poppr: Genetic Analysis of Populations with Mixed Reproduction

Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the 'adegenet' package.

AuthorZhian N. Kamvar [cre, aut], Javier F. Tabima [aut], Sydney E. Everhart [ctb, dtc], Jonah C. Brooks [aut], Stacy A. Krueger-Hadfield [ctb], Erik Sotka [ctb], Brian J. Knaus [ctb], Niklaus J. Grunwald [ths]
Date of publication2016-11-23 17:45:12
MaintainerZhian N. Kamvar <zkamvar@gmail.com>
LicenseGPL-2 | GPL-3
Version2.3.0
http://github.com/grunwaldlab/poppr, http://grunwaldlab.github.io/Population_Genetics_in_R/, http://grunwaldlab.cgrb.oregonstate.edu/poppr-r-package-population-genetics

View on CRAN

Man pages

aboot: Calculate a dendrogram with bootstrap support using any...

Aeut: Oomycete root rot pathogen _Aphanomyces euteiches_ AFLP data

bitwise.dist: Calculate a dissimilarity distance matrix for SNP data.

bitwise.ia: Calculate the index of association between samples in a...

bootgen-class: Bootgen object

bootgen-methods: Methods used for the bootgen object.

bruvo.boot: Create a tree using Bruvo's Distance with non-parametric...

bruvo.dist: Bruvo's distance for microsatellites

bruvomat-class: bruvomat object

bruvomat-methods: Methods used for the bruvomat object.

bruvo.msn: Create minimum spanning network of selected populations using...

clonecorrect: Remove potential bias caused by cloned genotypes in genind or...

coercion-methods: Switch between genind and genclone objects.

cutoff_predictor: Predict cutoff thresholds for use with mlg.filter

diss.dist: Calculate a distance matrix based on relative dissimilarity

diversity_boot: Perform a bootstrap analysis on diversity statistics

diversity_ci: Perform bootstrap statistics, calculate, and plot confidence...

diversity_stats: Produce a table of diversity statistics

filter_stats: Utilize all algorithms of mlg.filter

fix_replen: Find and fix inconsistent repeat lengths

genclone-class: GENclone and SNPclone classes

genclone-method: Methods used for the genclone object

genetic_distance: Calculate Genetic Distance for a genind or genclone object.

genind2genalex: Exporting data from genind objects to genalex formatted *.csv...

genotype_curve: Produce a genotype accumulation curve

getfile: Get a file name and path and store them in a list.

grapes-greater-than-grapes: magrittr forward-pipe operator

greycurve: Display a greyscale gradient adjusted to specific parameters

ia: Index of Association

imsn: Create minimum spanning networks interactively

incomp: Check for samples that are incomparable due to missing data

informloci: Remove all non-phylogentically informative loci

info_table: Create a table summarizing missing data or ploidy information...

is.clone: Check for validity of a genclone or snpclone object

levels-methods: Unique and Duplicated implementations for MLG objects

locus_table: Create a table of summary statistics per locus.

missingno: Treat missing data

mlg: Create counts, vectors, and matrices of multilocus genotypes.

MLG-accessors: Accessors for the MLG object

MLG-class: MLG class

mlg.filter: MLG definitions based on genetic distance

MLG-method: Methods used for MLG objects

mll.custom: Define custom multilocus lineages

mll-method: Access and manipulate multilocus lineages.

mll.reset-method: Reset multilocus lineages

monpop: Peach brown rot pathogen _Monilinia fructicola_

old2new_genclone: Convert an old genclone object to a new genclone object

partial_clone: Simulated data illustrating a Minimum Spanning Network based...

pgen: Genotype Probability

Pinf: Phytophthora infestans data from Mexico and South America.

plot_filter_stats: Plot the results of filter_stats

plot_poppr_msn: Plot minimum spanning networks produced in poppr.

poppr: Produce a basic summary table for population genetic...

poppr.all: Process a list of files with poppr

poppr.amova: Perform Analysis of Molecular Variance (AMOVA) on genind or...

poppr_has_parallel: Determines whether openMP is support on this system.

poppr.msn: Create a minimum spanning network of selected populations...

poppr-package: The 'poppr' R package.

popsub: Subset data by population

Pram: Phytophthora ramorum data from OR Forests and Nurseries (OR...

private_alleles: Tabulate alleles the occur in only one population.

