{ "_id": "6a5884ebff0138dec5d74851", "Package": "TITAN2", "Type": "Package", "Title": "Threshold Indicator Taxa Analysis", "Version": "2.4.4", "Authors@R": "c(person(\"Matthew E.\", \"Baker\", email = \"mbaker@umbc.edu\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-5069-0204\")),\nperson(\"Ryan S.\", \"King\",email = \"Ryan_S_King@baylor.edu\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-3159-9816\")),\nperson(\"David\", \"Kahle\", email = \"david@kahle.io\", role = c(\"aut\", \"cph\", \"cre\"), comment = c(ORCID = \"0000-0002-9999-1558\")))", "Description": "Uses indicator species scores across binary partitions of\na sample set to detect congruence in taxon-specific changes of\nabundance and occurrence frequency along an environmental\ngradient as evidence of an ecological community threshold.\nRelevant references include Baker and King (2010)\n, King and Baker (2010)\n, and Baker and King (2013)\n.", "VignetteBuilder": "knitr", "License": "GPL-2", "LazyData": "TRUE", "RoxygenNote": "7.3.2", "Roxygen": "list(markdown = TRUE)", "Encoding": "UTF-8", "Repository": "https://dkahle.r-universe.dev", "Date/Publication": "2025-10-16 20:24:37 UTC", "RemoteUrl": "https://github.com/dkahle/titan2", "RemoteRef": "HEAD", "RemoteSha": "0d6c89eda0643c0b1abb74551871adead7a1134d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-16 07:11:45 UTC", "User": "root" }, "Author": "Matthew E. Baker [aut, cph] (ORCID:\n),\nRyan S. King [aut, cph] (ORCID:\n),\nDavid Kahle [aut, cph, cre] (ORCID:\n)", "Maintainer": "David Kahle ", "_user": "dkahle", "_type": "src", "_file": "TITAN2_2.4.4.tar.gz", "_fileid": "https://r2.ropensci.org/66285aa06ace0027a6c9ae5c7b92c3961e7212ab6878d2c9cd6e5362b44aeec3", "_filesize": 5522144, "_sha256": "66285aa06ace0027a6c9ae5c7b92c3961e7212ab6878d2c9cd6e5362b44aeec3", "_expires": "2026-10-24T07:14:49.000Z", "_created": "2026-07-16T07:11:45.000Z", "_published": "2026-07-16T07:14:51.695Z", "_jobs": [ { "job": 87558636345, "time": 144, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8367795816" }, { "job": 87558636310, "time": 141, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8367795196" }, { "job": 87558636312, "time": 119, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8367786360" }, { "job": 87558636369, "time": 100, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8367779758" }, { "job": 87557908698, "time": 249, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8367744247" }, { "job": 87558636361, "time": 108, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8367783342" }, { "job": 87558636387, "time": 106, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8367782752" }, { "job": 87558636350, "time": 91, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8367776910" }, { "job": 87558636336, "time": 97, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8367779224" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/dkahle/actions/runs/29478882406", "_status": "success", "_upstream": "https://github.com/dkahle/titan2", "_commit": { "id": "0d6c89eda0643c0b1abb74551871adead7a1134d", "author": "David Kahle ", "committer": "David Kahle ", "message": "minor updates for maintenance release\n", "time": 1760646277 }, "_maintainer": { "name": "David Kahle", "email": "david@kahle.io", "login": "dkahle", "description": "", "uuid": 