{ "_id": "6aad020e3d719c1f8407493f", "Package": "phylopath", "Type": "Package", "Title": "Perform Phylogenetic Path Analysis", "Version": "1.4.0", "Authors@R": "person(\"Wouter\", \"van der Bijl\",\nemail = \"wouter@zoology.ubc.ca\",\nrole = c(\"aut\", \"cre\"))", "Maintainer": "Wouter van der Bijl ", "Description": "A comprehensive and easy to use R implementation of\nconfirmatory phylogenetic path analysis as described by Von\nHardenberg and Gonzalez-Voyer (2012)\n. Note that the required\npackage 'ggm' depends on 'graph' from Bioconductor, which is\nnot installed automatically; the simplest route is\ninstall.packages(\"BiocManager\");\nBiocManager::install(\"phylopath\").", "URL": "https://ax3man.github.io/phylopath/", "BugReports": "https://github.com/Ax3man/phylopath/issues", "License": "GPL-3", "LazyData": "TRUE", "biocViews": "", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev libglpk-dev\nlibicu-dev libxml2-dev", "Repository": "https://ax3man.r-universe.dev", "Date/Publication": "2026-08-19 20:21:17 UTC", "RemoteUrl": "https://github.com/ax3man/phylopath", "RemoteRef": "HEAD", "RemoteSha": "8d78f7cb2fe370cc8300854542abefae23b8f13d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-18 08:59:47 UTC", "User": "root" }, "Author": "Wouter van der Bijl [aut, cre]", "_user": "ax3man", "_type": "src", "_file": "phylopath_1.4.0.tar.gz", "_fileid": "https://r2.ropensci.org/5e4d57c72669371f3eaceedc77e9529f8a59ef74b14e8a5cf2930337b1aa9986", "_filesize": 3437869, "_sha256": "5e4d57c72669371f3eaceedc77e9529f8a59ef74b14e8a5cf2930337b1aa9986", "_expires": "2026-12-27T09:19:08.000Z", "_created": "2026-09-18T08:59:47.000Z", "_published": "2026-09-18T09:19:10.521Z", "_jobs": [ { "job": 105543043025, "time": 214, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10539936626" }, { "job": 105543042904, "time": 271, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10539996637" }, { "job": 105543042979, "time": 153, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10539899114" }, { "job": 105543042978, "time": 208, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10540341839" }, { "job": 105541957082, "time": 241, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10540280416" }, { "job": 105543042887, "time": 130, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10539596916" }, { "job": 105543042910, "time": 119, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10540185380" }, { "job": 105543043095, "time": 130, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10540270867" }, { "job": 105543042952, "time": 140, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10539437141" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/ax3man/actions/runs/35326881330", "_status": "success", "_upstream": "https://github.com/ax3man/phylopath", "_commit": { "id": "8d78f7cb2fe370cc8300854542abefae23b8f13d", "author": "Wouter van der Bijl ", "committer": "Wouter van der Bijl ", "message": "CRAN submission\n", "time": 1787170877 }, "_maintainer": { "name": "Wouter van der Bijl", "email": "wouter@zoology.ubc.ca", "login": "ax3man", "bluesky": "@vdbijl.bsky.social", "description": "Evolutionary biologist.", "uuid": 15309336 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "ape", "version": ">= 4.1", "role": "Imports" }, { "package": "future.apply", "role": "Imports" }, { "package": "ggm", "version": ">= 2.3", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.0.0", "role": "Imports" }, { "package": "ggraph", "version": ">= 1.0.0", "role": "Imports" }, { "package": "igraph", "version": ">= 1.0.1", "role": "Imports" }, { "package": "phylolm", "version": ">= 2.5", "role": "Imports" }, { "package": "purrr", "version": ">= 0.2.3", "role": "Imports" }, { "package": "rlang", "version": ">= 1.0.0", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "ax3man", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2026-33", "n": 12 }, { "week": "2026-34", "n": 28 } ], "_tags": [ { "name": "v1.4.0", "date": "2026-08-19" } ], "_topics": [ "analysis", "comparative-methods", "path", "phylogenetics" ], "_stars": 13, "_contributors": [ { "user": "ax3man", "count": 333, "uuid": 15309336 } ], "_userbio": { "uuid": 15309336, "type": "user", "name": "Wouter van der Bijl", "followers": 33, "description": "Evolutionary biologist." }, "_downloads": { "count": 793, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/phylopath" }, "_mentions": 8, "_devurl": "https://github.com/ax3man/phylopath", "_pkgdown": "https://ax3man.github.io/phylopath/", "_searchresults": 123, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/phylopath.html", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/ax3man/phylopath", "_realowner": "ax3man", "_cranurl": true, "_releases": [ { "version": "0.2.0", "date": "2016-10-07" }, { "version": "0.2.1", "date": "2016-11-10" }, { "version": "0.2.2", "date": "2017-01-04" }, { "version": "0.2.3", "date": "2017-03-23" }, { "version": "0.3.0", "date": "2017-07-06" }, { "version": "0.3.1", "date": "2017-08-09" }, { "version": "1.0.0", "date": "2017-11-03" }, { "version": "1.0.1", "date": "2018-07-08" }, { "version": "1.0.2", "date": "2019-01-02" }, { "version": "1.1.0", "date": "2019-07-12" }, { "version": "1.1.1", "date": "2019-08-28" }, { "version": "1.1.2", "date": "2019-12-07" }, { "version": "1.1.3", "date": "2021-10-04" }, { "version": "1.2.0", "date": "2023-10-10" }, { "version": "1.2.1", "date": "2024-03-19" }, { "version": "1.3.0", "date": "2024-06-14" }, { "version": "1.3.1", "date": "2025-09-06" }, { "version": "1.4.0", "date": "2026-08-20" } ], "_exports": [ "average", "average_DAGs", "best", "choice", "coef_plot", "DAG", "define_model_set", "est_DAG", "phylo_path", "plot_model_set", "show_warnings" ], "_datasets": [ { "name": "cichlids", "title": "Cichlid traits and the evolution of cooperative breeding.", "object": "cichlids", "class": [ "data.frame" ], "fields": [ "C", "M", "P", "G", "D" ], "rows": 69, "table": true, "tojson": true }, { "name": "cichlids_tree", "title": "Cichlid phylogeny.", "object": "cichlids_tree", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "red_list", "title": "Data on brain size, life history and vulnerability to extinction", "object": "red_list", "class": [ "data.frame" ], "fields": [ "Br", "B", "G", "L", "W", "P", "Status" ], "rows": 474, "table": true, "tojson": true }, { "name": "red_list_tree", "title": "Mammalian phylogeny", "object": "red_list_tree", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "rhino", "title": "Rhinogrades traits.", "object": "rhino", "class": [ "data.frame" ], "fields": [ "SP", "BM", "NL", "LS", "DD", "RS" ], "rows": 100, "table": true, "tojson": true }, { "name": "rhino_tree", "title": "Rhinogrades phylogeny.", "object": "rhino_tree", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "as.data.frame.fitted_DAG", "title": "Extract the paths of a fitted causal model.", "topics": [ "as.data.frame.fitted_DAG" ] }, { "page": "average", "title": "Extract and average the best supported models from a phylogenetic path analysis.", "topics": [ "average" ] }, { "page": "average_DAGs", "title": "Perform model averaging on a list of DAGs.", "topics": [ "average_DAGs" ] }, { "page": "best", "title": "Extract and estimate the best supported model from a phylogenetic path analysis.", "topics": [ "best" ] }, { "page": "choice", "title": "Extract and estimate an arbitrary model from a phylogenetic path analysis.", "topics": [ "choice" ] }, { "page": "cichlids", "title": "Cichlid traits and the evolution of cooperative breeding.", "topics": [ "cichlids" ] }, { "page": "cichlids_tree", "title": "Cichlid phylogeny.", "topics": [ "cichlids_tree" ] }, { "page": "coef_plot", "title": "Plot path coefficients and their confidence intervals or standard errors.", "topics": [ "coef_plot" ] }, { "page": "coef.fitted_DAG", "title": "Extract the coefficients and confidence intervals of a fitted causal model.", "topics": [ "coef.fitted_DAG", "confint.fitted_DAG" ] }, { "page": "DAG", "title": "Directed acyclic graphs (DAGs)", "topics": [ "DAG" ] }, { "page": "define_model_set", "title": "Define a model set.", "topics": [ "define_model_set" ] }, { "page": "est_DAG", "title": "Estimate path coefficients for a DAG.", "topics": [ "est_DAG" ] }, { "page": "phylo_path", "title": "Compare causal models in a phylogenetic context.", "topics": [ "phylo_path" ] }, { "page": "plot_model_set", "title": "Plot several causal hypothesis at once.", "topics": [ "plot_model_set" ] }, { "page": "plot.DAG", "title": "Plot a directed acyclic graph.", "topics": [ "plot.DAG" ] }, { "page": "plot.fitted_DAG", "title": "Plot a directed acyclic graph with path coefficients.", "topics": [ "plot.fitted_DAG" ] }, { "page": "plot.phylopath_summary", "title": "Plot the comparison of a set of causal models.", "topics": [ "plot.phylopath_summary" ] }, { "page": "red_list", "title": "Data on brain size, life history and vulnerability to extinction", "topics": [ "red_list" ] }, { "page": "red_list_tree", "title": "Mammalian phylogeny", "topics": [ "red_list_tree" ] }, { "page": "rhino", "title": "Rhinogrades traits.", "topics": [ "rhino" ] }, { "page": "rhino_tree", "title": "Rhinogrades phylogeny.", "topics": [ "rhino_tree" ] }, { "page": "show_warnings", "title": "Print out warnings from a