{ "_id": "6a12a600acfb0bcc41d13b35", "Package": "Select", "Title": "Determines Species Probabilities Based on Functional Traits", "Version": "1.6", "Authors@R": "c(\nperson(\"Daniel\", \"Laughlin\", email = \"danielclaughlin@gmail.com\", role = c(\"cre\",\"aut\")),\nperson(\"Loic\", \"Chalmandrier\", email = \"lchalman@uwyo.edu\", role = \"aut\"))", "Description": "The objective of these functions is to derive a species\nassemblage that satisfies a functional trait profile. Restoring\nresilient ecosystems requires a flexible framework for\nselecting assemblages that are based on the functional traits\nof species. However, current trait-based models have been\nlimited to algorithms that can only select species by\noptimising specific trait values, and could not elegantly\naccommodate the common desire among restoration ecologists to\nproduce functionally diverse assemblages. We have solved this\nproblem by applying a non-linear optimisation algorithm that\noptimises Rao Q, a closed-form functional trait diversity index\nthat incorporates species abundances, subject to other linear\nconstraints. This framework generalises previous models that\nonly optimised the entropy of the community, and can optimise\nboth functional diversity and entropy simultaneously. This\npackage can also be used to generate experimental assemblages\nto test the effects of community-level traits on community\ndynamics and ecosystem function. The method is based on theory\ndiscussed in Laughlin (2014, Ecology Letters) and Laughlin et\nal. (2018, Methods in Ecology and Evolution).", "License": "GPL (>= 2)", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-24 07:14:38 UTC", "User": "root" }, "Author": "Daniel Laughlin [cre, aut], Loic Chalmandrier [aut]", "Maintainer": "Daniel Laughlin ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-04-24 08:28:14 UTC", "RemoteUrl": "https://github.com/cran/Select", "RemoteRef": "HEAD", "RemoteSha": "a3ba6fe75c811827e30a46911fd19ca7d04b389e", "MD5sum": "d8ade20c837237b53c77b506b4bcb64a", "_user": "cran", "_type": "src", "_file": "Select_1.6.tar.gz", "_fileid": "01a3bef0f4dc07ad6ff308cbbb4b548123766c5448e9e7783e7d703cde10c0a3", "_filesize": 605468, "_sha256": "01a3bef0f4dc07ad6ff308cbbb4b548123766c5448e9e7783e7d703cde10c0a3", "_created": "2026-05-24T07:14:38.000Z", "_published": "2026-05-24T07:17:20.516Z", "_distro": "noble", "_jobs": [ { "job": 77579723809, 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trait data for species in serpentine grassland", "object": "serpentine", "class": [ "data.frame" ], "fields": [ "wue", "rootdepth" ], "rows": 48, "table": true, "tojson": true }, { "name": "tropicalforest", "title": "Functional trait data for tree species in tropical forest", "object": "tropicalforest", "class": [ "data.frame" ], "fields": [ "sla", "wd" ], "rows": 41, "table": true, "tojson": true } ], "_help": [ { "page": "pineforest", "title": "Functional trait data for understory species in ponderosa pine forest", "topics": [ "pineforest" ] }, { "page": "plotProbs", "title": "Plots results from the selectSpecies function", "topics": [ "plotProbs" ] }, { "page": "selectSpecies", "title": "Select species based on traits", "topics": [ "selectSpecies" ] }, { "page": "serpentine", "title": "Functional trait data for species in serpentine grassland", "topics": [ "serpentine" ] }, { "page": "tropicalforest", "title": "Functional trait data for tree species in tropical forest", "topics": [ "tropicalforest" ] } ], "_rundeps": [ "ade4", "codetools", "deldir", "digest", "future", "future.apply", "globals", "interp", "jpeg", "lattice", "latticeExtra", "listenv", "MASS", "numDeriv", "parallelly", "pixmap", "png", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rsolnp", "sp", "truncnorm" ], "_vignettes": [ { "source": "selectSpecies.Rmd", "filename": "selectSpecies.html", "title": "Vignette for using the selectSpecies( ) function", "author": "Daniel C. Laughlin, Loic Chalmandrier, Chaitanya Joshi, Michael Renton, John M. Dwyer, and Jennifer L. Funk", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "The selectSpecies( ) function takes the following arguments:", "The plotProbs() function takes the following arguments:", "Part 1. Examples using one trait with known structure (evenly spaced integers)", "Example 1: Derive species assemblage with the following trait profile:", "Example 2: Derive species assemblage with the following trait profile:", "Example 3: Derive species assemblage with the following trait profile:", "Example 4: Derive species assemblage with the following trait profile:", "Part 2. Examples using two traits with known structure (evenly spaced integers)", "Example 5: Derive species assemblage with the following trait profile:", "Example 6: Derive species assemblage with the following trait profile:", "Part 3. An example using a real dataset", "Example 7: Derive species assemblage for a California serpentine grassland with the following trait profile:" ], "created": "2018-04-02 18:36:41", "modified": "2026-04-24 08:28:14", "commits": 3 } ], "_score": 3.8573324964312685, "_indexed": true, "_nocasepkg": "select", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.6", "date": "2026-05-24T07:16:40.000Z", "distro": "noble", "commit": "a3ba6fe75c811827e30a46911fd19ca7d04b389e", "fileid": "5db8f1b101d587129680d90caf738e66b32f0968705793c38103439a8ccd8076", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26354822199" }, { "r": "4.6.0", "os": "linux", "version": "1.6", "date": "2026-05-24T07:16:53.000Z", "distro": "noble", "commit": "a3ba6fe75c811827e30a46911fd19ca7d04b389e", "fileid": "e08b09d9838bfd2191fccd45ce8d48b41c4fe27308fdbbcf6990be2a91e070fa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26354822199" }, { "r": "4.6.0", "os": "wasm", "version": "1.6", "date": "2026-05-24T07:16:55.000Z", "commit": "a3ba6fe75c811827e30a46911fd19ca7d04b389e", "fileid": "aeecab62e082c84b6f58afd1060a8d361a81b2ca42925fc80ebc71f46a1f5970", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26354822199" } ] }