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
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libssl-dev
        libx11-dev zlib1g-dev
Repository: https://mmollina.r-universe.dev
Date/Publication: 2026-01-12 01:15:11 UTC
RemoteUrl: https://github.com/mmollina/mappoly
RemoteRef: HEAD
RemoteSha: 09ec30a58a6b9d4b6edc8bc6af44021c94bb7ec0
NeedsCompilation: yes
Packaged: 2026-06-11 07:24:22 UTC; root
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)