Files in grunwaldlab/poppr
Genetic Analysis of Populations with Mixed Reproduction

.Rbuildignore
.gitignore
.travis.yml
CONDUCT.md CONTRIBUTING.md
DESCRIPTION
ISSUE_TEMPLATE.md
Makefile
NAMESPACE
NEWS
NEWS.md
R/.gitignore
R/Index_calculations.r R/aaaMLGclass.R R/aaaMLGmethods.R R/amova.r R/bitwise.r R/bootstraping.R R/bruvo.r R/check_data.R R/classes.r R/data_subset.r R/distances.r R/file_handling.r R/filter_stats.R R/global_memory.r R/ia_jackknife.R R/imsn.R R/internal.r R/internal_methods.R R/messages.r R/methods.r R/mlg.r R/msn_handlers.R R/pipe.R R/poppr.R R/print_methods.r R/round_robin.R R/sample_schemes.r R/visualizations.r R/zzz.r README.md cran-comments.md
data/Aeut.rda
data/Pinf.rda
data/Pram.rda
data/monpop.rda
data/old_Pinf.rda
data/old_partial_clone.rda
data/partial_clone.rda
docs/articles/algo-concordance.tex
docs/articles/algo.Rnw
docs/articles/algo.pdf
docs/articles/algo.synctex.gz
docs/articles/algo.tex
docs/articles/authordate1.bst
docs/articles/bruvo_upgma.png
docs/articles/figure/Aeut_MLG_Aeut-1.pdf docs/articles/figure/Aeut_MLG_Ahena-1.pdf docs/articles/figure/Aeut_MLG_Ahena.pdf docs/articles/figure/Aeut_MLG_Ahena1.pdf docs/articles/figure/Aeut_MLG_Ahena2.pdf docs/articles/figure/Aeut_MLG_black-1.pdf docs/articles/figure/Aeut_MLG_black.pdf docs/articles/figure/Aeut_MLG_theme-1.pdf docs/articles/figure/Aeut_MLG_theme_axis-1.pdf docs/articles/figure/Aeut_MLG_title-1.pdf docs/articles/figure/Aeut_MLG_title.pdf docs/articles/figure/Aeut_silly-1.pdf docs/articles/figure/bd_histogram-1.pdf docs/articles/figure/bd_histogram.pdf docs/articles/figure/bruvo_msn.pdf docs/articles/figure/bruvo_tree.pdf docs/articles/figure/ex_data_picture-1.pdf docs/articles/figure/ex_data_picture.pdf docs/articles/figure/ggplotchart.pdf docs/articles/figure/greycurve_normal.pdf docs/articles/figure/greycurve_small_heavy.pdf docs/articles/figure/greywidth_inverse.pdf docs/articles/figure/greywidth_large_heavy.pdf docs/articles/figure/initializing_poppr-1.pdf docs/articles/figure/initializing_poppr.pdf docs/articles/figure/mantel.pdf docs/articles/figure/mlgbarplot-1.pdf docs/articles/figure/mlgbarplot.pdf docs/articles/figure/mlgrareplot-1.pdf docs/articles/figure/mlgrareplot.pdf docs/articles/figure/mlgsub_flagshow-1.pdf docs/articles/figure/pinf_table-1.pdf docs/articles/figure/popcompare_bruvo2.pdf docs/articles/figure/poppr_msn_fig.pdf docs/articles/figure/subnor-1.pdf docs/articles/figure/subnor.pdf docs/articles/figure/unnamed-chunk-3-1.pdf docs/articles/figure/unnamed-chunk-3.pdf docs/articles/figure/unnamed-chunk-4.pdf docs/articles/figure/unnamed-chunk-5.pdf docs/articles/figure/unnamed-chunk-6.pdf docs/articles/figure/unnamed-chunk-7.pdf docs/articles/figure/unnamed-chunk-8.pdf docs/articles/figure/unnamed-chunk-9.pdf docs/articles/getfile.pdf
docs/articles/getfile.png
docs/articles/index.html
docs/articles/jalapeno-poppers.pdf
docs/articles/jalapeno_logo.png
docs/articles/jalapeno_logo.svg
docs/articles/mlg.html
docs/articles/mlg_files/figure-html/unnamed-chunk-12-1.png
