Package: mappoly
Type: Package
Title: Genetic Linkage Maps in Autopolyploids
Version: 0.3.0
Authors@R: c(person(given = "Marcelo",
                    family = "Mollinari",
                    role = c("aut", "cre"),
                    email = "mmollin@ncsu.edu",
                    comment = c(ORCID="0000-0002-7001-8498")),
            person(given = "Gabriel",
                    family = "Gesteira",
                    role = "aut",
                    email = "gdesiqu@ncsu.edu",
                    comment = c(ORCID="0000-0002-4106-7346")),
            person(given = "Guilhereme",
                    family = "Pereira",
                    role = "ctb",
                    comment = c(ORCID="0000-0002-7106-8630")),
            person(given = "Augusto",
                    family = "Garcia",
                    role = "ctb",
                    comment = c(ORCID="0000-0003-0634-3277")),
            person(given = "Zhao-Bang",
                    family = "Zeng",
                    role = "ctb",
                    comment = c(ORCID="0000-0002-3115-1149")),
            person(given = "Katharine",
                    family = "Preedy",
                    role = c("ctb", "cph"),
                    comment = "MDS ordering algorithm"),
            person(given = "Robert",
                   family = "Gentleman",
                    role = "cph",
                    comment = "C code for MLE optimization in src/pairwise_estimation.cpp"),
            person(given = "Ross",
                    family = "Ihaka",
                     role = "cph",
                    comment = "C code for MLE optimization in src/pairwise_estimation.cpp"),
            person(given = "R Foundation",
                    role = "cph",
                    comment = "C code for MLE optimization in src/pairwise_estimation.cpp"),
            person(given = "R-core",
                    role = "cph",
                    comment = "C code for MLE optimization in src/pairwise_estimation.cpp"))
Maintainer: Marcelo Mollinari <mmollin@ncsu.edu>
Description: Construction of genetic maps in autopolyploid full-sib populations. 
             Uses pairwise recombination fraction estimation as the first 
             source of information to sequentially position allelic variants 
             in specific homologues. For situations where pairwise analysis has 
             limited power, the algorithm relies on the multilocus likelihood 
             obtained through a hidden Markov model (HMM). For more detail,
             please see  Mollinari and Garcia (2019) <doi:10.1534/g3.119.400378> 
             and Mollinari et al. (2020) <doi:10.1534/g3.119.400620>.
License: GPL-3
LazyData: TRUE
LazyDataCompression: xz
Depends: R (>= 4.0.0)
Imports: Rcpp (>= 0.12.6), RcppParallel, RCurl, fields, ggpubr, ggsci,
        rstudioapi, scatterplot3d, dplyr, crayon, cli, magrittr,
        reshape2, ggplot2, smacof, princurve, dendextend, vcfR, zoo,
        plotly
LinkingTo: Rcpp, RcppParallel
RoxygenNote: 7.1.2
SystemRequirements: C++11, GNU make
Encoding: UTF-8
Suggests: testthat, updog, fitPoly, polymapR, AGHmatrix, gatepoints,
        knitr, rmarkdown
URL: https://github.com/mmollina/MAPpoly
BugReports: https://github.com/mmollina/MAPpoly/issues
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-01-11 01:16:20 UTC; marcelomollinari
Author: Marcelo Mollinari [aut, cre] (<https://orcid.org/0000-0002-7001-8498>),
  Gabriel Gesteira [aut] (<https://orcid.org/0000-0002-4106-7346>),
  Guilhereme Pereira [ctb] (<https://orcid.org/0000-0002-7106-8630>),
  Augusto Garcia [ctb] (<https://orcid.org/0000-0003-0634-3277>),
  Zhao-Bang Zeng [ctb] (<https://orcid.org/0000-0002-3115-1149>),
  Katharine Preedy [ctb, cph] (MDS ordering algorithm),
  Robert Gentleman [cph] (C code for MLE optimization in
    src/pairwise_estimation.cpp),
  Ross Ihaka [cph] (C code for MLE optimization in
    src/pairwise_estimation.cpp),
  R Foundation [cph] (C code for MLE optimization in
    src/pairwise_estimation.cpp),
  R-core [cph] (C code for MLE optimization in
    src/pairwise_estimation.cpp)
Repository: CRAN
Date/Publication: 2022-01-11 09:22:41 UTC
Built: R 4.0.5; x86_64-w64-mingw32; 2022-04-21 16:19:30 UTC; windows
Archs: i386, x64
