{ "_id": "6a1f2b1fb401979e73425075", "Package": "divDyn", "Type": "Package", "Title": "Diversity Dynamics using Fossil Sampling Data", "Version": "0.8.3", "Authors@R": "c(\nperson(given=\"Adam T.\", family=\"Kocsis\", role=c(\"cre\", \"aut\"), email=\"adam.t.kocsis@gmail.com\", comment=c(ORCID=\"0000-0002-9028-665X\")),\nperson(given=\"John\", family=\"Alroy\", role=c(\"aut\"), comment=c(ORCID=\"0000-0002-9882-2111\")),\nperson(given=\"Carl J.\", family=\"Reddin\", role=c(\"aut\"), comment=c(ORCID=\"0000-0001-5930-1164\")),\nperson(given=\"Wolfgang\", family=\"Kiessling\", role=c(\"aut\"), comment=c(ORCID=\"0000-0002-1088-2014\")),\nperson(given=\"Deutsche Forschungsgemeinschaft\", role=\"fnd\"),\nperson(given=\"FAU GeoZentrum Nordbayern\", role=\"fnd\"))", "Maintainer": "Adam T. Kocsis ", "Description": "Functions to describe sampling and diversity dynamics of\nfossil occurrence datasets (e.g. from the Paleobiology\nDatabase). The package includes methods to calculate range- and\noccurrence-based metrics of taxonomic richness, extinction and\norigination rates, along with traditional sampling measures. A\npowerful subsampling tool is also included that implements\nfrequently used sampling standardization methods in a multiple\nbin-framework. The plotting of time series and the occurrence\ndata can be simplified by the functions incorporated in the\npackage, as well as other calculations, such as environmental\naffinities and extinction selectivity testing. Details can be\nfound in: Kocsis, A.T.; Reddin, C.J.; Alroy, J. and Kiessling,\nW. (2019) .", "License": "CC BY 4.0", "Date": "2024-11-21", "BugReports": "https://github.com/divDyn/r-package/issues", "Encoding": "UTF-8", "LazyData": "false", "NeedsCompilation": "yes", "RoxygenNote": "7.3.0", "VignetteBuilder": "knitr", "Repository": "https://divdyn.r-universe.dev", "Date/Publication": "2024-11-22 09:38:30 UTC", "RemoteUrl": "https://github.com/divdyn/r-package", "RemoteRef": "HEAD", "RemoteSha": "0c453483caa6743b67a8f31ec20763bd145cec09", "Packaged": { "Date": "2026-05-15 10:23:37 UTC", "User": "root" }, "Author": "Adam T. Kocsis [cre, aut] (ORCID:\n),\nJohn Alroy [aut] (ORCID: ),\nCarl J. 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Kocsis, Carl J. Reddin, Wolfgang Kiessling", "engine": "knitr::rmarkdown", "headings": [ "1. Introduction", "1.1. Installation", "2. Necessary Data", "2.1. Time scales", "2.2. Occurrence table", "2.2.1. Stratigraphic assignment", "2.2.2. The example file", "3. Basic patterns", "3.1. Ranges", "3.2. Sampling parameters", "3.2.1. Basic descriptors", "3.2.2. Plotting of counts and proportions", "3.2.3. Single-collection and single reference taxa", "4. Raw diversity dynamics", "4.1. Diversity (taxonomic richness) with discrete time input", "4.1.1.Taxon counts", "4.1.2. Different metrics of richness", "4.2. Taxonomic rates with discrete time input", "4.2.1. Different metrics of turnover", "4.2.2. Selectivity testing for the per capita rates", "4.3. Diversity dynamics with age input", "4.3.1. Using the bin argument – unique values code intervals", "4.3.2. Slicing: slice() and the age argument of divDyn()", "4.3.3. Summary – about slicing and the direction of time", "4.4. Origination and extinction dates in binary response variables", "5. Sampling standardization", "5.1. Concepts", "5.1.1. The goal of sampling standardization", "5.1.2. The formal representation of subsampling", "5.2. Basic arguments", "5.2.1. Subsampling level", "5.2.2. The number of iterations/trials", "5.2.3. The duplicates argument", "5.2.4. The useFailed argument", "5.2.5. The keep and rem arguments", "5.2.6. Subsampling ‘output’ and plotting options", "5.3. The applied function during the subsampling", "5.3.1. Example 1: Checking the number of occurrences", "5.3.2. Example 2: maximum absolute paleolatitudes", "5.4. Different subsampling types", "5.4.1. Classical Rarefaction (CR)", "5.4.2. Occurrence-weighted by-list subsampling (O^x^W)", "5.4.3. Shareholder Quorum Subsampling (SQS)", "5.4.3.1. The ‘inexact’ approach to SQS", "5.4.3.2. Concluding remarks on SQS", "5.4.4. Subsampling trial functions", "6. Taxon-specific characteristics", "6.1. Environmental affinities", "6.1.1. Majority rule", "6.1.2. Binomial method", "6.2. Changing characteristics", "6.2.1. Geographic