RClone: Partially Clonal Populations Analysis

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).

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
https://github.com/dbailleul/RClone

View on CRAN

Functions

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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