424139, "orcid": "0000-0002-9999-1558" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "parallel", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "glue", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "ggridges", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "dkahle", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-42", "n": 1 } ], "_tags": [], "_stars": 16, "_contributors": [ { "user": "dkahle", "count": 117, "uuid": 424139 }, { "user": "matthewebaker", "count": 5, "uuid": 49703428 }, { "user": "ryan1138", "count": 1, "uuid": 44208728 } ], "_userbio": { "uuid": 424139, "type": "user", "name": "David Kahle", "followers": 178 }, "_downloads": { "count": 428, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TITAN2" }, "_mentions": 10, "_devurl": "https://github.com/dkahle/titan2", "_searchresults": 39, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/TITAN2.html", "manual.pdf" ], "_homeurl": "https://github.com/dkahle/titan2", "_realowner": "dkahle", "_cranurl": true, "_releases": [ { "version": "2.1", "date": "2015-12-19" }, { "version": "2.3", "date": "2019-08-29" }, { "version": "2.4", "date": "2019-12-05" }, { "version": "2.4.1", "date": "2020-12-07" }, { "version": "2.4.2", "date": "2023-05-31" }, { "version": "2.4.3", "date": "2023-11-15" }, { "version": "2.4.4", "date": "2025-10-16" } ], "_exports": [ "getivz", "plot_cps", "plot_sumz", "plot_sumz_density", "plot_taxa", "plot_taxa_ridges", "plotCPs", "plotSumz", "plotTaxa", "titan" ], "_datasets": [ { "name": "glades.env", "title": "glades.env title", "object": "glades.env", "class": [ "data.frame" ], "fields": [ "TP.ugL" ], "rows": 126, "table": true, "tojson": true }, { "name": "glades.taxa", "title": "glades.taxa title", "object": "glades.taxa", "class": [ "data.frame" ], "fields": [ "ABLARHAM", "ACENTRIA", "ANOPHELE", "APEDELAS", "APHAOPAC", "ARRENSP1", "ATRICHOP", "BEARTRUN", "BELO.IMM", "BELOLUTA", "BELOTEST", "BEROSU.L", "BEZZSP1", "BEZZSP2", "BEZZSP3", "BRACGRAV", "BRATUNID", "CAECIDOT", "CAENDIMI", "CALANOID", "CALLFLOR", "CANDANNA", "CELIEPON", "CELIIMIT", "CELINA.L", "CERIODAP", "CERNOTIN", "CHIRSTIG", "CHMUSSP", "CHYDORID", "CLADOPEL", "CLADOTAN", "COLLESP1", "COLLESP2", "COLLESP4", "CORYINGE", "CORYSPD", "CRANGONY", "CURCULIO", "CYBIFIMB", "CYCLPOID", "CYPRBREV", "CYPROKEE", "CYTHALOS", "DAPHNSP1", "DASYHELE", "DERAALTU", "DERODIGX", "DEROFURC", "DEROLODE", "DEROPECT", "DESMOP.A", "DESMOP.L", "DICROMOD", "DICROSIM", "ECLIPALU", "ENALCIVI", "ENOCHR.L", "ENOCOCHR", "ERYTHSIM", "EYLAIS", "FERRISSI", "FITTSERT", "FORCMYIA", "GASTRO1", "GOELDHOL", "GOELDNAT", "HAEMWALD", "HARPACTI", "HELOFUSC", "HELOLARV", "HELOTRIS", "HYALAZTE", "HYDBISP2", "HYDCAN.L", "HYDRA", "HYDROBLO", "HYDRPUST", "HYDRSP13", "ILYBIU.L", "ILYOSPIN", "ISCHNURA", "KIEFFDUX", "LABRNEOP", "LACCGENT", "LAEVPENI", "LAMPYRID", "LARSBERN", "LARSDECO", "LIBENEED", "LIMONIA", "MACROTHR", "MANSOSP1", "MANSOSP2", "MESOVELI", "MICRDILA", "MICRVELI", "MOORMICR", "NAMALABI", "NANOALTE", "NEMATODA", "NILOTHAU", "NOCTUSP1", "ODONTOMY", "OECETSP", "OECETSPE", "OSTRASP5", "OXYETHIR", "PACHLONG", "PALAPALU", "PARACALA", "PARAKSPC", "PARAMERI", "PARAPONY", "PARASPB", "PELOFEMO", "PHAEEXST", "PHAEMINO", "PHAENO.L", "PHYSCUBE", "PHYSELLA", "PLANDURY", "PLANSP1", "PLANTRIV", "POLYGYRA", "POLYHALT", "POLYILLI", "POLYPSPA", "POLYTRIG", "POLYTRIT", "POMAPALU", "PRISAEQU", "PRISLEID", "PROCFALL", "PROCLAD", "PSEUDCOL", "PSEUDOCH", "PSEUDOSI", "PSYCHODA", "PYRALSP1", "SCIRTES", "SIMYRA", "SPONGILL", "STAPHYLI", "SUPHISEL", "TANYLIMN", "TANYPCAR", "TANYSPF", "TANYSPG", "TANYSPJ", "TANYSPR", "TANYSPT", "TELEBYER", "TRICHORX", "TROPBLAT", "TROPIS.L", "TROPLATE", "TUBIFSP1", "TUBIFSP2", "TURBELLA", "UNIONICO", "URANOTAE", "VERTOVAT", "ZAVRMARM" ], "rows": 