psex: Probability of encountering a genotype more than once by...

rare_allele_correction: Correcting rare allele frequencies

read.genalex: Importing data from genalex formatted *.csv files.

recode_polyploids: Recode polyploid microsatellite data for use in frequency...

rraf: Round Robin Allele Frequencies

rrmlg: Round Robin Multilocus Genotypes

samp.ia: Calculate random samples of the index of association for...

shufflepop: Shuffle individuals in a 'genclone' or 'genind' object...

snpclone-coercion-methods: Create a snpclone object from a genlight object.

snpclone-method: Methods used for the snpclone object

test_replen: Test repeat length consistency.

unique-methods: Unique and Duplicated implementations for MLG objects

win.ia: Calculate windows of the index of association for genlight...

Files in this package

poppr
poppr/inst
poppr/inst/CITATION
poppr/inst/files
poppr/inst/files/simulated.dat
poppr/inst/files/rootrot2.csv
poppr/inst/files/rootrot.csv
poppr/inst/shiny
poppr/inst/shiny/utils.R
poppr/inst/shiny/msn_explorer
poppr/inst/shiny/msn_explorer/ui.R
poppr/inst/shiny/msn_explorer/server.R
poppr/inst/doc
poppr/inst/doc/mlg.R
poppr/inst/doc/poppr_manual.Rmd
poppr/inst/doc/poppr_manual.R
poppr/inst/doc/algo.R
poppr/inst/doc/mlg.html
poppr/inst/doc/poppr_manual.html
poppr/inst/doc/algo.Rnw
poppr/inst/doc/mlg.Rmd
poppr/inst/doc/algo.pdf
poppr/tests
poppr/tests/testthat
poppr/tests/testthat/test-greyscale.R
poppr/tests/testthat/test-amova.R
poppr/tests/testthat/test-import.R
poppr/tests/testthat/test-missing.R
poppr/tests/testthat/test-msn.R
poppr/tests/testthat/test-distpop.R
poppr/tests/testthat/test-popsub.R
poppr/tests/testthat/test-trees.R
poppr/tests/testthat/test-bitwise.R
poppr/tests/testthat/test-values.R
poppr/tests/testthat/test-genclone.R
poppr/tests/testthat/test-bootclass.R
poppr/tests/testthat/test-incomp.R
poppr/tests/testthat/test-filter.R
poppr/tests/testthat/test-informloci.R
poppr/tests/testthat/test-locustable.R
poppr/tests/testthat/test-MLG-class.R
poppr/tests/testthat/test-colors.R
poppr/tests/testthat/test-poppr.R
poppr/tests/testthat/test-mlg.R
poppr/tests/testthat/test-round-robin.R
poppr/tests/testthat/test-snpclone.R
poppr/tests/testthat/test-errors.R
poppr/tests/testthat/test-plots.R
poppr/tests/testthat/test-private.R
poppr/tests/testthat/test-polyploids.R
poppr/tests/testthat/test-sampling.R
poppr/tests/test-all.R
poppr/src
poppr/src/bitwise_distance.c
poppr/src/Makevars
poppr/src/mlg_counter.c
poppr/src/msn.c
poppr/src/poppr_distance.c
poppr/src/mlg_clustering.c
poppr/src/omp_test.c
poppr/src/permut_shuffler.c
poppr/NAMESPACE
poppr/NEWS
poppr/data
poppr/data/old_partial_clone.rda
poppr/data/Pinf.rda
poppr/data/old_Pinf.rda
poppr/data/partial_clone.rda
poppr/data/Aeut.rda
poppr/data/monpop.rda
poppr/data/Pram.rda
poppr/R
poppr/R/sandbox.r
poppr/R/aaaMLGmethods.R poppr/R/poppr.R
poppr/R/amova.r
poppr/R/round_robin.R poppr/R/pipe.R
poppr/R/distances.r
poppr/R/filter_stats.R
poppr/R/classes.r
poppr/R/Index_calculations.r
poppr/R/bootstraping.R
poppr/R/mlg.r
poppr/R/bruvo.r
poppr/R/imsn.R poppr/R/aaaMLGclass.R
