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.

Install the latest version of this package by entering the following in R:
install.packages("poppr")
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 publication2017-04-14 18:11:14 UTC
MaintainerZhian N. Kamvar <zkamvar@gmail.com>
LicenseGPL-2 | GPL-3
Version2.4.1
http://github.com/grunwaldlab/poppr, http://grunwaldlab.github.io/Population_Genetics_in_R/

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

jack.ia: Index of association with reduced data

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...

Functions

\%>\% Man page
aboot Man page
Aeut Man page
amova Man page
as.genclone Man page
as.genclone,genind-method Man page
as.snpclone Man page
as.snpclone,genlight-method Man page
bitwise.dist Man page
bitwise.ia Man page
bootgen2genind Man page
bootgen2genind,bootgen-method Man page
[,bootgen,ANY,ANY,ANY-method Man page
bootgen-class Man page
$,bootgen-method Man page
bootstrap Man page
bruvo.boot Man page
bruvo.dist Man page
[,bruvomat,ANY,ANY,ANY-method Man page
bruvomat-class Man page
bruvo.msn Man page
clonecorrect Man page
cutoff Man page
cutoff<- Man page
cutoff<-,MLG-method Man page
cutoff,MLG-method Man page
cutoff_predictor Man page
dim,bootgen-method Man page
dim,bruvomat-method Man page
diss.dist Man page
distalgo Man page
distalgo<- Man page
distalgo<-,MLG-method Man page
distalgo,MLG-method Man page
distargs Man page
distargs<- Man page
distargs<-,MLG-method Man page
distargs,MLG-method Man page
distname Man page
distname<- Man page
distname<-,MLG-method Man page
distname,MLG-method Man page
diversity_boot Man page
diversity_ci Man page
diversity_stats Man page
duplicated,MLG-method Man page
edwards.dist Man page
filter_stats Man page
fix_replen Man page
genclone Man page
genclone2genind Man page
genclone2genind,genclone-method Man page
[,genclone,ANY,ANY,ANY-method Man page
genclone-class Man page
genind2genalex Man page
genotype_curve Man page
getfile Man page
greycurve Man page
ia Man page
imsn Man page
incomp Man page
informloci Man page
info_table Man page
initialize,bootgen-method Man page
initialize,bruvomat-method Man page
initialize,genclone-method Man page
initialize,MLG-method Man page
initialize,snpclone-method Man page
is.clone Man page
is.genclone Man page
is.snpclone Man page
jack.ia Man page
length,MLG-method Man page
levels<-,MLG-method Man page
levels,MLG-method Man page
locus_table Man page
Math2,MLG-method Man page
Math,MLG-method Man page
missingno Man page
mlg Man page
MLG Man page
MLG2df Man page
MLG2df,MLG-method Man page
[<-,MLG,ANY,ANY,ANY-method Man page
[,MLG,ANY,ANY,ANY-method Man page
MLG-class Man page
mlg.crosspop Man page
mlg.filter Man page
mlg.filter<- Man page
mlg.filter<-,genclone-method Man page
mlg.filter,genclone-method Man page
mlg.filter<-,genind-method Man page
mlg.filter,genind-method Man page
mlg.filter<-,genlight-method Man page
mlg.filter,genlight-method Man page
mlg.filter<-,snpclone-method Man page
mlg.filter,snpclone-method Man page
mlg.id Man page
mlg.table Man page
mlg.vector Man page
mll Man page
mll<- Man page
mll.custom Man page
mll.custom<- Man page
mll.custom<-,genclone-method Man page
mll.custom,genclone-method Man page
mll.custom<-,snpclone-method Man page
mll.custom,snpclone-method Man page
mll<-,genclone-method Man page
mll,genclone-method Man page
mll,genind-method Man page
mll,genlight-method Man page
mll.levels Man page
mll.levels<- Man page
mll.levels<-,genclone-method Man page
mll.levels,genclone-method Man page
mll.levels<-,snpclone-method Man page
mll.levels,snpclone-method Man page
mll.reset Man page
mll.reset,genclone-method Man page
mll.reset,snpclone-method Man page
mll<-,snpclone-method Man page
mll,snpclone-method Man page
monpop Man page
msn.bruvo Man page
msn.poppr Man page
nei.dist Man page
nmll Man page
nmll,genclone-method Man page
nmll,genind-method Man page
nmll,genlight-method Man page
nmll,snpclone-method Man page
old2new_genclone Man page
old_partial_clone Man page
old_Pinf Man page
Ops,MLG,ANY-method Man page
pair.ia Man page
partial_clone Man page
pgen Man page
Pinf Man page
plot_filter_stats Man page
plot_poppr_msn Man page
poppr Man page
poppr.all Man page
poppr.amova Man page
poppr_has_parallel Man page
poppr.msn Man page
poppr-package Man page
popsub Man page
Pram Man page
prevosti.dist Man page
print,genclone-method Man page
private_alleles Man page
provesti.dist Man page
psex Man page
rare_allele_correction Man page
read.genalex Man page
recode_polyploids Man page
reynolds.dist Man page
rogers.dist Man page
rraf Man page
rrmlg Man page
samp.ia Man page
show,genclone-method Man page
show,MLG-method Man page
show,snpclone-method Man page
shufflepop Man page
snpclone Man page
[,snpclone,ANY,ANY,ANY-method Man page
snpclone-class Man page
Summary,MLG-method Man page
test_replen Man page
unique,MLG-method Man page
visible Man page
visible<- Man page
visible<-,MLG-method Man page
visible,MLG-method Man page
win.ia Man page

Files

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

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