126, "table": true, "tojson": true }, { "name": "glades.titan", "title": "glades.titan title", "object": "glades.titan", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "boot.titan", "title": "Controls the allocation of bootstrap replicates", "topics": [ "boot.titan" ] }, { "page": "env.part", "title": "Partitions environmental gradient for analysis", "topics": [ "env.part" ] }, { "page": "getivz", "title": "Performs calculation of IndVal z scores from observed and permuted values", "topics": [ "getivz" ] }, { "page": "glades.env", "title": "glades.env title", "topics": [ "glades.env" ] }, { "page": "glades.taxa", "title": "glades.taxa title", "topics": [ "glades.taxa" ] }, { "page": "glades.titan", "title": "glades.titan title", "topics": [ "glades.titan" ] }, { "page": "indval", "title": "IndVal scores based on relative abundance across, and occurrence frequency within, groups", "topics": [ "indval", "indvals" ] }, { "page": "indvalp", "title": "Calculate permuted IndVal scores using a group matrix", "topics": [ "indvalp", "indvalps" ] }, { "page": "ivzsums", "title": "Sum IndVal z scores across taxa", "topics": [ "ivzsums", "ivzsums.f" ] }, { "page": "obs.summ", "title": "Summarizes results from TITAN's analaysis of observed data", "topics": [ "obs.summ" ] }, { "page": "permiv", "title": "Permutation of group membership for a single candidate partition", "topics": [ "permiv" ] }, { "page": "plot_sumz_density", "title": "Plot community level change", "topics": [ "plot_sumz_density" ] }, { "page": "plot_taxa_ridges", "title": "Taxon change point ridge plots", "topics": [ "plot_taxa_ridges" ] }, { "page": "plot-cps", "title": "Plots probability densities of empirical distributions of bootstrapped change points", "topics": [ "plot-cps", "plotCPs", "plot_cps" ] }, { "page": "plot-sumz", "title": "Plots the pattern of community change along an environmental gradient", "topics": [ "plot-sumz", "plotSumz", "plot_sumz" ] }, { "page": "plot-taxa", "title": "Plots taxon-specific change points", "topics": [ "plot-taxa", "plotTaxa", "plot_taxa" ] }, { "page": "smallBigBoot", "title": "Summarizes raw output from TITAN's bootstrap procedure", "topics": [ "big.boot", "small.boot", "smallBigBoot" ] }, { "page": "sumz.tab", "title": "Summarizes the results of the community-level sum(z) analysis", "topics": [ "sumz.tab" ] }, { "page": "tboot", "title": "Calculate bootstrapped IndVal z scores", "topics": [ "tboot" ] }, { "page": "titan", "title": "Perform a threshold indicator taxa analysis", "topics": [ "titan" ] }, { "page": "TITAN2", "title": "Threshold Indicator Taxa Analysis", "topics": [ "TITAN2-package", "TITAN2" ] }, { "page": "txa.screen", "title": "Screening of site by taxa matrix", "topics": [ "txa.screen" ] } ], "_readme": "https://github.com/dkahle/titan2/raw/HEAD/README.md", "_rundeps": [ "cli", "cowplot", "cpp11", "dplyr", "farver", "generics", "ggplot2", "ggridges", "glue", "gtable", "isoband", "labeling", "lifecycle", "magrittr", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "rlang", "S7", "scales", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "titan2-intro.Rmd", "filename": "titan2-intro.pdf", "title": "An