RClone: Partially Clonal Populations Analysis

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R version of 'GenClone' (a computer program to analyse genotypic data, test for clonality and describe spatial clonal organization, Arnaud-Haond & Belkhir 2007, <http://wwz.ifremer.fr/clonix/content/download/68205/903914/file/GenClone2.0.setup.zip>), this package allows clone handling as 'GenClone' does, plus the possibility to work with several populations, MultiLocus Lineages (MLL) custom definition and use, and p-value calculation for psex statistic (probability of originating from distinct sexual events) and psex_Fis statistic (taking account of Hardy-Weinberg equilibrium departure) as 'MLGsim'/'MLGsim2' (a program for detecting clones using a simulation approach, Stenberg et al. 2003).

Author
Sophie Arnaud-Haond [aut], Diane Bailleul [aut, cre], Solenn Stoeckel [ctb]
Date of publication
2016-06-06 12:57:15
Maintainer
Diane Bailleul <diane.bailleul.pro@gmail.com>
License
GPL (>= 2.0)
Version
1.0.2
URLs

View on CRAN

Man pages

agg_index
Aggregation of clones
autocorrelation
Spatial Autocorrelation
clonal_index
Indices for clonal data
clonal_sub
Clonal Subrange
convert_GC
File conversion into RClone files
edge_effect
Edge Effect
export_genclone
export data file to Adegenet, Genetix and Arlequin
Fis
Fis
freq_RR
Allelic Frequencies
genclone
Summary function of RClone package
genet_dist
Genetic distance
kinship
Loiselle and Ritland kinship coefficients
list_all
Listing unique alleles
MLG_tab
Table of MLG (MultiLocus Genotypes)
MLL_generator
Clonal Lineage Generation
Pareto_index
Pareto index
pgen
Probability of a Genotype
psex
Probability of originating from distinct sexual events
RClone-package
RClone
sample_LU
Sample Loci or Units
sort_all
Sorting alleles
transcript_GC
Transcript GenClone files

Files in this package

RClone
RClone/inst
RClone/inst/doc
RClone/inst/doc/RClone_qmsevpops.pdf
RClone/inst/doc/RClone_quickmanual.pdf
RClone/inst/doc/RClone_qmsevpops.R
RClone/inst/doc/RClone_quickmanual.R
RClone/inst/doc/RClone_qmsevpops.Rmd
RClone/inst/doc/RClone_quickmanual.rmd
RClone/tests
RClone/tests/testthat_p3.R
RClone/tests/testthat_p2.R
RClone/tests/testthat_p1.R
RClone/tests/testthat_p4.R
RClone/tests/testthat
RClone/tests/testthat/test_package_RClone_p3.R
RClone/tests/testthat/test_package_RClone_p6.R
RClone/tests/testthat/test_package_RClone_p2.R
RClone/tests/testthat/test_package_RClone_p5.R
RClone/tests/testthat/test_package_RClone_p4.R
RClone/tests/testthat/test_package_RClone_p1.R
RClone/tests/testthat/test_package_RClone_p7.R
RClone/tests/testthat_p5.R
RClone/NAMESPACE
RClone/data
RClone/data/coord_posidonia.rda
RClone/data/resvigncont2.rda
RClone/data/infile.rda
RClone/data/resvigncont.rda
RClone/data/popsim.rda
RClone/data/posidonia.rda
RClone/data/datalist
RClone/data/zostera.rda
RClone/R
RClone/R/RClone.R
RClone/vignettes
RClone/vignettes/RClone_qmsevpops.Rmd
RClone/vignettes/RClone_quickmanual.rmd
RClone/README.md
RClone/MD5
RClone/build
RClone/build/vignette.rds
RClone/DESCRIPTION
RClone/man
RClone/man/clonal_sub.Rd
RClone/man/freq_RR.Rd
RClone/man/transcript_GC.Rd
RClone/man/resvigncont.rd
RClone/man/genclone.Rd
RClone/man/sample_LU.Rd
RClone/man/sort_all.Rd
RClone/man/infile.rd
RClone/man/agg_index.Rd
RClone/man/zostera.rd
RClone/man/RClone-package.Rd
RClone/man/coord_posidonia.rd
RClone/man/Pareto_index.Rd
RClone/man/genet_dist.Rd
RClone/man/edge_effect.Rd
RClone/man/list_all.Rd
RClone/man/Fis.Rd
RClone/man/MLL_generator.Rd
RClone/man/pgen.Rd
RClone/man/kinship.Rd
RClone/man/clonal_index.Rd
RClone/man/posidonia.rd
RClone/man/export_genclone.Rd
RClone/man/autocorrelation.Rd
RClone/man/psex.Rd
RClone/man/convert_GC.Rd
RClone/man/popsim.rd
RClone/man/MLG_tab.Rd