docs/articles/mlg_files/figure-html/unnamed-chunk-17-1.png
docs/articles/mlg_files/figure-html/unnamed-chunk-17-2.png
docs/articles/mlg_files/figure-html/unnamed-chunk-18-1.png
docs/articles/mlg_files/figure-html/unnamed-chunk-26-1.png
docs/articles/mlg_files/figure-html/unnamed-chunk-28-1.png
docs/articles/mlg_files/figure-html/unnamed-chunk-29-1.png
docs/articles/mlg_files/figure-html/unnamed-chunk-31-1.png
docs/articles/mlg_files/figure-html/unnamed-chunk-32-1.png
docs/articles/mlg_files/figure-html/unnamed-chunk-34-1.png
docs/articles/mlg_files/figure-html/unnamed-chunk-37-1.png
docs/articles/mlg_files/figure-html/unnamed-chunk-40-1.png
docs/articles/mod_dat.png
docs/articles/msg.txt
docs/articles/nancybruvo.rda
docs/articles/pnas.bst
docs/articles/poppr.css
docs/articles/poppr_manual-concordance.tex
docs/articles/poppr_manual.html
docs/articles/poppr_manual.synctex.gz
docs/articles/poppr_manual_files/figure-html/Aeut_MLG_Aeut-1.png
docs/articles/poppr_manual_files/figure-html/Aeut_MLG_theme-1.png
docs/articles/poppr_manual_files/figure-html/Aeut_MLG_theme_axis-1.png
docs/articles/poppr_manual_files/figure-html/Aeut_MLG_title-1.png
docs/articles/poppr_manual_files/figure-html/Aeut_silly-1.png
docs/articles/poppr_manual_files/figure-html/bd_histogram-1.png
docs/articles/poppr_manual_files/figure-html/ex_data_picture-1.png
docs/articles/poppr_manual_files/figure-html/initializing_poppr-1.png
docs/articles/poppr_manual_files/figure-html/mlgbarplot-1.png
docs/articles/poppr_manual_files/figure-html/mlgrareplot-1.png
docs/articles/poppr_manual_files/figure-html/mlgsub_flagshow-1.png
docs/articles/poppr_manual_files/figure-html/pinf_table-1.png
docs/articles/popprlogo.png
docs/articles/rootrot2.png
docs/articles/small_logo.png
docs/articles/the_bibliography.bib
docs/articles/unmod_dat.png
docs/authors.html
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/reference/Aeut.html
docs/reference/MLG-accessors.html
docs/reference/MLG-class.html
docs/reference/MLG-method.html
docs/reference/Pinf.html
docs/reference/Pram.html
docs/reference/aboot-1.png
docs/reference/aboot-2.png
docs/reference/aboot-37.png
docs/reference/aboot-40.png
docs/reference/aboot.html
docs/reference/bitwise.dist.html
docs/reference/bitwise.ia.html
docs/reference/boot.ia.html
docs/reference/bootgen-class.html
docs/reference/bootgen-methods.html
docs/reference/bruvo.boot-1.png
docs/reference/bruvo.boot-3.png
docs/reference/bruvo.boot.html
docs/reference/bruvo.dist.html
docs/reference/bruvo.msn-1.png
docs/reference/bruvo.msn-2.png
docs/reference/bruvo.msn.html
docs/reference/bruvomat-class.html
docs/reference/bruvomat-methods.html
docs/reference/clonecorrect.html
docs/reference/coercion-methods.html
docs/reference/cutoff_predictor.html
docs/reference/diss.dist.html
docs/reference/diversity_boot.html
docs/reference/diversity_ci-1.png
docs/reference/diversity_ci-3.png
docs/reference/diversity_ci.html
docs/reference/diversity_stats.html
docs/reference/filter_stats-1.png
