{ "_id": "6a27b2c424555f66ed5377ba", "Package": "fibre", "Title": "Fast Evolutionary Trait Modelling on Phylogenies using Branch\nRegression Models", "Version": "0.0.0.9000", "Authors@R": "person(given = \"Russell\",\nfamily = \"Dinnage\",\nrole = c(\"aut\", \"cre\"),\nemail = \"r.dinnage@gmail.com\",\ncomment = c(ORCID = \"0000-0003-0846-2819\"))", "Description": "Implements Phylogenetic Branch Regression models which\nallow for flexible and versatile models of evolution along a\nphylogeny. The model can be used to detect shifts in rates of\nevolution along branches. The model uses a continuous and\nlinear model structure and so can be easily combined with other\nnon-phylogenetic statistical structures, as long as they are\nimplemented using the R package INLA. One major uses of this\nare to condition on phylogeny in a standard regression between\ntwo traits, thus 'accounting' for phylogenetic structure in the\nresponse variable, similar to how pgls is used but allowing for\na more flexible phylogenetic model. This also allows the\nphylogenetic model to be combined with the spatial models that\nINLA excels at (and with comparable flexibility to those\nspatial models).", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Remotes": [ "rdinnager/phyf" ], "URL": "https://rdinnager.github.io/fibre/", "Additional_repositories": "https://inla.r-inla-download.org/R/stable", "Config/pak/sysreqs": "libabsl-dev libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libgdal-dev gdal-bin libgeos-dev libglpk-dev\nmake libicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nlibproj-dev libsqlite3-dev libudunits2-dev", "Repository": "https://rdinnager.r-universe.dev", "Date/Publication": "2024-12-10 13:23:58 UTC", "RemoteUrl": "https://github.com/rdinnager/fibre", "RemoteRef": "HEAD", "RemoteSha": "069e04c036172e1a6a0c39472bd499a33d231a4f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-09 05:53:04 UTC", "User": "root" }, "Author": "Russell Dinnage [aut, cre] (ORCID:\n)", "Maintainer": "Russell Dinnage ", "MD5sum": "f175949856dc35e2151e662133f32716", "_user": "rdinnager", "_type": "src", "_file": "fibre_0.0.0.9000.tar.gz", "_fileid": "833d17c8801c693c1a3113c4b41e6ae942b4d6c85f8424a99105093fedf6a984", "_filesize": 4403654, "_sha256": "833d17c8801c693c1a3113c4b41e6ae942b4d6c85f8424a99105093fedf6a984", "_created": "2026-06-09T05:53:04.000Z", "_published": "2026-06-09T06:29:24.288Z", "_distro": "noble", "_jobs": [ { "job": 80257341027, "time": 241, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7499614397" }, { "job": 80257340943, "time": 234, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7499612590" }, { "job": 80257340944, "time": 143, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7499921822" }, { "job": 80257340966, "time": 157, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7500098249" }, { "job": 80256803853, "time": 277, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7499557971" }, { "job": 80257341014, "time": 206, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7499606086" }, { "job": 80257340993, "time": 170, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7499597923" }, { "job": 80257341002, "time": 137, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7499590263" }, { "job": 80257341033, "time": 166, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7499596814" } ], "_buildurl": "https://github.com/r-universe/rdinnager/actions/runs/27123038961", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/rdinnager/fibre", "_commit": { "id": "069e04c036172e1a6a0c39472bd499a33d231a4f", "author": "rdinnager ", "committer": "rdinnager ", "message": "updating documentation\n", "time": 1733837038 }, "_maintainer": { "name": "Russell Dinnage", "email": "r.dinnage@gmail.com", "login": "rdinnager", "orcid": "0000-0003-0846-2819", "twitter": "@ecologician", "description": "", "uuid": 5945401 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "ape", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "fastmatch", "role": "Imports" }, { "package": "MCMCglmm", "role": "Imports" }, { "package": "phytools", "role": "Imports" }, { "package": "phangorn", "role": "Imports" }, { "package": "ivs", "role": "Imports" }, { "package": "phyf", "version": ">= 