phylopath analysis.", "topics": [ "show_warnings" ] } ], "_readme": "https://github.com/ax3man/phylopath/raw/HEAD/README.md", "_rundeps": [ "ape", "base64enc", "BiocGenerics", "BiocManager", "cachem", "cli", "codetools", "cpp11", "digest", "dplyr", "farver", "fastmap", "future", "future.apply", "generics", "ggforce", "ggm", "ggplot2", "ggraph", "ggrepel", "globals", "glue", "graph", "graphlayouts", "gridExtra", "gtable", "igraph", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "listenv", "magrittr", "MASS", "Matrix", "memoise", "nlme", "parallelly", "phylolm", "pillar", "pkgconfig", "polyclip", "purrr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "S7", "scales", "stringi", "stringr", "systemfonts", "tibble", "tidygraph", "tidyr", "tidyselect", "tweenr", "utf8", "vctrs", "viridis", "viridisLite", "withr" ], "_vignettes": [ { "source": "binary_models.Rmd", "filename": "binary_models.html", "title": "Comparing causal models of binary traits using phylopath", "author": "Wouter van der Bijl", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "On phylogenetic logistic regression", "On the interpretation of coefficients", "Example analysis", "Data and hypotheses", "Defining the causal models", "Comparing the models", "Evaluating variable importance" ], "created": "2017-07-06 13:57:06", "modified": "2026-08-19 17:44:58", "commits": 17 }, { "source": "intro_to_phylopath.Rmd", "filename": "intro_to_phylopath.html", "title": "Introduction to phylogenetic path analysis with phylopath", "author": "Wouter van der Bijl", "engine": "knitr::rmarkdown", "headings": [ "Some starting notes", "Starting up", "Models of evolution", "An example analysis", "Specifying the model set", "Evaluating the model set", "Selecting and fitting a final model" ], "created": "2016-08-09 17:47:42", "modified": "2026-08-17 18:38:32", "commits": 18 } ], "_score": 7.885089701121823, "_indexed": true, "_nocasepkg": "phylopath", "_universes": [ "ax3man" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4.0", "date": "2026-09-18T09:02:30.000Z", "distro": "resolute", "commit": "8d78f7cb2fe370cc8300854542abefae23b8f13d", "fileid": "https://r2.ropensci.org/29c3bd7786242ba34fbc6575d3ff2c376fcd1dff8de9d26b8f744dbaf68bd8ba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ax3man/actions/runs/35326881330" }, { "r": "4.6.1", "os": "linux", "version": "1.4.0", "date": "2026-09-18T09:03:31.000Z", "distro": "resolute", "commit": "8d78f7cb2fe370cc8300854542abefae23b8f13d", "fileid": "https://r2.ropensci.org/6e38f616cc1abe74d51bab86bdb1027dee5f6dc46a4b620b49d5feacf4c2290e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ax3man/actions/runs/35326881330" }, { "r": "4.5.3", "os": "mac", "version": "1.4.0", "date": "2026-09-18T09:17:53.000Z", "commit": "8d78f7cb2fe370cc8300854542abefae23b8f13d", "fileid": "https://r2.ropensci.org/22112fa334162ee0c8ad2d1adc41fcf1df5038aa1a7a9231399c3f4a3532327c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ax3man/actions/runs/35326881330" }, { "r": "4.6.1", "os": "mac", "version": "1.4.0", "date": "2026-09-18T09:15:30.000Z", "commit": "8d78f7cb2fe370cc8300854542abefae23b8f13d", "fileid": "https://r2.ropensci.org/265a2c60761e656fb068d3197b0a1b2d516e762768614cef97357bfd5bd2a904", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ax3man/actions/runs/35326881330" }, { "r": "4.6.0", "os": "wasm", "version": "1.4.0", "date": "2026-09-18T09:02:17.000Z", "commit": "8d78f7cb2fe370cc8300854542abefae23b8f13d", "fileid": "https://r2.ropensci.org/d5346ed30fdd3d6748d838abb88033c64f33248cf81a2e3b8c99623323ce8693", "status": "success", "buildurl": "https://github.com/r-universe/ax3man/actions/runs/35326881330" }, { "r": "4.7.0", "os": "win", "version": "1.4.0", "date": "2026-09-18T09:00:55.000Z", "commit": "8d78f7cb2fe370cc8300854542abefae23b8f13d", "fileid": "https://r2.ropensci.org/eb759293f748ecd7f0e165cd2480ee6479775c33cdaa6b92be8c006bef6ec0c0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ax3man/actions/runs/35326881330" }, { "r": "4.5.3", "os": "win", "version": "1.4.0", "date": "2026-09-18T09:01:24.000Z", "commit": "8d78f7cb2fe370cc8300854542abefae23b8f13d", "fileid": "https://r2.ropensci.org/dc3f45d226fb466ba855f9560ca71b56c6d3bbc802abf121f8213742d32f77f8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ax3man/actions/runs/35326881330" }, { "r": "4.6.1", "os": "win", "version": "1.4.0", "date": "2026-09-18T09:01:04.000Z", "commit": "8d78f7cb2fe370cc8300854542abefae23b8f13d", "fileid": "https://r2.ropensci.org/9197bf509c7135036bf5b1bfb8322bfcfdbc39b2881a8ac3a00153ca04b8c7f4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ax3man/actions/runs/35326881330" } ] }