Package: mappoly
Type: Package
Title: Genetic Linkage Maps in Autopolyploids
Version: 0.4.2
Authors@R: c(person(given = "Marcelo",
                    family = "Mollinari",
                    role = c("aut", "cre"),
                    email = "marcelo.mollinari@proton.me",
                    comment = c(ORCID="0000-0002-7001-8498")),
            person(given = "Gabriel",
                    family = "Gesteira",
                    role = "aut",
                    comment = c(ORCID="0000-0002-4106-7346")),
            person(given = "Cristiane",
                    family = "Taniguti",
                    role = "aut",
                    comment = c(ORCID="0000-0002-2021-6883")),
            person(given = "Jeekin",
                    family = "Lau",
                    role = "aut",
                    comment = c(ORCID="0000-0003-1114-6892")),
            person(given = "Oscar",
                    family = "Riera-Lizarazu",
                    role = "ctb",
                    comment = c(ORCID="0000-0002-7477-4063")),
            person(given = "Guilherme",
                    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("R Core Team", role = "cph",
                   comment = "Portions of C/C++ code adapted from R sources; see src/pairwise_estimation.cpp"),
            person("R Foundation for Statistical Computing", role = "cph",
                   comment = "Portions of C/C++ code adapted from R sources; see src/pairwise_estimation.cpp"))
Maintainer: Marcelo Mollinari <marcelo.mollinari@proton.me>
Description: Constructs genetic linkage maps in autopolyploid full-sib populations. 
             Uses pairwise recombination fraction estimation as the first 
             source of information to sequentially position allelic variants 
             in specific homologous chromosomes. For situations where pairwise 
             analysis has limited power, the algorithm relies on the multilocus 
             likelihood obtained through a hidden Markov model (HMM). 
             Methods are described in 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, dplyr, crayon, cli, magrittr, reshape2, ggplot2,
        smacof, princurve, dendextend, vcfR, zoo, plotly
LinkingTo: Rcpp, RcppParallel
RoxygenNote: 7.3.3
SystemRequirements: GNU make
Encoding: UTF-8
Suggests: updog, plot3D, fitPoly, polymapR, AGHmatrix, gatepoints,
        knitr, rmarkdown, stringr
URL: https://github.com/mmollina/MAPpoly
BugReports: https://github.com/mmollina/MAPpoly/issues
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2026-01-12 01:16:26 UTC; mmoll
Author: Marcelo Mollinari [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-7001-8498>),
  Gabriel Gesteira [aut] (ORCID: <https://orcid.org/0000-0002-4106-7346>),
  Cristiane Taniguti [aut] (ORCID:
    <https://orcid.org/0000-0002-2021-6883>),
  Jeekin Lau [aut] (ORCID: <https://orcid.org/0000-0003-1114-6892>),
  Oscar Riera-Lizarazu [ctb] (ORCID:
    <https://orcid.org/0000-0002-7477-4063>),
  Guilherme Pereira [ctb] (ORCID:
    <https://orcid.org/0000-0002-7106-8630>),
  Augusto Garcia [ctb] (ORCID: <https://orcid.org/0000-0003-0634-3277>),
  Zhao-Bang Zeng [ctb] (ORCID: <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 Core Team [cph] (Portions of C/C++ code adapted from R sources; see
    src/pairwise_estimation.cpp),
  R Foundation for Statistical Computing [cph] (Portions of C/C++ code
    adapted from R sources; see src/pairwise_estimation.cpp)
Repository: CRAN
Date/Publication: 2026-01-12 10:20:14 UTC
Built: R 4.6.0; x86_64-w64-mingw32; 2026-01-20 05:59:11 UTC; windows
Archs: x64