range", "6.2.2. The tabinate() iterator function", "Acknowledgements", "References" ], "created": "2024-11-22 09:08:15", "modified": "2024-11-22 09:08:15", "commits": 1 } ], "_score": 6.054613054556888, "_indexed": true, "_nocasepkg": "divdyn", "_universes": [ "divdyn", "adamkocsis" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.8.3", "date": "2026-05-15T10:26:10.000Z", "distro": "noble", "arch": "aarch64", "commit": "0c453483caa6743b67a8f31ec20763bd145cec09", "fileid": "325cfe6890f72f7e7a3ff327fab01c7e6c7b1fd175d2c997a0b32e1e4681c375", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/divdyn/actions/runs/25912687287" }, { "r": "4.7.0", "os": "linux", "version": "0.8.3", "date": "2026-05-15T10:26:01.000Z", "distro": "noble", "arch": "x86_64", "commit": "0c453483caa6743b67a8f31ec20763bd145cec09", "fileid": "b073c38813977e8b60584cdcf2db2b0939979bd4c3e0ca344ec5a4e54d2d937d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/divdyn/actions/runs/25912687287" }, { "r": "4.6.0", "os": "linux", "version": "0.8.3", "date": "2026-05-15T10:26:06.000Z", "distro": "noble", "arch": "aarch64", "commit": "0c453483caa6743b67a8f31ec20763bd145cec09", "fileid": "efc29df00b1a0dc66560d287a2c1033da30ad6fbd3933183b4f72b24e2ae00d5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/divdyn/actions/runs/25912687287" }, { "r": "4.6.0", "os": "linux", "version": "0.8.3", "date": "2026-05-15T10:25:59.000Z", "distro": "noble", "arch": "x86_64", "commit": "0c453483caa6743b67a8f31ec20763bd145cec09", "fileid": "d4a0e708bc010a0476da2ed222c1050252c6e8d015fae864f0e4251def2b3860", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/divdyn/actions/runs/25912687287" }, { "r": "4.5.3", "os": "mac", "version": "0.8.3", "date": "2026-05-15T10:26:26.000Z", "arch": "aarch64", "commit": "0c453483caa6743b67a8f31ec20763bd145cec09", "fileid": "f2e0719385809537c424da2e64e9d747021350f8640f6b7cc5902880151abbb3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/divdyn/actions/runs/25912687287" }, { "r": "4.5.3", "os": "mac", "version": "0.8.3", "date": "2026-05-15T10:27:52.000Z", "arch": "x86_64", "commit": "0c453483caa6743b67a8f31ec20763bd145cec09", "fileid": "1026cf5834a7c252be8cb73e130314c9e7c8072379a29d7f0a7784ab60fab76c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/divdyn/actions/runs/25912687287" }, { "r": "4.6.0", "os": "mac", "version": "0.8.3", "date": "2026-05-15T10:26:30.000Z", "arch": "aarch64", "commit": "0c453483caa6743b67a8f31ec20763bd145cec09", "fileid": "3c8dc3e0e0313320113e3d558842d2aefad148fb44bf8709de9ca210b0d5c9e7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/divdyn/actions/runs/25912687287" }, { "r": "4.6.0", "os": "mac", "version": "0.8.3", "date": "2026-05-15T10:27:27.000Z", "arch": "x86_64", "commit": "0c453483caa6743b67a8f31ec20763bd145cec09", "fileid": "7aff9c8aedf19fa861e7886c714a1b65fe94049373b0fb4b99bf12d2fd587125", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/divdyn/actions/runs/25912687287" }, { "r": "4.7.0", "os": "win", "version": "0.8.3", "date": "2026-05-15T10:25:16.000Z", "arch": "x86_64", "commit": "0c453483caa6743b67a8f31ec20763bd145cec09", "fileid": "34be736d4f342c46d00743470d6edd48658ab4e62a6ed9682aea22b22aca9516", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/divdyn/actions/runs/25912687287" }, { "r": "4.5.3", "os": "win", "version": "0.8.3", "date": "2026-05-15T10:25:18.000Z", "arch": "x86_64", "commit": "0c453483caa6743b67a8f31ec20763bd145cec09", "fileid": "751098893c076d65fd84c339fadcb70e5667ed0647b30a22578858107624928a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/divdyn/actions/runs/25912687287" }, { "r": "4.6.0", "os": "win", "version": "0.8.3", "date": "2026-05-15T10:25:16.000Z", "arch": "x86_64", "commit": "0c453483caa6743b67a8f31ec20763bd145cec09", "fileid": "797af4f0b3f32f1841bc01fcc7c1f3dbfdde892520f632b774978e818ee4ce52", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/divdyn/actions/runs/25912687287" }, { "r": "4.6.0", "os": "wasm", "version": "0.8.3", "date": "2026-06-02T19:12:08.000Z", "arch": "emscripten", "commit": "0c453483caa6743b67a8f31ec20763bd145cec09", "fileid": "a63dddc5ccf72ccdb986a0a72deea4e0968fdb7401ad36bbe0e6c32a2999b1ba", "status": "success", "buildurl": "https://github.com/r-universe/divdyn/actions/runs/25912687287" } ] }