Package: adegenet
Version: 2.1.2
Encoding: UTF-8
Title: Exploratory Analysis of Genetic and Genomic Data
Author: Thibaut Jombart, Zhian N. Kamvar, Caitlin Collins, Roman Lustrik, Marie-
Pauline Beugin, Brian J. Knaus, Peter Solymos, Vladimir Mikryukov, Klaus Schliep, Tiago Maié, Libor Morkovsky, Ismail Ahmed, Anne Cori, Federico Calboli, RJ Ewing, Frédéric Michaud, Rebecca DeCamp
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Suggests: pegas, hierfstat, akima, maps, splancs, tripack, testthat,
poppr
Depends: R (>= 2.14), methods, ade4
Imports: utils, stats, grDevices, MASS, igraph, ape, shiny, ggplot2,
seqinr, parallel, spdep, boot, reshape2, dplyr (>= 0.4.1),
vegan
URL: https://github.com/thibautjombart/adegenet
Description: Toolset for the exploration of genetic and genomic data. Adegenet
provides formal (S4) classes for storing and handling various genetic data,
including genetic markers with varying ploidy and hierarchical population
structure ('genind' class), alleles counts by populations ('genpop'), and
genome-wide SNP data ('genlight'). It also implements original multivariate
methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance
and similarity measures, and several spatial methods. A range of both empirical
and simulated datasets is also provided to illustrate various methods.
Collate: adegenet.package.R datasets.R dist.genlight.R orthobasis.R
classes.R constructors.R accessors.R basicMethods.R handling.R
auxil.R minorAllele.R setAs.R SNPbin.R strataMethods.R
hierarchyMethods.R glHandle.R glFunctions.R glSim.R
find.clust.R hybridize.R scale.R fstat.R import.R seqTrack.R
chooseCN.R genind2genpop.R loadingplot.R sequences.R
gstat.randtest.R makefreq.R colorplot.R monmonier.R spca.R
coords.monmonier.R haploGen.R old2new.R global_local_tests.R
dapc.R compoplot.R xvalDapc.R haploPop.R PCtest.R dist.genpop.R
Hs.R propShared.R export.R HWE.R propTyped.R inbreeding.R
glPlot.R gengraph.R simOutbreak.R mutations.R snpposi.R
snpzip.R pairDist.R snapclust.R AIC.snapclust.R
AICc.snapclust.R BIC.snapclust.R KIC.snapclust.R
snapclust.choose.k.R servers.R showmekittens.R spca_randtest.R
export_to_mvmapper.R doc_C_routines.R zzz.R
License: GPL (>= 2)
LazyLoad: yes
RoxygenNote: 7.0.2
NeedsCompilation: yes
Packaged: 2020-01-20 07:41:20 UTC; zhian
Repository: CRAN
Date/Publication: 2020-01-20 19:50:02 UTC