{ "_id": "6a1f2a10b401979e734243d6", "Package": "apex", "Title": "Phylogenetic Methods for Multiple Gene Data", "Version": "1.0.7", "Authors@R": "c(KS=person(\"Klaus\", \"Schliep\", email=\"klaus.schliep@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-2941-0161\")),\nTJ=person(\"Thibaut\", \"Jombart\", , \"t.jombart@imperial.ac.uk\", role = c(\"aut\")),\nZK=person(\"Zhian Namir\", \"Kamvar\", email = \"kamvarz@science.oregonstate.edu\", role = c(\"aut\")),\nEA=person(\"Eric\", \"Archer\", email=\"eric.archer@noaa.gov\", role = c(\"aut\")),\nRH=person(\"Rebecca\", \"Harris\", email=\"rbharris@uw.edu\", role = c(\"aut\")))", "Description": "Toolkit for the analysis of multiple gene data (Jombart et\nal. 2017) . 'apex' implements the\nnew S4 classes 'multidna', 'multiphyDat' and associated methods\nto handle aligned DNA sequences from multiple genes.", "License": "GPL (>=2)", "URL": "https://github.com/thibautjombart/apex", "BugReports": "https://github.com/thibautjombart/apex/issues", "Collate": "doc.R internal.R multidna.class.R multiphyDat.class.R\nadd.gaps.R rm.gaps.R show.R multidna.constructor.R\nmultiphyDat.constructor.R accessors.R subset.R concatenate.R\nplot.R readfiles.R datasets.R dist.R getTree.R exports.R", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Roxygen": "list(old_usage = TRUE)", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev zlib1g-dev", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2025-07-24 11:58:06 UTC", "RemoteUrl": "https://github.com/thibautjombart/apex", "RemoteRef": "HEAD", "RemoteSha": "63c67138aaad3b6ed92ee428595a9844b9d83555", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 19:02:26 UTC", "User": "root" }, "Author": "Klaus Schliep [aut, cre] (ORCID:\n),\nThibaut Jombart [aut],\nZhian Namir Kamvar [aut],\nEric Archer [aut],\nRebecca Harris [aut]", "Maintainer": "Klaus Schliep ", "MD5sum": "313aac90dbf1ed7aa877840a4b1daec5", "_user": "phylotastic", "_type": "src", "_file": "apex_1.0.7.tar.gz", "_fileid": "5c64029475efc9d6081bde9981cf56f6e24f905e0a4486f7a5c674de0437ea19", "_filesize": 3348316, "_sha256": "5c64029475efc9d6081bde9981cf56f6e24f905e0a4486f7a5c674de0437ea19", "_created": "2026-06-02T19:02:26.000Z", "_published": "2026-06-02T19:08:00.822Z", "_distro": "noble", "_jobs": [ { "job": 79150233687, "time": 189, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7367281171" }, { "job": 79150233719, "time": 187, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7367280290" }, { "job": 79150233737, "time": 141, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7367308970" }, { "job": 79150233746, "time": 160, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7367317716" }, { "job": 79149544811, "time": 215, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7367211575" }, { "job": 79150233751, "time": 137, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7367261803" }, { "job": 79150233756, "time": 153, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7367268363" }, { "job": 79150233714, "time": 127, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7367258369" }, { "job": 79150233766, "time": 132, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7367260211" } ], "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841484168", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/thibautjombart/apex", "_commit": { "id": "63c67138aaad3b6ed92ee428595a9844b9d83555", "author": "Klaus Schliep ", "committer": "Klaus Schliep ", "message": "fix Rd cross-references\n", "time": 1753358286 }, "_maintainer": { "name": "Klaus Schliep", "email": "klaus.schliep@gmail.com", "login": "klausvigo", "description": "Senior Scientist at TU Graz", "uuid": 3372431, "orcid": "0000-0003-2941-0161" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.1.3", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "ape", "role": "Depends" }, { "package": "phangorn", "role": "Depends" }, { "package": "utils", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "adegenet", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "thibautjombart", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 } ], "_tags": [], "_stars": 5, "_contributors": [ { "user": "thibautjombart", "count": 168, "uuid": 10757154 }, { "user": "klausvigo", "count": 38, "uuid": 3372431 }, { "user": "zkamvar", "count": 14, "uuid": 3639446 }, { "user": "ericarcher", "count": 12, "uuid": 4854603 }, { "user": "rebzzy", "count": 3, "uuid": 4985167 }, { "user": "yihui", "count": 1, "uuid": 163582 } ], "_userbio": { "uuid": 