mappoly: Genetic Linkage Maps in Autopolyploids

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>.

Version: 0.2.1
Depends: R (≥ 3.5.0)
Imports: Rcpp (≥ 0.12.6), RCurl, plotly, fields, ggpubr, ggsci, rstudioapi, scatterplot3d, dplyr, crayon, cli, magrittr, reshape2, ggplot2, smacof, princurve, dendextend, vcfR, zoo
LinkingTo: Rcpp
Suggests: testthat, RColorBrewer, updog, covr, polymapR, fitPoly
Published: 2020-11-23
Author: Marcelo Mollinari ORCID iD [aut, cre], Gabriel Gesteira ORCID iD [aut], Guilhereme Pereira ORCID iD [ctb], Augusto Garcia ORCID iD [ctb], Zhao-Bang Zeng ORCID iD [ctb], 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)
Maintainer: Marcelo Mollinari <mmollin at ncsu.edu>
BugReports: https://github.com/mmollina/MAPpoly/issues
License: GPL-3
URL: https://github.com/mmollina/MAPpoly
NeedsCompilation: yes
SystemRequirements: C++11
Citation: mappoly citation info
Materials: README NEWS
CRAN checks: mappoly results

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Reference manual: mappoly.pdf
Package source: mappoly_0.2.1.tar.gz
Windows binaries: r-devel: mappoly_0.2.1.zip, r-release: mappoly_0.2.1.zip, r-oldrel: mappoly_0.2.1.zip
macOS binaries: r-release: mappoly_0.2.1.tgz, r-oldrel: mappoly_0.2.1.tgz
Old sources: mappoly archive

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