Package: MSCquartets
Title: Analyzing Gene Tree Quartets under the Multi-Species Coalescent
Version: 1.1.1
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: RandomFieldsUtils, zipfR, graphics, stats, Rdpack, foreach,
        doParallel, methods
RdMacros: Rdpack
Encoding: UTF-8
RoxygenNote: 7.1.2
NeedsCompilation: no
Depends: R (>= 3.2.0), ape (>= 5.0), phangorn
Packaged: 2022-04-14 00:41:23 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: 2022-04-19 14:22:30 UTC
Built: R 4.0.5; ; 2022-04-20 16:35:02 UTC; windows