Introduction to TITAN2", "author": "Matthew Baker (UMBC), Ryan King (Baylor), and David Kahle (Baylor)", "engine": "knitr::rmarkdown", "headings": [ "Introduction to Threshold Indicator Taxa Analysis with TITAN2", "First Steps", "Note on Loading Your Own Data", "Tabular Results", "Visualizing Results", "plot_sumz()", "plot_taxa_ridges()", "plot_taxa()", "plot_cps()" ], "created": "2019-04-04 22:47:01", "modified": "2023-11-14 21:26:23", "commits": 12 } ], "_score": 6.795184589682424, "_indexed": true, "_nocasepkg": "titan2", "_universes": [ "dkahle" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.4.4", "date": "2026-07-16T07:13:59.000Z", "distro": "resolute", "commit": "0d6c89eda0643c0b1abb74551871adead7a1134d", "fileid": "https://r2.ropensci.org/707afd0bb10005908267dd3443674dbfd038127af23387118534941dc4be6f87", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dkahle/actions/runs/29478882406" }, { "r": "4.6.1", "os": "linux", "version": "2.4.4", "date": "2026-07-16T07:13:57.000Z", "distro": "resolute", "commit": "0d6c89eda0643c0b1abb74551871adead7a1134d", "fileid": "https://r2.ropensci.org/14d329d3b6930274f89ac3fe1b2d45f6d4b7e3b85089f579e9df79082a372e62", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dkahle/actions/runs/29478882406" }, { "r": "4.5.3", "os": "mac", "version": "2.4.4", "date": "2026-07-16T07:13:36.000Z", "commit": "0d6c89eda0643c0b1abb74551871adead7a1134d", "fileid": "https://r2.ropensci.org/249b2a13886e9cf7726bb10ad4fccd28215fb5bbafea3dc8be380cf545c60497", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dkahle/actions/runs/29478882406" }, { "r": "4.6.1", "os": "mac", "version": "2.4.4", "date": "2026-07-16T07:13:19.000Z", "commit": "0d6c89eda0643c0b1abb74551871adead7a1134d", "fileid": "https://r2.ropensci.org/fa6da565bb85af8223fb6f5448b266a38d43f21c2994650943f9d27e6ae04725", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dkahle/actions/runs/29478882406" }, { "r": "4.6.0", "os": "wasm", "version": "2.4.4", "date": "2026-07-16T07:13:58.000Z", "commit": "0d6c89eda0643c0b1abb74551871adead7a1134d", "fileid": "https://r2.ropensci.org/2750d8236eac2748788c4dd8f54ab7d519b168474c57a0fed4369c206c9547e1", "status": "success", "buildurl": "https://github.com/r-universe/dkahle/actions/runs/29478882406" }, { "r": "4.7.0", "os": "win", "version": "2.4.4", "date": "2026-07-16T07:13:19.000Z", "commit": "0d6c89eda0643c0b1abb74551871adead7a1134d", "fileid": "https://r2.ropensci.org/e8666513ae742fc9e5d7c040b20a713eb83cede924339990414af9fc072188f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dkahle/actions/runs/29478882406" }, { "r": "4.5.3", "os": "win", "version": "2.4.4", "date": "2026-07-16T07:12:59.000Z", "commit": "0d6c89eda0643c0b1abb74551871adead7a1134d", "fileid": "https://r2.ropensci.org/1efc6310a5137029932093b8d66e61826203ea61eccbb0849c01ef1ba5987bb9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dkahle/actions/runs/29478882406" }, { "r": "4.6.1", "os": "win", "version": "2.4.4", "date": "2026-07-16T07:13:17.000Z", "commit": "0d6c89eda0643c0b1abb74551871adead7a1134d", "fileid": "https://r2.ropensci.org/d43cb84232653358d61de5c3b92966ec8fa6ec125300535654cf7edc1d0069c7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dkahle/actions/runs/29478882406" } ] }