docs/reference/filter_stats-2.png
docs/reference/filter_stats.html
docs/reference/fix_replen.html
docs/reference/genclone-class.html
docs/reference/genclone-method.html
docs/reference/genetic_distance.html
docs/reference/genind2genalex.html
docs/reference/genotype_curve-1.png
docs/reference/genotype_curve-3.png
docs/reference/genotype_curve.html
docs/reference/getfile.html
docs/reference/grapes-greater-than-grapes.html
docs/reference/greycurve-1.png
docs/reference/greycurve-2.png
docs/reference/greycurve.html
docs/reference/ia-1.png
docs/reference/ia-2.png
docs/reference/ia-5.png
docs/reference/ia-7.png
docs/reference/ia.html
docs/reference/imsn.html
docs/reference/incomp.html
docs/reference/index.html
docs/reference/info_table-1.png
docs/reference/info_table-2.png
docs/reference/info_table-4.png
docs/reference/info_table.html
docs/reference/informloci.html
docs/reference/is.clone.html
docs/reference/jack.ia.html
docs/reference/levels-methods.html
docs/reference/locus_table.html
docs/reference/missingno.html
docs/reference/mlg-1.png
docs/reference/mlg-8.png
docs/reference/mlg.filter.html
docs/reference/mlg.html
docs/reference/mll-method.html
docs/reference/mll.custom.html
docs/reference/mll.reset-method.html
docs/reference/monpop.html
docs/reference/old2new_genclone.html
docs/reference/partial_clone.html
docs/reference/pgen.html
docs/reference/plot_filter_stats.html
docs/reference/plot_poppr_msn-1.png
docs/reference/plot_poppr_msn-2.png
docs/reference/plot_poppr_msn-6.png
docs/reference/plot_poppr_msn-7.png
docs/reference/plot_poppr_msn.html
docs/reference/poppr-package.html
docs/reference/poppr.all.html
docs/reference/poppr.amova-1.png
docs/reference/poppr.amova-8.png
docs/reference/poppr.amova.html
docs/reference/poppr.html
docs/reference/poppr.msn-1.png
docs/reference/poppr.msn-2.png
docs/reference/poppr.msn.html
docs/reference/poppr.plot.html
docs/reference/poppr_has_parallel.html
docs/reference/popsub.html
docs/reference/private_alleles.html
docs/reference/psex-1.png
docs/reference/psex-4.png
docs/reference/psex.html
docs/reference/rare_allele_correction.html
docs/reference/read.genalex.html
docs/reference/recode_polyploids.html
docs/reference/rraf.html
docs/reference/rrmlg.html
docs/reference/samp.ia-1.png
docs/reference/samp.ia-2.png
docs/reference/samp.ia-4.png
docs/reference/samp.ia-8.png
docs/reference/samp.ia.html
docs/reference/shufflepop.html
docs/reference/snpclone-coercion-methods.html
docs/reference/snpclone-method.html
docs/reference/test_replen.html
docs/reference/unique-methods.html
docs/reference/win.ia-1.png
docs/reference/win.ia-4.png
docs/reference/win.ia.html
inst/CITATION
inst/files/rootrot.csv
inst/files/rootrot2.csv
inst/files/simulated.dat