poppr/R/visualizations.r
poppr/R/internal.r
poppr/R/sample_schemes.r
poppr/R/file_handling.r
poppr/R/internal_methods.R
poppr/R/zzz.r
poppr/R/check_data.R
poppr/R/methods.r
poppr/R/messages.r
poppr/R/global_memory.r
poppr/R/print_methods.r
poppr/R/msn_handlers.R
poppr/R/bitwise.r
poppr/R/data_subset.r
poppr/vignettes
poppr/vignettes/poppr_manual.Rmd
poppr/vignettes/unmod_dat.png
poppr/vignettes/algo-concordance.tex
poppr/vignettes/poppr_manual.synctex.gz
poppr/vignettes/getfile.pdf
poppr/vignettes/jalapeno-poppers.pdf
poppr/vignettes/popprlogo.png
poppr/vignettes/nancybruvo.rda
poppr/vignettes/jalapeno_logo.png
poppr/vignettes/bruvo_upgma.png
poppr/vignettes/getfile.png
poppr/vignettes/authordate1.bst
poppr/vignettes/poppr.css
poppr/vignettes/pnas.bst
poppr/vignettes/algo.Rnw
poppr/vignettes/the_bibliography.bib
poppr/vignettes/mlg.Rmd
poppr/vignettes/jalapeno_logo.svg
poppr/vignettes/poppr_manual-concordance.tex
poppr/vignettes/rootrot2.png
poppr/vignettes/mod_dat.png
poppr/vignettes/msg.txt
poppr/README.md
poppr/MD5
poppr/build
poppr/build/vignette.rds
poppr/DESCRIPTION
poppr/man
poppr/man/plot_filter_stats.Rd poppr/man/grapes-greater-than-grapes.Rd poppr/man/mll.reset-method.Rd poppr/man/genclone-method.Rd poppr/man/private_alleles.Rd poppr/man/bruvo.boot.Rd poppr/man/mll.custom.Rd poppr/man/bruvomat-class.Rd poppr/man/locus_table.Rd poppr/man/getfile.Rd poppr/man/diversity_boot.Rd poppr/man/clonecorrect.Rd poppr/man/levels-methods.Rd poppr/man/unique-methods.Rd poppr/man/mlg.filter.Rd poppr/man/diversity_stats.Rd poppr/man/Aeut.Rd poppr/man/info_table.Rd poppr/man/poppr.all.Rd poppr/man/monpop.Rd poppr/man/MLG-class.Rd poppr/man/poppr-package.Rd poppr/man/incomp.Rd poppr/man/greycurve.Rd poppr/man/ia.Rd poppr/man/aboot.Rd poppr/man/is.clone.Rd poppr/man/genind2genalex.Rd poppr/man/coercion-methods.Rd poppr/man/bruvo.dist.Rd poppr/man/diversity_ci.Rd poppr/man/bootgen-class.Rd poppr/man/genclone-class.Rd poppr/man/read.genalex.Rd poppr/man/popsub.Rd poppr/man/MLG-method.Rd poppr/man/pgen.Rd poppr/man/plot_poppr_msn.Rd poppr/man/imsn.Rd poppr/man/bitwise.dist.Rd poppr/man/bootgen-methods.Rd poppr/man/win.ia.Rd poppr/man/partial_clone.Rd poppr/man/poppr_has_parallel.Rd poppr/man/test_replen.Rd poppr/man/Pinf.Rd poppr/man/old2new_genclone.Rd poppr/man/filter_stats.Rd poppr/man/samp.ia.Rd poppr/man/poppr.Rd poppr/man/cutoff_predictor.Rd poppr/man/rrmlg.Rd poppr/man/informloci.Rd poppr/man/recode_polyploids.Rd poppr/man/poppr.amova.Rd poppr/man/genetic_distance.Rd poppr/man/snpclone-coercion-methods.Rd poppr/man/snpclone-method.Rd poppr/man/rraf.Rd poppr/man/poppr.msn.Rd poppr/man/mll-method.Rd poppr/man/MLG-accessors.Rd poppr/man/bruvo.msn.Rd poppr/man/psex.Rd poppr/man/bitwise.ia.Rd poppr/man/fix_replen.Rd poppr/man/genotype_curve.Rd poppr/man/missingno.Rd poppr/man/shufflepop.Rd poppr/man/Pram.Rd poppr/man/mlg.Rd poppr/man/bruvomat-methods.Rd poppr/man/diss.dist.Rd poppr/man/rare_allele_correction.Rd

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

All documentation is copyright its authors; we didn't write any of that.