DESCRIPTION

Package: rphenoscate
Title: Semantics for Comparative Analyses of Trait Evolution
Version: 1.0.0
Authors@R: 
    c(person(c("Diego", "S."), "Porto",
             email = "diegosporto@gmail.com",
             role = c("aut"),
             comment = c(ORCID="0000-0002-1657-9606")
           ),
      person("Sergei", "Tarasov",
             email = "sergei.tarasov@helsinki.fi",
             role = c("aut"),
             comment = c(ORCID="0000-0001-5237-2330")
           ),
	  person("Caleb", "Charpentier",
             email = "calebc22@vt.edu",
             role = c("aut"),
             comment = c(ORCID="0000-0002-9787-7081")
           ),
	  person("Hilmar", "Lapp",
             email = "hilmar.lapp@duke.edu",
             role = c("aut"),
             comment = c(ORCID="0000-0001-9107-0714")
           ),
      person(c("Benjamin", "D."), "Redelings",
	     email = "benjamin.redelings@gmail.com",
	     role = c("ctb"),
	     comment = c(ORCID="0000-0002-3278-4343")
	     ),
      person("Josef", "Uyeda",
             email = "juyeda@vt.edu",
             role = c("aut", "cre"),
             comment = c(ORCID="0000-0003-4624-9680")
           ))
Description: Provides tools for semantic-aware evolutionary analyses of anatomical traits.
  It integrates semantic tools from rphenoscape and the whole-anatomy approach from PARAMO into a common framework for studying integrated anatomical traits.
  Current available capabilities include: setting structured Markov models for sets of characters based on a dependency matrix;
  recoding dependent traits as a single multistate character; building files to perform analyses on RevBayes or corHMM;
  visualizing dependency structure among characters with graphs and stochastic maps.
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-US
URL: https://github.com/uyedaj/rphenoscate
BugReports: https://github.com/uyedaj/rphenoscate/issues
Depends: R (>= 3.5.0)
Imports: ape, phytools, corHMM, pracma, dplyr, tidyr, stringr, MASS, numbers,
        treeplyr, rphenoscape, ontologyIndex, grDevices, graphics, igraph
Suggests: ontoFAST, tidyverse, rmarkdown, knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
Remotes: uyedaj/rphenoscate
RoxygenNote: 7.2.3
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2023-04-19; diego