{ "_id": "6a1f0287b401979e7341b2ae", "Package": "ontophylo", "Title": "Ontology-Informed Phylogenetic Comparative Analyses", "Version": "1.0.0", "Authors@R": "c(person(c(\"Diego\", \"S.\"), \"Porto\",\nemail = \"diegosporto@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID=\"0000-0002-1657-9606\")\n),\nperson(\"Sergei\", \"Tarasov\",\nemail = \"sergei.tarasov@helsinki.fi\",\nrole = c(\"aut\"),\ncomment = c(ORCID=\"0000-0001-5237-2330\")\n)\n)", "Description": "This package provides new phylogenetic tools for analyzing\ndiscrete trait data integrating bio-ontologies and\nphylogenetics. It expands on the previous work of Tarasov et\nal. (2019). The PARAMO pipeline allows to reconstruct ancestral\nphenomes treating groups of morphological traits as a single\ncomplex character. The pipeline incorporates knowledge from\nontologies during the amalgamation of individual character\nstochastic maps. Here we expand the current PARAMO\nfunctionality by adding new statistical methods for inferring\nevolutionary phenome dynamics using non-homogeneous Poisson\nprocess (NHPP). The new functionalities include: (1)\nreconstruction of evolutionary rate shifts of phenomes across\nlineages and time; (2) reconstruction of morphospace dynamics\nthrough time; and (3) estimation of rates of phenome evolution\nat different levels of anatomical hierarchy (e.g., entire body\nor specific regions only). The package also includes\nuser-friendly tools for visualizing evolutionary rates of\ndifferent anatomical regions using PNG vector images of the\norganisms of interest.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Language": "en-US", "URL": "https://github.com/diegosasso/ontophylo", "BugReports": "https://github.com/diegosasso/ontophylo/issues", "VignetteBuilder": "knitr", "Remotes": [ "diegosasso/ontophylo" ], "LazyData": "true", "RoxygenNote": "7.2.3", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev", "Repository": "https://diegosasso.r-universe.dev", "Date/Publication": "2023-12-08 09:49:35 UTC", "RemoteUrl": "https://github.com/diegosasso/ontophylo", "RemoteRef": "HEAD", "RemoteSha": "49565f518d1057473fe3470d8bc50b67030e0d49", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-18 08:24:14 UTC", "User": "root" }, "Author": "Diego S. Porto [aut, cre] (ORCID:\n),\nSergei Tarasov [aut] (ORCID: )", "Maintainer": "Diego S. 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Porto", "email": "diegosporto@gmail.com", "login": "diegosasso", "twitter": "@PortoSasso", "description": "", "uuid": 59983061, "orcid": "0000-0002-1657-9606" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "magrittr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "stringdist", "role": "Imports" }, { "package": "phytools", "role": "Imports" }, { "package": "ontologyIndex", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "truncnorm", "role": "Imports" }, { "package": "fANCOVA", "role": "Imports" }, { "package": "grImport", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "roxygen2", "role": "Suggests" }, 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