ontophylo: Ontology-Informed Phylogenetic Comparative Analyses

Provides new tools for analyzing discrete trait data integrating bio-ontologies and phylogenetics. It expands on the previous work of Tarasov et al. (2019) <doi:10.1093/isd/ixz009>. The PARAMO pipeline allows to reconstruct ancestral phenomes treating groups of morphological traits as a single complex character. The pipeline incorporates knowledge from ontologies during the amalgamation of individual character stochastic maps. Here we expand the current PARAMO functionality by adding new statistical methods for inferring evolutionary phenome dynamics using non-homogeneous Poisson process (NHPP). The new functionalities include: (1) reconstruction of evolutionary rate shifts of phenomes across lineages and time; (2) reconstruction of morphospace dynamics through time; and (3) estimation of rates of phenome evolution at different levels of anatomical hierarchy (e.g., entire body or specific regions only). The package also includes user-friendly tools for visualizing evolutionary rates of different anatomical regions using vector images of the organisms of interest.

Version: 1.1.3
Depends: R (≥ 3.5.0)
Imports: magrittr, dplyr, tidyr, purrr, tibble, ggplot2, stringdist, ape, phytools, ontologyIndex, RColorBrewer, grid, truncnorm, fANCOVA, grImport
Suggests: rmarkdown, knitr, roxygen2, testthat (≥ 3.0.0), stringr
Published: 2024-01-10
Author: Diego S. Porto ORCID iD [aut, cre], Sergei Tarasov ORCID iD [aut]
Maintainer: Diego S. Porto <diegosporto at gmail.com>
BugReports: https://github.com/diegosasso/ontophylo/issues
License: MIT + file LICENSE
URL: https://github.com/diegosasso/ontophylo
NeedsCompilation: no
Language: en-US
Materials: README
CRAN checks: ontophylo results

Documentation:

Reference manual: ontophylo.pdf

Downloads:

Package source: ontophylo_1.1.3.tar.gz
Windows binaries: r-devel: ontophylo_1.1.3.zip, r-release: ontophylo_1.1.3.zip, r-oldrel: ontophylo_1.1.3.zip
macOS binaries: r-release (arm64): ontophylo_1.1.3.tgz, r-oldrel (arm64): ontophylo_1.1.3.tgz, r-release (x86_64): ontophylo_1.1.3.tgz
Old sources: ontophylo archive

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