inst/shiny/msn_explorer/server.R inst/shiny/msn_explorer/ui.R inst/shiny/utils.R man/Aeut.Rd man/MLG-accessors.Rd man/MLG-class.Rd man/MLG-method.Rd man/Pinf.Rd man/Pram.Rd man/aboot.Rd man/bitwise.dist.Rd man/bitwise.ia.Rd man/boot.ia.Rd man/bootgen-class.Rd man/bootgen-methods.Rd man/bruvo.boot.Rd man/bruvo.dist.Rd man/bruvo.msn.Rd man/bruvomat-class.Rd man/bruvomat-methods.Rd man/clonecorrect.Rd man/coercion-methods.Rd man/cutoff_predictor.Rd man/diss.dist.Rd man/diversity_boot.Rd man/diversity_ci.Rd man/diversity_stats.Rd man/filter_stats.Rd man/fix_replen.Rd man/genclone-class.Rd man/genclone-method.Rd man/genetic_distance.Rd man/genind2genalex.Rd man/genotype_curve.Rd man/getfile.Rd man/grapes-greater-than-grapes.Rd man/greycurve.Rd man/ia.Rd man/imsn.Rd man/incomp.Rd man/info_table.Rd man/informloci.Rd man/is.clone.Rd man/levels-methods.Rd man/locus_table.Rd man/missingno.Rd man/mlg.Rd man/mlg.filter.Rd man/mll-method.Rd man/mll.custom.Rd man/mll.reset-method.Rd man/monpop.Rd man/old2new_genclone.Rd man/partial_clone.Rd man/pgen.Rd man/plot_filter_stats.Rd man/plot_poppr_msn.Rd man/poppr-package.Rd man/poppr.Rd man/poppr.all.Rd man/poppr.amova.Rd man/poppr.msn.Rd man/poppr.plot.Rd man/poppr_has_parallel.Rd man/popsub.Rd man/private_alleles.Rd man/psex.Rd man/rare_allele_correction.Rd man/read.genalex.Rd man/recode_polyploids.Rd man/rraf.Rd man/rrmlg.Rd man/samp.ia.Rd man/shufflepop.Rd man/snpclone-coercion-methods.Rd man/snpclone-method.Rd man/test_replen.Rd man/unique-methods.Rd man/win.ia.Rd
poppr.Rproj
src/.gitignore
src/Makevars
src/bitwise_distance.c
src/init.c
src/mlg_clustering.c
src/mlg_counter.c
src/msn.c
src/omp_test.c
src/permut_shuffler.c
src/poppr_distance.c
tests/test-all.R tests/testthat/test-MLG-class.R tests/testthat/test-amova.R tests/testthat/test-bitwise.R tests/testthat/test-bootclass.R tests/testthat/test-colors.R tests/testthat/test-distpop.R tests/testthat/test-errors.R tests/testthat/test-filter.R tests/testthat/test-genclone.R tests/testthat/test-genotype_curve.R tests/testthat/test-greyscale.R tests/testthat/test-import.R tests/testthat/test-incomp.R tests/testthat/test-informloci.R tests/testthat/test-jackia.R tests/testthat/test-locustable.R tests/testthat/test-missing.R tests/testthat/test-mlg.R tests/testthat/test-msn.R tests/testthat/test-plots.R tests/testthat/test-polyploids.R tests/testthat/test-poppr.R tests/testthat/test-popsub.R tests/testthat/test-private.R tests/testthat/test-replen.R tests/testthat/test-round-robin.R tests/testthat/test-sampling.R tests/testthat/test-snpclone.R tests/testthat/test-trees.R tests/testthat/test-values.R tests/testthat/test-winia.R
tools/convertversion.sh
tools/getversion.sh
vignettes/.gitignore
vignettes/algo-concordance.tex
vignettes/algo.Rnw
vignettes/algo.pdf
vignettes/algo.tex
vignettes/authordate1.bst
vignettes/bruvo_upgma.png
vignettes/getfile.pdf
vignettes/getfile.png
vignettes/jalapeno-poppers.pdf
vignettes/jalapeno_logo.png
vignettes/jalapeno_logo.svg
vignettes/mlg.Rmd
vignettes/mod_dat.png
vignettes/msg.txt
vignettes/nancybruvo.rda
vignettes/pnas.bst
vignettes/poppr.css
vignettes/poppr_manual.Rmd
vignettes/popprlogo.png
vignettes/rootrot2.png
vignettes/small_logo.png
vignettes/the_bibliography.bib
vignettes/unmod_dat.png
grunwaldlab/poppr documentation built on Jan. 9, 2018, 10:48 p.m.