RClone: Partially Clonal Populations Analysis
Version 1.0.2

R version of 'GenClone' (a computer program to analyse genotypic data, test for clonality and describe spatial clonal organization, Arnaud-Haond & Belkhir 2007, ), 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).

AuthorSophie Arnaud-Haond [aut], Diane Bailleul [aut, cre], Solenn Stoeckel [ctb]
Date of publication2016-06-06 12:57:15
MaintainerDiane Bailleul <diane.bailleul.pro@gmail.com>
LicenseGPL (>= 2.0)
Version1.0.2
URL https://github.com/dbailleul/RClone
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RClone")

Getting started

Package overview
README.md
RClone quickmanual: several populations"

Popular man pages

clonal_index: Indices for clonal data
convert_GC: File conversion into RClone files
export_genclone: export data file to Adegenet, Genetix and Arlequin
kinship: Loiselle and Ritland kinship coefficients
Pareto_index: Pareto index
psex: Probability of originating from distinct sexual events
sample_LU: Sample Loci or Units
See all...

All man pages Function index File listing

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
coord_posidonia: Posidonia coordinates
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
infile: Infile GenClone style file
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
popsim: Posidonia
posidonia: Posidonia
psex: Probability of originating from distinct sexual events
RClone-package: RClone
resvigncont: Results contained in vignette Quick Manual
sample_LU: Sample Loci or Units
sort_all: Sorting alleles
transcript_GC: Transcript GenClone files
zostera: Zostera Dataset

Functions

Fis Man page Source code
Fis_core Man page Source code
GenClone Man page Source code
GenClone_core Man page Source code
MLG_list Man page Source code
MLG_list_core Man page Source code
MLG_tab Man page Source code
MLG_tab_core Man page Source code
MLL_generator Man page Source code
MLL_generator2 Man page Source code
MLL_generator2_core Man page Source code
MLL_generator_core Man page Source code
Pareto_index Man page Source code
Pareto_index_core Man page Source code
RClone Man page
RClone-package Man page
RClone_quickmanual Man page
agg_index Man page Source code
agg_index_core Man page Source code
autocorrelation Man page Source code
autocorrelation_core Man page Source code
clonal_index Man page Source code
clonal_index_core Man page Source code
clonal_sub Man page Source code
clonal_sub_core Man page Source code
convert_GC Man page Source code
coord_posidonia Man page
corresp_loci Man page Source code
edge_effect Man page Source code
edge_effect_core Man page Source code
export_genclone_arlequin Man page Source code
export_genclone_genetix Man page Source code
export_genclone_genind Man page Source code
freq_RR Man page Source code
freq_RR_core Man page Source code
freq_finder Man page Source code
genclone Man page
genclone_core Man page
genet_dist Man page Source code
genet_dist_core Man page Source code
genet_dist_sim Man page Source code
genet_dist_sim_core Man page Source code
graph_autocorrelation Man page Source code
graph_genet_dist Man page Source code
id_clonal Man page Source code
id_clonal_MLL Man page Source code
id_clonal_mod Man page Source code
id_clonal_mod_MLL Man page Source code
infile Man page
kinship Man page
kinship_Loiselle Man page Source code
kinship_Loiselle_core Man page Source code
kinship_Ritland Man page Source code
kinship_Ritland_core Man page Source code
list_all Man page
list_all_obj Man page Source code
list_all_obj_core Man page Source code
list_all_tab Man page Source code
list_all_tab2 Man page Source code
list_all_tab2_core Man page Source code
list_all_tab_core Man page Source code
nearest_unit Man page Source code
pgen Man page Source code
pgen_Fis Man page Source code
pgen_Fis_core Man page Source code
pgen_core Man page Source code
popsim Man page
popsimgen Man page Source code
posidonia Man page
psex Man page Source code
psex_Fis Man page Source code
psex_Fis_core Man page Source code
psex_core Man page Source code
red_MLL Man page Source code
red_MLL_mod Man page Source code
resvigncont Man page
resvigncont2 Man page
sample_LU Man page
sample_loci Man page Source code
sample_loci_core Man page Source code
sample_units Man page Source code
sample_units_core Man page Source code
sort_all Man page Source code
transcript_GC Man page Source code
zostera Man page

Files

inst
inst/doc
inst/doc/RClone_qmsevpops.pdf
inst/doc/RClone_quickmanual.pdf
inst/doc/RClone_qmsevpops.R
inst/doc/RClone_quickmanual.R
inst/doc/RClone_qmsevpops.Rmd
inst/doc/RClone_quickmanual.rmd
tests
tests/testthat_p3.R
tests/testthat_p2.R
tests/testthat_p1.R
tests/testthat_p4.R
tests/testthat
tests/testthat/test_package_RClone_p3.R
tests/testthat/test_package_RClone_p6.R
tests/testthat/test_package_RClone_p2.R
tests/testthat/test_package_RClone_p5.R
tests/testthat/test_package_RClone_p4.R
tests/testthat/test_package_RClone_p1.R
tests/testthat/test_package_RClone_p7.R
tests/testthat_p5.R
NAMESPACE
data
data/coord_posidonia.rda
data/resvigncont2.rda
data/infile.rda
data/resvigncont.rda
data/popsim.rda
data/posidonia.rda
data/datalist
data/zostera.rda
R
R/RClone.R
vignettes
vignettes/RClone_qmsevpops.Rmd
vignettes/RClone_quickmanual.rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/clonal_sub.Rd
man/freq_RR.Rd
man/transcript_GC.Rd
man/resvigncont.rd
man/genclone.Rd
man/sample_LU.Rd
man/sort_all.Rd
man/infile.rd
man/agg_index.Rd
man/zostera.rd
man/RClone-package.Rd
man/coord_posidonia.rd
man/Pareto_index.Rd
man/genet_dist.Rd
man/edge_effect.Rd
man/list_all.Rd
man/Fis.Rd
man/MLL_generator.Rd
man/pgen.Rd
man/kinship.Rd
man/clonal_index.Rd
man/posidonia.rd
man/export_genclone.Rd
man/autocorrelation.Rd
man/psex.Rd
man/convert_GC.Rd
man/popsim.rd
man/MLG_tab.Rd
RClone documentation built on May 19, 2017, 3:27 p.m.

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