n[![CRAN status](https://www.r-pkg.org/badges/version-ago/fundiversity)](https://CRAN.R-project.org/package=fundiversity)\n[![DOI](https://zenodo.org/badge/300231216.svg)](https://zenodo.org/badge/latestdoi/300231216)\n\u003c!-- badges: end --\u003e\n\n`fundiversity` provides a lightweight package to compute common functional\ndiversity indices. To a get a glimpse of what `fundiversity` can do refer to the\n[introductory vignette](https://funecology.github.io/fundiversity/articles/fundiversity.html).\nThe package is built using clear, public \n[design principles](https://funecology.github.io/fundiversity/articles/fundiversity_4-design-principles.html)\ninspired from our own experience and user feedback.\n\n\n## Installation\n\nYou can install the stable version from CRAN with:\n\n```{r, eval = FALSE}\ninstall.packages(\"fundiversity\")\n```\n\nAlternatively, you can install the development version with:\n\n```{r eval = FALSE}\ninstall.packages(\"fundiversity\", repos = \"https://bisaloo.r-universe.dev\")\n```\n\n\n## Examples\n\n`fundiversity` lets you compute six functional diversity indices: Functional Richness with `fd_fric()`, intersection with between convex hulls with `fd_fric_intersect()`, Functional Divergence with\n`fd_fdiv()`, Rao's Quadratic Entropy with `fd_raoq()`, Functional Dispersion with `fd_fdis()` and Functional Evenness with `fd_feve()`. You can have a brief overview of the indices in the [introductory vignette](https://funecology.github.io/fundiversity/articles/fundiversity.html).\n\nAll indices can be computed either using global trait data or at the site-level:\n\n```{r example}\nlibrary(\"fundiversity\")\n\n# If only the trait dataset is specified, considers all species together\n# by default\nfd_fric(traits_birds)\n\n# We can also compute diversity across sites\nfd_fric(traits_birds, site_sp_birds)\n```\n\nTo compute Rao's Quadratic Entropy, the user can also provide a distance matrix between species directly:\n\n```{r rao-distance-matrix}\ndist_traits_birds = as.matrix(dist(traits_birds))\n\nfd_raoq(traits = NULL, dist_matrix = dist_traits_birds)\n```\n\n## Function Summary\n\n```{r child=\"man/rmdchunks/_fundiversity_functions.Rmd\"}\n```\n\n## Parallelization\n\nThanks to the `future.apply` package, all functions (except `fd_raoq()`) within `fundiversity` support parallelization through the `future` backend. To toggle parallelization follow the [`future` syntax](https://cran.r-project.org/package=future):\n\n```{r future-syntax, render=FALSE}\nfuture::plan(future::multisession)\nfd_fdiv(traits_birds)\n```\n\nFor more details please refer to the [parallelization vignette](https://funecology.github.io/fundiversity/articles/fundiversity_1-parallel.html) or use `vignette(\"fundiversity_1-parallel\", package = \"fundiversity\")` within R. **Note**: parallelization and memoization are **mutually exclusive**, when doing computation in parallel, fundiversity falls back on **unmemoised** versions of function.\n\n\n## Available functional diversity indices\n\nAccording to Pavoine \u0026 Bonsall (2011) classification, functional diversity indices can be classified in three \"domains\" that assess different properties of the functional space: richness, divergence, and regularity. We made sure that the computations in the package are correct in our [correctness vignette](https://funecology.github.io/fundiversity/articles/fundiversity_3-correctness.html).