Package: MSCquartets
Type: Package
Title: Analyzing Gene Tree Quartets under the Multi-Species Coalescent
Version: 1.3.1
Authors@R: c(
     person("Elizabeth", "Allman", email = "esallman@alaska.edu",
                  role = "aut"),
     person("Hector", "Banos", email = "hbassnos@gmail.com",
                  role =  "aut"),
     person("Jonathan", "Mitchell", email = "jonathanmitchell88@gmail.com",
                  role =  "aut"),
     person("John", "Rhodes", email = "j.rhodes@alaska.edu",
                  role = c("aut", "cre"),comment=c(ORCID = "0000-0001-9921-1091"))  )
Description: Methods for analyzing and using quartets displayed on a collection of gene trees, 
      primarily to make inferences about the species tree or network under the multi-species 
      coalescent model. These include quartet hypothesis tests for the model, as developed by 
      Mitchell et al. (2019) <doi:10.1214/19-EJS1576>, simplex plots of quartet concordance factors
      as presented by Allman et al. (2020) <doi:10.1101/2020.02.13.948083>, species tree inference 
      methods based on quartet distances of Rhodes (2019) <doi:10.1109/TCBB.2019.2917204> and 
      Yourdkhani and Rhodes (2019) <doi:10.1007/s11538-020-00773-4>, and the NANUQ algorithm for inference 
      of level-1 species networks of Allman et al. (2019) <doi:10.1186/s13015-019-0159-2>. Software announcement by Rhodes et al. (2020) 
      <doi:10.1093/bioinformatics/btaa868>.
License: MIT + file LICENSE
Imports: zipfR, graphics, stats, Rdpack, foreach, doParallel, methods,
        Rcpp (>= 1.0.10)
RdMacros: Rdpack
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
NeedsCompilation: yes
LinkingTo: Rcpp
Depends: R (>= 3.5.0), ape (>= 5.0), phangorn
Packaged: 2023-06-12 18:44:21 UTC; johnrhodes
Author: Elizabeth Allman [aut],
  Hector Banos [aut],
  Jonathan Mitchell [aut],
  John Rhodes [aut, cre] (<https://orcid.org/0000-0001-9921-1091>)
Maintainer: John Rhodes <j.rhodes@alaska.edu>
Repository: CRAN
Date/Publication: 2023-06-12 19:10:01 UTC
Built: R 4.2.0; x86_64-apple-darwin17.0; 2023-06-13 11:19:14 UTC; unix
Archs: MSCquartets.so.dSYM
