Description
Ontology-Informed Phylogenetic Comparative Analyses.
Description
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.
README.md
Ontology-Informed Phylogenetic Comparative Analyses
- Authors: Diego Porto and Sergei Tarasov
- Maintainer: Diego Porto
This is the release version of the package. Please, feel free to try it out.
- Install package:
install.packages("remotes")
require(remotes)
remotes::install_github("diegosasso/ontophylo")
Please report any bugs or issues at: https://github.com/diegosasso/ontophylo/issues
Tutorial and examples: https://github.com/diegosasso/ontophylo_tutorials
Manuscript describing package: http://doi.org/10.1111/2041-210X.14283