1652822, "type": "organization", "name": "phylotastic" }, "_downloads": { "count": 5077, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/apex" }, "_mentions": 3, "_devurl": "https://github.com/thibautjombart/apex", "_searchresults": 60, "_rbuild": "4.6.0", "_assets": [ "extra/apex.html", "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", "manual.pdf" ], "_homeurl": "https://github.com/thibautjombart/apex", "_realowner": "thibautjombart", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2015-04-15" }, { "version": "1.0.1", "date": "2015-09-07" }, { "version": "1.0.2", "date": "2016-03-31" }, { "version": "1.0.3", "date": "2017-09-23" }, { "version": "1.0.4", "date": "2020-04-11" }, { "version": "1.0.6", "date": "2024-01-31" }, { "version": "1.0.7", "date": "2025-07-24" } ], "_exports": [ "add.gaps", "concatenate", "dist.multidna", "getLocusNames", "getNumInd", "getNumLoci", "getNumSequences", "getSequenceNames", "getSequences", "getTree", "initialize", "multidna2alignment", "multidna2genind", "multidna2multiphyDat", "multiphyDat2alignment", "multiphyDat2genind", "multiphyDat2multidna", "plot", "read.multidna", "read.multiFASTA", "read.multiphyDat", "rm.gaps", "setLocusNames<-", "show" ], "_help": [ { "page": "subset.multidna", "title": "Subset multidna objects", "topics": [ "[,multidna,ANY,ANY,ANY-method", "[,multidna-method", "[,multiphyDat,ANY,ANY,ANY-method", "[,multiphyDat-method", "[.multidna", "[.multiphyDat" ] }, { "page": "accessors", "title": "multidna Accessors", "topics": [ "accessors", "getLocusNames", "getLocusNames,multidna", "getLocusNames,multidna-method", "getLocusNames,multiphyDat", "getLocusNames,multiphyDat-method", "getNumInd", "getNumInd,multidna", "getNumInd,multidna-method", "getNumInd,multiphyDat", "getNumInd,multiphyDat-method", "getNumLoci", "getNumLoci,multidna", "getNumLoci,multidna-method", "getNumLoci,multiphyDat", "getNumLoci,multiphyDat-method", "getNumSequences", "getNumSequences,multidna", "getNumSequences,multidna-method", "getNumSequences,multiphyDat", "getNumSequences,multiphyDat-method", "getSequenceNames", "getSequenceNames,multidna", "getSequenceNames,multidna-method", "getSequenceNames,multiphyDat", "getSequenceNames,multiphyDat-method", "getSequences", "getSequences,multidna", "getSequences,multidna-method", "getSequences,multiphyDat", "getSequences,multiphyDat-method", "setLocusNames<-", "setLocusNames<-,multidna", "setLocusNames<-,multidna-method", "setLocusNames<-,multiphyDat", "setLocusNames<-,multiphyDat-method" ] }, { "page": "add.gaps", "title": "Add gap-only sequences for missing data", "topics": [ "add.gaps", "add.gaps,multidna-method", "add.gaps,multiphyDat-method", "add.gaps.generic", "add.gaps.multidna", "add.gaps.multiphyDat" ] }, { "page": "concatenate", "title": "Concatenate genes into a single matrix", "topics": [ "concatenate", "concatenate,multidna-method", "concatenate,multiphyDat-method", "concatenate.generic", "concatenate.multidna", "concatenate.multiphyDat" ] }, { "page": "dist.multidna", "title": "Pairwise distances for multiple gene data", "topics": [ "dist.multidna" ] }, { "page": "getTree", "title": "Build phylogenies from multiple gene data", "topics": [ "getTree" ] }, { "page": "initialize-multidna-method", "title": "multidna constructor", "topics": [ "initialize,multidna-method", "initialize,multidna-methods", "new.multidna" ] }, { "page": "initialize-multiphyDat-method", "title": "multiphyDat constructor", "topics": [ "initialize,multiphyDat-method", "initialize,multiphyDat-methods", "new.multiphyDat" ] }, { "page": "multidna", "title": "multidna: class for multiple gene data", "topics": [ "data.frameOrNULL", "listOrNULL", "multidna", "multidna-class" ] }, { "page": "multidna2alignment", "title": "Convert from multidna into alignment (seqinr)", "topics": [ "multidna2alignment", "multiphyDat2alignment" ] }, { "page": "multidna2genind", "title": "Convert multidna into genind", "topics": [ "multidna2genind", "multiphyDat2genind" ] }, { "page": "multidna2multiphyDat", "title": "Conversions between multidna and multiphyDat", "topics": [ "multidna2multiphyDat", "multiphyDat2multidna" ] }, { "page": "multiphyDat", "title": "multiphyDat: class for multiple gene data", "topics": [ "multiphyDat", "multiphyDat-class" ] }, { "page": "plot-multidna-method", "title": "Display multidna objects", "topics": [ "plot,multidna-method", "plot.multidna" ] }, { "page": "readfiles", "title": "Read multiple DNA alignments", "topics": [ "read.multidna", "read.multiFASTA", "read.multiphyDat" ] }, { "page": "rm.gaps", "title": "Remove gap-only sequences for missing data", "topics": [ "rm.gaps", "rm.gaps,multidna-method", "rm.gaps,multiphyDat-method", "rm.gaps.generic", "rm.gaps.multidna", "rm.gaps.multiphyDat" ] }, { "page": "show-multidna-method", "title": "Display multidna objects", "topics": [ "show,multidna-method", "show.multidna" ] }, { "page": "show-multiphyDat-method", "title": "Display multiphyDat objects", "topics": [ "show,multiphyDat-method", "show.multiphyDat" ] } ], "_readme": "https://github.com/thibautjombart/apex/raw/HEAD/README.md", "_rundeps": [ "ade4", "adegenet", "ape", "backports", "base64enc", "boot", "bslib", "cachem", "checkmate", "cli", "cluster", "codetools", "commonmark", "cpp11", "digest", "dplyr", "farver", "fastmap", "fontawesome", "fs", "future", "future.apply", "generics", "ggplot2", "globals", "glue", "gtable", "htmltools", "httpuv", "igraph", "isoband", "jquerylib", "jsonlite", "labeling", "later", "lattice", "lifecycle", "listenv", "magrittr", "MASS", "Matrix", "memoise", "mgcv", "mime", "nlme", "osqp", "otel", "parallelly", "permute", "phangorn", "pillar", "pixmap", "pkgconfig", "plyr", "progressr", "promises", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "reshape2", "rlang", "S7", "sass", "scales", "segmented", "seqinr", "shiny", "sourcetools", "sp", "stringi", "stringr", "tibble", "tidyselect", "utf8", "vctrs", "vegan", "viridisLite", "withr", "xtable" ], "_vignettes": [ { "source": "apex.Rmd", "filename": "apex.html", "title": "Phylogenetic Methods for Multiple Gene Data", "author": "Thibaut Jombart", "engine": "knitr::rmarkdown", "headings": [ "apex: Phylogenetic Methods for Multiple Gene Data", "Installing apex", "Importing data", "ape wrappers", "phangorn wrappers", "New object classes", "multidna", "multiphyDat", "Handling data", "Building trees", "Distance-based trees", "Likelihood-based trees", "Exporting data" ], "created": "2015-03-26 17:46:47", "modified": "2024-01-29 13:25:09", "commits": 21 } ], "_score": 7.057789681515968, "_indexed": false, "_nocasepkg": "apex", "_universes": [ "phylotastic" ], "_indexurl": "https://thibautjombart.r-universe.dev/apex", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.7", "date": "2026-06-02T19:05:04.000Z", "distro": "noble", "commit": "63c67138aaad3b6ed92ee428595a9844b9d83555", "fileid": "0e40e3c4532dbb23b90ef4a49d394ec95957371ac63b66ecfa90eefd51b73cff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841484168" }, { "r": "4.6.0", "os": "linux", "version": "1.0.7", "date": "2026-06-02T19:05:02.000Z", "distro": "noble", "commit": "63c67138aaad3b6ed92ee428595a9844b9d83555", "fileid": "2f0da9396c8604e8bfac523f7eea7b9f4912e73de755d06ff3c4237bc1612555", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841484168" }, { "r": "4.5.3", "os": "mac", "version": "1.0.7", "date": "2026-06-02T19:06:22.000Z", "commit": "63c67138aaad3b6ed92ee428595a9844b9d83555", "fileid": "9cb852778681949973399958edc7ef4bf07933472cb2e255bf1dc3bc0ef64509", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841484168" }, { "r": "4.6.0", "os": "mac", "version": "1.0.7", "date": "2026-06-02T19:06:44.000Z", "commit": "63c67138aaad3b6ed92ee428595a9844b9d83555", "fileid": "8d6a84039c18650eff12122c55024cb1ad33a9104f961512f042ea2c6a448e67", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841484168" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.7", "date": "2026-06-02T19:05:07.000Z", "commit": "63c67138aaad3b6ed92ee428595a9844b9d83555", "fileid": "6036fe019a7f562c602ce9f17f92c441fbffeeee1874c7068f70adb8fa102f56", "status": "success", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841484168" }, { "r": "4.7.0", "os": "win", "version": "1.0.7", "date": "2026-06-02T19:04:12.000Z", "commit": "63c67138aaad3b6ed92ee428595a9844b9d83555", "fileid": "48c31dc1e0d0573841527493e54e6c82e3994b3deb8386c1c600f1bb99c17686", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841484168" }, { "r": "4.5.3", "os": "win", "version": "1.0.7", "date": "2026-06-02T19:03:47.000Z", "commit": "63c67138aaad3b6ed92ee428595a9844b9d83555", "fileid": "0f001abca0949ecebfdfd770ef04790a87a27c596b6e3b78acefe668e6e22700", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841484168" }, { "r": "4.6.0", "os": "win", "version": "1.0.7", "date": "2026-06-02T19:03:55.000Z", "commit": "63c67138aaad3b6ed92ee428595a9844b9d83555", "fileid": "b558b5be61f5339ac25fb7d44b869a9ba835eb78f5e32c828253df9078ef8eb1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841484168" } ] }