Geneland: Detection of Structure from Multilocus Genetic Data

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Stochastic simulation and MCMC inference of structure from genetic data.

Author
Gilles Guillot, Filipe Santos, Arnaud Estoup
Date of publication
2016-09-01 19:31:58
Maintainer
Gilles Guillot <gigu@dtu.dk>
License
GPL
Version
4.0.6
URLs

View on CRAN

Man pages

coordinates
Example of coordinate file
EstimateFreqNA
Estimate frequencies of null alleles.
FormatGenotypes
Formatting file of genotype data.
Fstat
Computes F statistics on a population genetics dataset given...
Fstat.output
Computes F statistics on the output of an inference by MCMC...
Geneland.GUI
Graphical interface for package Geneland
Geneland-package
Simulation and inference for subdivided populations
genotypes
Example of coordinate file
gl2gp
Geneland to Genepop conversion
HZ
Estimate parameters of the hybrid zone model by MCMC...
MCMC
Markov Chain Monte-Carlo inference of clusters from genotpype...
nullify
Simulates null alleles
PlotDrift
Plot the drift factors
PlotFreq
Plot the trace of allele frequencies in present time...
PlotFreqA
Plots allele frequencies in ancestral population along the...
Plotnpop
Plot of number of populations along the MCMC run
Plotntile
Plot of number of tiles along the MCMC run
PlotTessDyn
Plot tessellation along an MCMC run.
PlotTessellation
Maps of posterior probability of membership
PosteriorMode
Map of mode of posterior distribution of population...
PostProcessChain
Computation for maps of posterior probability of population...
show.estimate.hz
Show estimate of parameters of the hybrid zone model by MCMC...
show.simdata
Graphical display of data simulated by simdata
simdata
Simulation of georeferenced genotypes under an IBD + barrier...
simFmodel
Simulation of multi-locus genetic data from the spatial...

Files in this package

Geneland
Geneland/inst
Geneland/inst/CITATION
Geneland/inst/images
Geneland/inst/images/icon-configure.gif
Geneland/inst/images/icon-hybridzone.gif
Geneland/inst/images/icon-run.gif
Geneland/inst/images/line.gif
Geneland/inst/images/icon-convert.gif
Geneland/inst/images/icon-fmodel.gif
Geneland/inst/images/icon-fstat.gif
Geneland/inst/images/illustration_geneland.JPG
Geneland/inst/images/icon-postprocess.gif
Geneland/inst/images/icon-run2.gif
Geneland/inst/images/icon-output.gif
Geneland/inst/images/geneland6.gif
Geneland/inst/images/icon-draw.gif
Geneland/inst/images/icon-plot.gif
Geneland/inst/images/icon-ok.gif
Geneland/inst/images/pleasewait.gif
Geneland/inst/images/geneland6.gif.SAVE
Geneland/inst/images/icon-ibd.gif
Geneland/src
Geneland/src/alarousset.f
Geneland/src/main.f
Geneland/src/ggfstat.f
Geneland/src/hz.f
Geneland/src/wrapper.c
Geneland/NAMESPACE
Geneland/data
Geneland/data/coordinates.txt.gz
Geneland/data/genotypes.txt.gz
Geneland/R
Geneland/R/PlotFreqA.R
Geneland/R/show.estimate.hz.R
Geneland/R/Plotnpop.R
Geneland/R/PosteriorMode.R
Geneland/R/PlotTessellation.R
Geneland/R/MCMC.R
Geneland/R/PostProcessChain.R
Geneland/R/HZ.R
Geneland/R/simdata.R
Geneland/R/PlotDrift.R
Geneland/R/FormatGenotypes.R
Geneland/R/nullify.R
Geneland/R/PlotTessDyn.R
Geneland/R/show.simdata.R
Geneland/R/simFmodel.R
Geneland/R/Fstat.output.R
Geneland/R/Geneland.GUI.R
Geneland/R/gl2gp.R
Geneland/R/PlotFreq.R
Geneland/R/EstimateFreqNA.R
Geneland/R/Plotntile.R
Geneland/R/Fstat.R
Geneland/vignettes
Geneland/vignettes/Geneland-Doc.tex
Geneland/vignettes/dag3.pdf
Geneland/vignettes/fig
Geneland/vignettes/fig/postproc.jpg
Geneland/vignettes/fig/multip_run.jpg
Geneland/vignettes/fig/dag-final.pdf_t
Geneland/vignettes/fig/MyMap_zoom7.jpeg
Geneland/vignettes/fig/wdl1.jpeg
Geneland/vignettes/fig/example_spatial3_bis.jpeg
Geneland/vignettes/fig/map.jpeg
Geneland/vignettes/fig/power.jpeg
Geneland/vignettes/fig/npop.jpeg
Geneland/vignettes/fig/vor2.jpeg
Geneland/vignettes/fig/example_spatial3_ter.jpeg
Geneland/vignettes/fig/choosesep.jpg
Geneland/vignettes/fig/MCMC.jpg
Geneland/vignettes/fig/multip_run2.jpg
Geneland/vignettes/fig/choosefiles.jpg
Geneland/vignettes/fig/vor1.jpeg
Geneland/vignettes/fig/exp_q_quart.jpeg
Geneland/vignettes/fig/initial.jpg
Geneland/vignettes/fig/example_spatial2_bis.jpeg
Geneland/vignettes/fig/parallel.jpg
Geneland/vignettes/fig/dag3.pdf_t
Geneland/vignettes/fig/example_spatial_bis.jpeg
Geneland/vignettes/fig/MyMap_zoom10.jpeg
Geneland/vignettes/fig/output.jpg
Geneland/vignettes/dag-final.pdf
Geneland/vignettes/Geneland-Doc.pdf
Geneland/MD5
Geneland/DESCRIPTION
Geneland/ChangeLog
Geneland/man
Geneland/man/show.simdata.Rd
Geneland/man/Fstat.output.Rd
Geneland/man/Plotnpop.Rd
Geneland/man/PostProcessChain.Rd
Geneland/man/PlotFreq.Rd
Geneland/man/PlotTessDyn.Rd
Geneland/man/MCMC.Rd
Geneland/man/Plotntile.Rd
Geneland/man/PosteriorMode.Rd
Geneland/man/Fstat.Rd
Geneland/man/PlotDrift.Rd
Geneland/man/nullify.Rd
Geneland/man/Geneland.GUI.Rd
Geneland/man/genotypes.Rd
Geneland/man/coordinates.Rd
Geneland/man/simdata.Rd
Geneland/man/HZ.Rd
Geneland/man/gl2gp.Rd
Geneland/man/simFmodel.Rd
Geneland/man/EstimateFreqNA.Rd
Geneland/man/Geneland-package.Rd
Geneland/man/PlotFreqA.Rd
Geneland/man/FormatGenotypes.Rd
Geneland/man/PlotTessellation.Rd
Geneland/man/show.estimate.hz.Rd