{ "_id": "6ae85ad29ceaa78f2009b5ed", "Package": "phylosignal", "Type": "Package", "Title": "Exploring the Phylogenetic Signal in Continuous Traits", "Version": "1.3.2", "Date": "2023-10-11", "Author": "Francois Keck ", "Maintainer": "Francois Keck ", "Description": "A collection of tools to explore the phylogenetic signal\nin univariate and multivariate data. The package provides\nfunctions to plot traits data against a phylogenetic tree,\ndifferent measures and tests for the phylogenetic signal,\nmethods to describe where the signal is located and a\nphylogenetic clustering method.", "License": "GPL-3", "RoxygenNote": "7.2.1", "LazyLoad": "yes", "LazyData": "true", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libssl-dev zlib1g-dev", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2025-06-10 09:32:01 UTC", "RemoteUrl": "https://github.com/fkeck/phylosignal", "RemoteRef": "HEAD", "RemoteSha": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-11-02 08:51:05 UTC", "User": "root" }, "_user": "phylotastic", "_type": "src", "_file": "phylosignal_1.3.2.tar.gz", "_fileid": "https://r2.ropensci.org/0fbc208c5e674a4917be605c5cf68a6d6015d6e67df19607725d175f2d38d027", "_filesize": 3134672, "_sha256": "0fbc208c5e674a4917be605c5cf68a6d6015d6e67df19607725d175f2d38d027", "_expires": "2027-02-10T09:41:36.000Z", "_created": "2026-11-02T08:51:05.000Z", "_published": "2026-11-02T09:41:37.888Z", "_upstream": "https://github.com/fkeck/phylosignal", "_status": "success", "_maintainer": { "name": "Francois Keck", "email": "francois.keck@gmail.com", "login": "fkeck", "bluesky": "@francoiskeck.bsky.social", "orcid": "0000-0002-3323-4167", "description": "", "uuid": 9269625 }, "_jobs": [ { "job": 125180388738, "time": 188, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "13127736872" }, { "job": 125180388806, "time": 175, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13128300743" }, { "job": 125180388941, "time": 184, "config": "linux-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "13127777607" }, { "job": 125180389184, "time": 187, "config": "linux-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13127338123" }, { "job": 125180388685, "time": 176, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "13130576252" }, { "job": 125180389146, "time": 570, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "13129407295" }, { "job": 125180388684, "time": 221, "config": "macos-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "13130616613" }, { "job": 125180388995, "time": 316, "config": "macos-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13129805825" }, { "job": 125178387477, "time": 301, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13128245377" }, { "job": 125180388964, "time": 133, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13126954182" }, { "job": 125180389026, "time": 265, "config": "windows-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "13127334598" }, { "job": 125180388906, "time": 246, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13127967468" }, { "job": 125180389228, "time": 181, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "13127756769" }, { "job": 125180388712, "time": 340, "config": "windows-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "13127423127" }, { "job": 125180388704, "time": 163, "config": "windows-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13128495194" } ], "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/41415469359", "_commit": { "id": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "author": "fkeck ", "committer": "fkeck ", "message": "Increase to 1.3.2\n", "time": 1749547921 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.11.0", "role": "Imports" }, { "package": "adephylo", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "phylobase", "role": "Imports" }, { "package": "boot", "role": "Imports" }, { "package": "DBI", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "fkeck", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 19, "_contributors": [ { "user": "fkeck", "count": 138, "uuid": 9269625 }, { "user": "mrhelmus", "count": 2, "uuid": 5468482 } ], "_userbio": { "uuid": 1652822, "type": "organization", "name": "phylotastic", "followers": 5 }, "_downloads": { "count": 499, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/phylosignal" }, "_mentions": 39, "_devurl": "https://github.com/fkeck/phylosignal", "_searchresults": 136, "_topics": [ "openblas", "cpp" ], "_abi": { "exports": [], "imports": [ { "key": "Rcpp::Rcpp_precious_preserve()", "hash": "33a97ea62b293da6" }, { "key": "Rcpp::Rcpp_precious_remove()", "hash": "63d26947ba7e1377" }, { "key": "Rcpp::dataptr()", "hash": "54e69ad2e6668c83" }, { "key": "Rcpp::demangle()", "hash": "b0cfd6754c5ebc4e" }, { "key": "Rcpp::enterRNGScope()", "hash": "a04a299137cef947" }, { "key": "Rcpp::exitRNGScope()", "hash": "a04a299137cef947" }, { "key": "Rcpp::rcpp_get_stack_trace()", "hash": "c684a9bbe15cdc52" }, { "key": "Rcpp::rcpp_set_stack_trace()", "hash": "33a97ea62b293da6" } ] }, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/phylosignal.html", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/fkeck/phylosignal", "_realowner": "fkeck", "_cranurl": true, "_releases": [ { "version": "1.1", "date": "2015-10-26" }, { "version": "1.2", "date": "2018-01-10" }, { "version": "1.2.1", "date": "2019-01-23" }, { "version": "1.3", "date": "2020-02-03" }, { "version": "1.3.1", "date": "2023-10-12" } ], "_exports": [ "barplot.phylo4d", "descentsNames", "directDescents", "distEq", "dotplot", "dotplot.phylo4d", "evenColors", "focusStop", "focusTips", "focusTraits", "focusTree", "graphClust", "gridplot", "gridplot.phylo4d", "kStarTest", "kTest", "lambdaTest", "lipaMoran", "mantelStat", "matchTipsAndTraits", "moranTest", "multiplot.phylo4d", "pagelLogLik", "phyloCorrelogram", "phyloSignal", "phyloSignalBS", "phyloSignalINT", "phyloSim", "phyloSimSignal", "phyloWeights", "plot.graphclust", "plot.phylocorrelogram", "plot.phylosim", "plot.phylosimsignal", "print.graphclust", "print.phylosimsignal", "read.p4d", "rTraitContWeight", "subsetPhyloSimSignal", "white2red" ], "_datasets": [ { "name": "navic", "title": "Phylogeny and pollution sensitivity of diatoms", "object": "navic", "class": [ "phylo4d" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "layouterize", "title": "Set layout for plots", "topics": [ ".layouterize" ] }, { "page": "layouterizeRatio", "title": "Set layout for plots", "topics": [ ".layouterizeRatio" ] }, { "page": "orderGrArg", "title": "Reordering vector or matrix of settings.", "topics": [ ".orderGrArg" ] }, { "page": "barplot.phylo4d", "title": "Barplot of Traits Values along a Phylogeny", "topics": [ "barplot.phylo4d" ] }, { "page": "descentsNames", "title": "Names of descents", "topics": [ "descentsNames" ] }, { "page": "directDescents", "title": "ID of direct descents", "topics": [ "directDescents" ] }, { "page": "distEq", "title": "Pairwise Distance from Regularly Distributed Points", "topics": [ "distEq" ] }, { "page": "dotplot", "title": "Dotplot", "topics": [ "dotplot" ] }, { "page": "dotplot.phylo4d", "title": "Dotplot of Traits Values along a Phylogeny", "topics": [ "dotplot.phylo4d" ] }, { "page": "evenColors", "title": "Palette of evenly distributed colors", "topics": [ "evenColors" ] }, { "page": "focus", "title": "Focus on sub parts of a plot", "topics": [ "focusStop", "focusTips", "focusTraits", "focusTree" ] }, { "page": "graphClust", "title": "Phylogenetically constrained clustering", "topics": [ "graphClust" ] }, { "page": "gridplot", "title": "Gridplot", "topics": [ "gridplot" ] }, { "page": "gridplot.phylo4d", "title": "Gridplot of Traits Values along a Phylogeny", "topics": [ "gridplot.phylo4d" ] }, { "page": "kStarTest", "title": "Computes permutation test for Blomberg's K Star", "topics": [ "kStarTest" ] }, { "page": "kTest", "title": "Computes permutation test for Blomberg's K", "topics": [ "kTest" ] }, { "page": "lambdaTest", "title": "Test Pagel's Lambda Optimize Pagel's Lambda and do a likelihood ratio test.", "topics": [ "lambdaTest" ] }, { "page": "lipaMoran", "title": "Local Indicator of Phylogenetic Association", "topics": [ "lipaMoran" ] }, { "page": "mantelStat", "title": "Mantel statistic", "topics": [ "mantelStat" ] }, { "page": "matchTipsAndTraits", "title": "Match matrix row/col names with phylo4d tips/traits", "topics": [ "matchTipsAndTraits" ] }, { "page": "moranTest", "title": "Computes permutation test for Moran's I", "topics": [ "moranTest" ] }, { "page": "multiplot.phylo4d", "title": "Plots of Traits Values along a Phylogeny", "topics": [ "multiplot.phylo4d" ] }, { "page": "navic", "title": "Phylogeny and pollution sensitivity of diatoms", "topics": [ "navic" ] }, { "page": "pagelLogLik", "title": "Computes log-likelihood for data and a given value of Pagel's Lambda", "topics": [ "pagelLogLik" ] }, { "page": "phyloCorrelogram", "title": "Phylogenetic