0.0.0.9000", "role": "Imports" }, { "package": "hardhat", "role": "Imports" }, { "package": "rlang", "version": ">= 0.4.11", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "vctrs", "role": "Imports" }, { "package": "zeallot", "role": "Imports" }, { "package": "torch", "role": "Imports" }, { "package": "glue", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "generics", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "glmnet", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "skimr", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "bench", "role": "Suggests" }, { "package": "RPANDA", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "INLA", "role": "Suggests" }, { "package": "tidytree", "role": "Suggests" }, { "package": "recipes", "role": "Suggests" }, { "package": "learnr", "role": "Suggests" }, { "package": "roxygen2", "role": "Suggests" }, { "package": "rgl", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" }, { "package": "rmarchingcubes", "role": "Suggests" }, { "package": "Rvcg", "role": "Suggests" }, { "package": "orientlib", "role": "Suggests" }, { "package": "Morpho", "role": "Suggests" }, { "package": "einsum", "role": "Suggests" }, { "package": "imager", "role": "Suggests" }, { "package": "movMF", "role": "Suggests" }, { "package": "furrr", "role": "Suggests" }, { "package": "ggridges", "role": "Suggests" }, { "package": "ggforce", "role": "Suggests" } ], "_owner": "rdinnager", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 3, "_contributors": [ { "user": "rdinnager", "count": 47, "uuid": 5945401 } ], "_userbio": { "uuid": 5945401, "type": "user", "name": "Russell Dinnage" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/fibre" }, "_devurl": "https://github.com/rdinnager/fibre", "_pkgdown": "https://rdinnager.github.io/fibre/", "_searchresults": 35, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/fibre.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ ":=", ".data", "%>%", "as_label", "as_name", "augment", "autoplot", "bre", "bre_brownian", "bre_second_order", "default_camera", "default_light", "enquo", "enquos", "evo_autodecoder", "fibre", "fibre_formula_blueprint", "get_aces", "get_camera_position", "get_rates", "get_tces", "get_tips", "glance", "load_bird_beak_model", "load_model", "re", "sdf_net", "simulate_traits", "tidy" ], "_help": [ { "page": "bre", "title": "Specify a branch length (random) effect", "topics": [ "bre" ] }, { "page": "bre_brownian", "title": "Specify a branch length (random) effect for a Brownian motion model", "topics": [ "bre_brownian" ] }, { "page": "bre_second_order", "title": "Specify a branch length (random) effect for a 'Second Order' Brownian motion model", "topics": [ "bre_second_order" ] }, { "page": "evo_autodecoder", "title": "Create a Evolutionary Autodecoder Model", "topics": [ "evo_autodecoder" ] }, { "page": "fibre", "title": "Fit a 'fibre'", "topics": [ "fibre", "fibre.data.frame", "fibre.default", "fibre.formula", "fibre.matrix", "fibre.recipe" ] }, { "page": "get_aces", "title": "Title", "topics": [ "get_aces" ] }, { "page": "get_rates", "title": "Title", "topics": [ "get_rates" ] }, { "page": "get_tces", "title": "Title", "topics": [ "get_tces" ] }, { "page": "get_tips", "title": "Title", "topics": [ "get_tips" ] }, { "page": "load_model", "title": "Load a model", "topics": [ "load_model" ] }, { "page": "predict.fibre", "title": "Predict from a 'fibre'", "topics": [ "predict.fibre" ] }, { "page": "re", "title": "Specify a random effect", "topics": [ "re" ] }, { "page": "sdf_net", "title": "A signed distance field based neural network model for generating 3d shapes", "topics": [ "sdf_net" ] }, { "page": "simulate_traits", "title": "Function to simulate continuous trait value histories on a phylogeny.", "topics": [ "simulate_traits" ] }, { "page": "tidy.fibre", "title": "Tidy Model Results", "topics": [ "tidy.fibre" ] } ], "_pkglogo": "https://github.com/rdinnager/fibre/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/rdinnager/fibre/raw/HEAD/README.md", "_rundeps": [ "ape", "aplot", "assertthat", "base64enc", "bit", "bit64", "bslib", "cachem", "callr", "class", "classInt", "cli", "clusterGeneration", "coda", "codetools", "combinat", "coro", "corpcor", "cpp11", "cubature", "DBI", "DEoptim", "desc", "digest", "doParallel", "dplyr", "e1071", "evaluate", "expm", "farver", "fastmap", "fastmatch", "fmesher", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "foreach", "fs", "gdtools", "generics", "ggfun", "ggiraph", "ggplot2", "ggplotify", "ggtree", "glmnet", "glue", "gridGraphics", "gtable", "hardhat", "highr", "htmltools", "htmlwidgets", "igraph", "inlabru", "isoband", "iterators", "ivs", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "lattice", "lazyeval", "lifecycle", "magrittr", "maps", "MASS", "Matrix", "MatrixModels", "MCMCglmm", "memoise", "mime", "mnormt", "nlme", "numDeriv", "optimParallel", "otel", "patchwork", "phangorn", "phyf", "phytools", "pillar", "pkgconfig", "plyr", "processx", "proxy", "ps", "purrr", "quadprog", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppEigen", "repr", "rlang", "rmarkdown", "s2", "S7", "safetensors", "sass", "scales", "scatterplot3d", "sf", "shape", "skimr", "sp", "sparsevctrs", "splancs", "stringi", "stringr", "survival", "systemfonts", "tensorA", "tibble", "tidyr", "tidyselect", "tidytree", "tinytex", "torch", "treeio", "units", "utf8", "vctrs", "viridisLite", "withr", "wk", "xfun", "yaml", "yulab.utils", "zeallot" ], "_score": 2.720159303405957, "_indexed": true, "_nocasepkg": "fibre", "_universes": [ "rdinnager" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.0.9000", "date": "2026-06-09T05:56:28.000Z", "distro": "noble", "commit": "069e04c036172e1a6a0c39472bd499a33d231a4f", "fileid": "0d922cc2bc0dd2f65d8749d62e323586d31e8d33c97e331f241cb1f9c1c1e8f4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/rdinnager/actions/runs/27123038961" }, { "r": "4.6.0", "os": "linux", "version": "0.0.0.9000", "date": "2026-06-09T05:56:21.000Z", "distro": "noble", "commit": "069e04c036172e1a6a0c39472bd499a33d231a4f", "fileid": "de90790084824af04703539b6e2b8b411a23da1de38d58fd078c6019745a79b2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/rdinnager/actions/runs/27123038961" }, { "r": "4.5.3", "os": "mac", "version": "0.0.0.9000", "date": "2026-06-09T06:17:19.000Z", "commit": "069e04c036172e1a6a0c39472bd499a33d231a4f", "fileid": "a26c378bdc31bfd446b0a277222f5228f5a9892a693b7547731e90bb8753bbe1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/rdinnager/actions/runs/27123038961" }, { "r": "4.6.0", "os": "mac", "version": "0.0.0.9000", "date": "2026-06-09T06:28:17.000Z", "commit": "069e04c036172e1a6a0c39472bd499a33d231a4f", "fileid": "18aa3af0be426c41d631fa0832bb3c326a1b43bb43c8565bd8517e18d6467c39", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/rdinnager/actions/runs/27123038961" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.0.9000", "date": "2026-06-09T05:56:46.000Z", "commit": "069e04c036172e1a6a0c39472bd499a33d231a4f", "fileid": "97ee69c9ec9d59e2f09e7bf6acb804cb10930af165fea0957502dcaf5d2a38c1", "status": "success", "buildurl": "https://github.com/r-universe/rdinnager/actions/runs/27123038961" }, { "r": "4.7.0", "os": "win", "version": "0.0.0.9000", "date": "2026-06-09T05:55:28.000Z", "commit": "069e04c036172e1a6a0c39472bd499a33d231a4f", "fileid": "1b47163a4d6e7a556f19efb35975dd2e8e3238041adad077530d0cfafa14af05", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/rdinnager/actions/runs/27123038961" }, { "r": "4.5.3", "os": "win", "version": "0.0.0.9000", "date": "2026-06-09T05:54:42.000Z", "commit": "069e04c036172e1a6a0c39472bd499a33d231a4f", "fileid": "b7896fc361498799c6de948eb4a349805b80c515197aeb229baabb93e20da9e6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/rdinnager/actions/runs/27123038961" }, { "r": "4.6.0", "os": "win", "version": "0.0.0.9000", "date": "2026-06-09T05:55:26.000Z", "commit": "069e04c036172e1a6a0c39472bd499a33d231a4f", "fileid": "ccddcddb29042f0e99c57d33dd9e6b7ac57b26b986b163904c996e139e2c03d4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/rdinnager/actions/runs/27123038961" } ] }