\n`fundiversity` provides function to compute indices that assess this three facets at the site scale:\n\n| Scale | Richness | Divergence | Evenness |\n|------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------|\n| Ξ±-diversity\u003cbr /\u003e(= among sites) | FRic with [`fd_fric()`](https://funecology.github.io/fundiversity/reference/fd_fric.html) | FDiv with [`fd_fdiv()`](https://funecology.github.io/fundiversity/reference/fd_fdiv.html)\u003cbr /\u003eRao's QE with [`fd_raoq()`](https://funecology.github.io/fundiversity/reference/fd_raoq.html)\u003cbr /\u003eFDis with [`fd_fdis()`](https://funecology.github.io/fundiversity/reference/fd_fdis.html) | FEve with [`fd_feve()`](https://funecology.github.io/fundiversity/reference/fd_feve.html) |\n| Ξ²-diversity\u003cbr /\u003e(= between sites) | FRic pairwise intersection with [`fd_fric_intersect()`](https://funecology.github.io/fundiversity/reference/fd_fric_intersect.html)\u003cbr /\u003ealternatives available in `betapart` | available in `entropart`, `betapart` or `hillR` | available in `BAT` |\n \n## Related Packages\n\n```{r pkg-vign-tests, include = FALSE}\nadiv = pkg_has_vignettes_and_test(\"adiv\")\nbat = pkg_has_vignettes_and_test(\"BAT\")\nbetapart = pkg_has_vignettes_and_test(\"betapart\")\nentropart = pkg_has_vignettes_and_test(\"entropart\")\nfd = pkg_has_vignettes_and_test(\"FD\")\nhilldiv = pkg_has_vignettes_and_test(\"hilldiv\")\nhillr = pkg_has_vignettes_and_test(\"hillR\")\nhypervolume = pkg_has_vignettes_and_test(\"hypervolume\")\ntpd = pkg_has_vignettes_and_test(\"TPD\")\nvegan = pkg_has_vignettes_and_test(\"vegan\")\n```\n\nSeveral other packages exist that compute functional diversity indices. We did a [performance comparison](https://funecology.github.io/fundiversity/articles/fundiversity_2-performance.html) between related packages. We here mention some of them (but do not mention the numerous wrappers around these packages): \n\n| Package Name | Indices included | Has vignettes | Has tests | On GitHub | On CRAN (last updated) |\n|-------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------|--------------------|--------------------|-----------|-----------------------------------------------------------|\n| [`adiv`](https://github.com/cran/adiv) | Functional Entropy, Functional Redundancy |`r adiv[[1]]` |`r adiv[[2]]` | ❌ | ![](https://www.r-pkg.org/badges/last-release/adiv) |\n| [`BAT`](https://github.com/cardosopmb/BAT) | Ξ²-diversity indices, Richness, divergence, and evenness with hypervolumes |`r bat[[1]]` |`r bat[[2]]` | βœ… | ![](https://www.r-pkg.org/badges/last-release/BAT) | \n| [`betapart`](https://github.com/cran/betapart) | Functional Ξ²-diversity |`r betapart[[1]]` |`r betapart[[2]]` | ❌ | ![](https://www.r-pkg.org/badges/last-release/betapart) |\n| [`entropart`](https://github.com/EricMarcon/entropart)| Functional Entropy |`r entropart[[1]]` |`r entropart[[2]]` | βœ… | ![](https://www.r-pkg.org/badges/last-release/entropart) | \n| [`FD`](https://github.com/cran/FD) | FRic, FDiv, FDis, FEve, Rao's QE, Functional Group Richness |`r fd[[1]]` |`r fd[[2]]` | ❌ | ![](https://www.r-pkg.org/badges/last-release/FD) |\n| [`hilldiv`](https://github.com/anttonalberdi/hilldiv) | Dendrogram-based Hill numbers for functional diversity |`r hilldiv[[1]]` |`r hilldiv[[2]]` | βœ… | ![](https://www.r-pkg.org/badges/last-release/hilldiv) | \n| [`hillR`](https://github.com/daijiang/hillR) | Functional Diversity Hill Numbers |`r hillr[[1]]` |`r hillr[[2]]` | βœ… | ![](https://www.r-pkg.org/badges/last-release/hillR) | \n| [`hypervolume`](https://github.com/cran/hypervolume) | Hypervolume measure of functional diversity (~FRic) |`r hypervolume[[1]]`|`r hypervolume[[2]]`| βœ… | ![](https://www.r-pkg.org/badges/last-release/hypervolume)|\n| [`mFD`](https://github.com/CmlMagneville/mFD) | Functional Ξ±- and Ξ²-diversity indices, including FRic, FDiv, FDis, FEve, FIde, FMPD, FNND, FOri, FSpe, Hill Numbers | βœ… | ❌ | βœ… | ![](https://www.r-pkg.org/badges/last-release/mFD) |\n| [`TPD`](https://github.com/cran/TPD) | FRic, FDiv, FEve but for probability distributions |`r tpd[[1]]` |`r tpd[[2]]` | ❌ | ![](https://www.r-pkg.org/badges/last-release/TPD) |\n| [`vegan`](https://github.com/vegandevs/vegan) | Only dendrogram-based FD (`treedive()`) |`r vegan[[1]]` |`r vegan[[2]]` | βœ… | ![](https://www.r-pkg.org/badges/last-release/vegan) | \n\n---\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["taxonomy"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/12246","html_url":"https://ost.ecosyste.ms/projects/12246"}