correlogram", "topics": [ "phyloCorrelogram" ] }, { "page": "phylosignal", "title": "phylosignal", "topics": [ "phylosignal" ] }, { "page": "phylosignalStats", "title": "Computes phylogenetic signal with different methods", "topics": [ "phyloSignal" ] }, { "page": "phyloSignalBS", "title": "Computes phylogenetic signal for bootstrapped replicates of a phylogeny.", "topics": [ "phyloSignalBS" ] }, { "page": "phyloSignalINT", "title": "Computes phylogenetic signal at each internal node of a phylogeny", "topics": [ "phyloSignalINT" ] }, { "page": "phyloSim", "title": "Simulate the behaviour of phylogenetic signal statistics with a given phylogeny", "topics": [ "phyloSim" ] }, { "page": "phyloSimSignal", "title": "Phylogenetic signal estimation as a fraction of a Brownian Motion process.", "topics": [ "phyloSimSignal" ] }, { "page": "phyloWeights", "title": "Phylogenetic weights matrix", "topics": [ "phyloWeights" ] }, { "page": "plot.graphclust", "title": "Plot phylogenetically constrained clustering", "topics": [ "plot.graphclust" ] }, { "page": "plot.phylocorrelogram", "title": "Plot a phylogenetic correlogram", "topics": [ "plot.phylocorrelogram" ] }, { "page": "plot.phylosim", "title": "Plot 'phylosim' object", "topics": [ "plot.phylosim" ] }, { "page": "plot.phylosimsignal", "title": "Plot signal estimation as a fraction of a Brownian Motion process.", "topics": [ "plot.phylosimsignal" ] }, { "page": "print.graphclust", "title": "#' Print results of phylogenetically constrained clustering", "topics": [ "print.graphclust" ] }, { "page": "print.phylosimsignal", "title": "Print signal estimation as a fraction of a Brownian Motion process.", "topics": [ "print.phylosimsignal" ] }, { "page": "read.p4d", "title": "Read a phylo4d object from files", "topics": [ "read.p4d" ] }, { "page": "rTraitContWeight", "title": "Traits Values Simulation", "topics": [ "rTraitContWeight" ] }, { "page": "subsetPhyloSimSignal", "title": "phyloSimSignal subsetting", "topics": [ "subsetPhyloSimSignal" ] }, { "page": "white2red", "title": "Color Palette", "topics": [ "white2red" ] } ], "_readme": "https://github.com/fkeck/phylosignal/raw/HEAD/README.md", "_rundeps": [ "ade4", "adegenet", "adephylo", "ape", "askpass", "base64enc", "boot", "bslib", "cachem", "cli", "cluster", "commonmark", "cpp11", "crayon", "curl", "DBI", "digest", "dplyr", "farver", "fastmap", "fontawesome", "fs", "generics", "ggplot2", "glue", "gtable", "hms", "htmltools", "httpuv", "httr", "igraph", "isoband", "jquerylib", "jsonlite", "labeling", "later", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "memoise", "mgcv", "mime", "nlme", "openssl", "otel", "permute", "phylobase", "pillar", "pixmap", "pkgconfig", "plyr", "prettyunits", "progress", "promises", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "reshape2", "rlang", "rncl", "RNeXML", "S7", "sass", "scales", "segmented", "seqinr", "shiny", "sourcetools", "sp", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "utf8", "uuid", "vctrs", "vegan", "viridisLite", "withr", "XML", "xml2", "xtable" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "Basics.Rmd", "filename": "Basics.html", "title": "Package overview", "author": "Francois Keck", "engine": "knitr::rmarkdown", "headings": [ "Data", "Visualizing the data", "Measuring and testing the signal for each trait and different methods", "Assessing the behavior of these methods with this phylogeny along a Brownian-Motion influence gradient", "Assessing the signal depth with correlograms", "Locating the signal with LIPA" ], "created": "2018-01-09 15:07:17", "modified": "2019-01-02 12:46:19", "commits": 2 }, { "source": "Demo_plots.Rmd", "filename": "Demo_plots.html", "title": "Plotting functions", "author": "Francois Keck", "engine": "knitr::rmarkdown", "headings": [ "Data", "Basics", "Colors", "Advanced tuning" ], "created": "2018-01-09 15:07:17", "modified": "2019-01-02 12:46:19", "commits": 2 } ], "_score": 7.412292509323047, "_indexed": false, "_nocasepkg": "phylosignal", "_universes": [ "phylotastic" ], "_indexurl": "https://fkeck.r-universe.dev/phylosignal", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.2", "date": "2026-11-02T08:53:56.000Z", "distro": "resolute", "arch": "aarch64", "commit": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "fileid": "https://r2.ropensci.org/25388fbc55a07e60bd6429fdb7f6c6b147e0e349b0d9af1489ace673f13d1e43", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/41415469359" }, { "r": "4.7.0", "os": "linux", "version": "1.3.2", "date": "2026-11-02T08:53:45.000Z", "distro": "resolute", "arch": "x86_64", "commit": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "fileid": "https://r2.ropensci.org/5b3bb8af7b617afa587c7f62c4dc1f8acf54f21c5c1e1069555bcd13a5d58a1a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/41415469359" }, { "r": "4.6.2", "os": "linux", "version": "1.3.2", "date": "2026-11-02T08:53:55.000Z", "distro": "resolute", "arch": "aarch64", "commit": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "fileid": "https://r2.ropensci.org/95b0d73b6cdba214369b20dd3c648b277a300b443ccdd74bcb96e6f21a816b3a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/41415469359" }, { "r": "4.6.2", "os": "linux", "version": "1.3.2", "date": "2026-11-02T08:53:56.000Z", "distro": "resolute", "arch": "x86_64", "commit": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "fileid": "https://r2.ropensci.org/85a5c3143cda4871378c32d72118626b718f38f1b986e85f2e1ce39179e495fd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/41415469359" }, { "r": "4.5.3", "os": "mac", "version": "1.3.2", "date": "2026-11-02T09:37:03.000Z", "arch": "aarch64", "commit": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "fileid": "https://r2.ropensci.org/4439bbb86cabea48b079f103808543ed7d5d2e54967d9973247fc3f9932f77cb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/41415469359" }, { "r": "4.5.3", "os": "mac", "version": "1.3.2", "date": "2026-11-02T09:23:09.000Z", "arch": "x86_64", "commit": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "fileid": "https://r2.ropensci.org/5543d0edffd71e7e26a99a5b31d9373152d838ea069775b898e01b6af904d9d9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/41415469359" }, { "r": "4.6.2", "os": "mac", "version": "1.3.2", "date": "2026-11-02T09:39:25.000Z", "arch": "aarch64", "commit": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "fileid": "https://r2.ropensci.org/c11e281debbf7336a45a57bf3e3fb2fb732854762f01e22f3010533980ce4091", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/41415469359" }, { "r": "4.6.2", "os": "mac", "version": "1.3.2", "date": "2026-11-02T09:19:41.000Z", "arch": "x86_64", "commit": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "fileid": "https://r2.ropensci.org/06e2347b09f19ea82ca75c3d157df0a150f48f485fbe079eb36fa2d842aa0b74", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/41415469359" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.2", "date": "2026-11-02T08:54:06.000Z", "arch": "emscripten", "commit": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "fileid": "https://r2.ropensci.org/28d4bce6b8b36e9844eacc6456def11083e717ee9eac537200e2453c9be1b6c5", "status": "success", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/41415469359" }, { "r": "4.7.0", "os": "win", "version": "1.3.2", "date": "2026-11-02T08:54:47.000Z", "arch": "aarch64", "commit": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "fileid": "https://r2.ropensci.org/bb1459af3552f80e1f88b9ae7bcd485c8c4900af438fb22bc5a5c764bf1785ff", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/41415469359" }, { "r": "4.7.0", "os": "win", "version": "1.3.2", "date": "2026-11-02T08:53:05.000Z", "arch": "x86_64", "commit": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "fileid": "https://r2.ropensci.org/1b35e889619f09a33a16ee31064c927dbad74266a4d5c65a7fdc67957828b4ba", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/41415469359" }, { "r": "4.5.3", "os": "win", "version": "1.3.2", "date": "2026-11-02T08:53:06.000Z", "arch": "x86_64", "commit": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "fileid": "https://r2.ropensci.org/49392dac753c83c956f17881643613b78879e1c8435adb9850ca03525ec5fdf7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/41415469359" }, { "r": "4.6.2", "os": "win", "version": "1.3.2", "date": "2026-11-02T08:56:12.000Z", "arch": "aarch64", "commit": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "fileid": "https://r2.ropensci.org/506f9aae4044a660d4c2cabb3626fc6e9a982f2a0164d80abe7e46c2e9176c90", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/41415469359" }, { "r": "4.6.2", "os": "win", "version": "1.3.2", "date": "2026-11-02T08:52:47.000Z", "arch": "x86_64", "commit": "3f3377341240dfe7b344bd957e4b3c1831d0a108", "fileid": "https://r2.ropensci.org/062efa8a83f5f2624e3c55ea1d91b71e1fe4470d587736d93d13183e47305b4f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/41415469359" } ] }