CRAN/E | ontophylo

ontophylo

Ontology-Informed Phylogenetic Comparative Analyses

Installation

About

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.

github.com/diegosasso/ontophylo
Bug report File report

Key Metrics

Version 1.1.3
R ≥ 3.5.0
Published 2024-01-10 276 days ago
Needs compilation? no
License MIT
License File
CRAN checks ontophylo results
Language en-US

Downloads

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Last 90 days 487 -3%
Last 365 days 1.913

Maintainer

Maintainer

Diego S. Porto

Authors

Diego S. Porto

aut / cre

Sergei Tarasov

aut

Material

README
Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

ontophylo archive

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