poppr: Genetic Analysis of Populations with Mixed Reproduction

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

Author
Zhian 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 publication
2016-11-23 17:45:12
Maintainer
Zhian N. Kamvar <zkamvar@gmail.com>
License
GPL-2 | GPL-3
Version
2.3.0
URLs

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