Package: poppr 2.9.6

Zhian N. Kamvar

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. Originally described in Kamvar, Tabima, and Grünwald (2014) <doi:10.7717/peerj.281> with version 2.0 described in Kamvar, Brooks, and Grünwald (2015) <doi:10.3389/fgene.2015.00208>.

Authors: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], Patrick G. Meirmans [ctb], Frédéric D. Chevalier [ctb], David Folarin [aut], Niklaus J. Grünwald [ths]

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NEWS

# Install 'poppr' in R:
install.packages('poppr', repos = c('https://grunwaldlab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/grunwaldlab/poppr/issues

Uses libs:
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • Aeut - Oomycete root rot pathogen *Aphanomyces euteiches* AFLP data
  • Pinf - Phytophthora infestans data from Mexico and South America.
  • Pram - Phytophthora ramorum data from OR Forests and Nurseries
  • monpop - Peach brown rot pathogen *Monilinia fructicola*
  • old_Pinf - Phytophthora infestans data from Mexico and South America.
  • old_partial_clone - Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance
  • partial_clone - Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance

On CRAN:

clonalitygenetic-analysisgenetic-distancesminimum-spanning-networksmultilocus-genotypesmultilocus-lineagespopulation-geneticspopulations

10.67 score 68 stars 576 scripts 4.6k downloads 251 mentions 99 exports 75 dependencies

Last updated 6 months agofrom:aa90f4f4e2. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-win-x86_64NOTENov 12 2024
R-4.5-linux-x86_64NOTENov 12 2024
R-4.4-win-x86_64OKNov 12 2024
R-4.4-mac-x86_64OKNov 12 2024
R-4.4-mac-aarch64OKNov 12 2024
R-4.3-win-x86_64OKNov 12 2024
R-4.3-mac-x86_64OKNov 12 2024
R-4.3-mac-aarch64OKNov 12 2024

Exports:%>%abootas.genambigas.gencloneas.snpclonebitwise.distbitwise.iaboot.iabootgen2genindbruvo.betweenbruvo.bootbruvo.distbruvo.msnclonecorrectcutoffcutoff_predictorcutoff<-diss.distdistalgodistalgo<-distargsdistargs<-distenvdistenv<-distnamedistname<-diversity_bootdiversity_cidiversity_statsduplicatededwards.distfilter_statsfix_replengenclone2genindgenind2genalexgenotype_curvegetfilegreycurveiaimsnincompinfo_tableinformlociis.cloneis.gencloneis.snpclonejack.ialevelslocus_tablemake_haplotypesmissingnomlgmlg.crosspopmlg.filtermlg.filter<-mlg.idmlg.tablemlg.vectorMLG2dfmllmll.custommll.custom<-mll.levelsmll.levels<-mll.resetmll<-nei.distnmllold2new_genclonepair.iapgenplot_filter_statsplot_poppr_msnpopprpoppr_has_parallelpoppr.allpoppr.amovapoppr.msnpopsubprevosti.distprintprivate_allelesprovesti.distpsexread.genalexrecode_polyploidsresample.iareynolds.distrogers.distrrafrrmlgsamp.iashufflepoptest_replenuniqueupgmavisiblevisible<-win.ia

Dependencies:ade4adegenetapebase64encbootbslibcachemcliclustercolorspacecommonmarkcpp11crayondigestdplyrfansifarverfastmapfontawesomefsgenericsggplot2gluegtablehtmltoolshttpuvigraphisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepegaspermutepillarpixmappkgconfigplyrpolysatprogressrpromisesR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangsassscalessegmentedseqinrshinysourcetoolsspstringistringrtibbletidyselectutf8vctrsveganviridisLitewithrxtable

Algorightms and Equations

Rendered fromalgo.Rnwusingknitr::knitron Nov 12 2024.

Last update: 2024-01-16
Started: 2014-05-24

Readme and manuals

Help Manual

Help pageTopics
The 'poppr' R packagepoppr-package
Calculate a dendrogram with bootstrap support using any distance applicable to genind or genclone objects.aboot bootstrap
Oomycete root rot pathogen *Aphanomyces euteiches* AFLP dataAeut
Create a snpclone object from a genlight object.as.snpclone as.snpclone,genlight-method
Calculate dissimilarity or Euclidean distance for genlight objectsbitwise.dist
Bootstrap the index of associationboot.ia
Switch between genind and genclone objects.as.genambig as.genambig,genind-method as.genclone as.genclone,genind-method bootgen2genind bootgen2genind,bootgen-method genclone2genind genclone2genind,genclone-method
Create a tree using Bruvo's Distance with non-parametric bootstrapping.bruvo.boot
Bruvo's distance for microsatellitesbruvo.between bruvo.dist
Create minimum spanning network of selected populations using Bruvo's distance.bruvo.msn msn.bruvo
Remove potential bias caused by cloned genotypes in genind or genclone object.clonecorrect
Predict cutoff thresholds for use with mlg.filtercutoff_predictor
Calculate a distance matrix based on relative dissimilaritydiss.dist
Perform a bootstrap analysis on diversity statisticsdiversity_boot
Perform bootstrap statistics, calculate, and plot confidence intervals.diversity_ci
Produce a table of diversity statisticsdiversity_stats
Utilize all algorithms of mlg.filterfilter_stats
Find and fix inconsistent repeat lengthsfix_replen
GENclone and SNPclone classesgenclone genclone-class snpclone snpclone-class
Export data from genind objects to genalex formatted \*.csv files.genind2genalex
Produce a genotype accumulation curvegenotype_curve
Get a file name and path and store them in a list.getfile
Display a greyscale gradient adjusted to specific parametersgreycurve
Index of Associationia jack.ia pair.ia resample.ia
Create minimum spanning networks interactivelyimsn
Check for samples that are incomparable due to missing dataincomp
Create a table summarizing missing data or ploidy information of a genind or genclone objectinfo_table
Remove all non-phylogentically informative lociinformloci
Check for validity of a genclone or snpclone objectis.clone is.genclone is.snpclone
Create a table of summary statistics per locus.locus_table
Split samples from a genind object into pseudo-haplotypesmake_haplotypes make_haplotypes,ANY-method make_haplotypes,genclone-method make_haplotypes,genind-method make_haplotypes,genlight-method make_haplotypes,snpclone-method
Treat missing datamissingno
Create counts, vectors, and matrices of multilocus genotypes.mlg mlg.crosspop mlg.id mlg.table mlg.vector
MLG definitions based on genetic distancemlg.filter mlg.filter,genclone-method mlg.filter,genind-method mlg.filter,genlight-method mlg.filter,snpclone-method mlg.filter<- mlg.filter<-,genclone-method mlg.filter<-,genind-method mlg.filter<-,genlight-method mlg.filter<-,snpclone-method
Access and manipulate multilocus lineages.mll mll,genclone-method mll,genind-method mll,genlight-method mll,snpclone-method mll<- mll<-,genclone-method mll<-,snpclone-method nmll nmll,genclone-method nmll,genind-method nmll,genlight-method nmll,snpclone-method
Define custom multilocus lineagesmll.custom mll.custom,genclone-method mll.custom,snpclone-method mll.custom<- mll.custom<-,genclone-method mll.custom<-,snpclone-method mll.levels mll.levels,genclone-method mll.levels,snpclone-method mll.levels<- mll.levels<-,genclone-method mll.levels<-,snpclone-method
Reset multilocus lineagesmll.reset mll.reset,genclone-method mll.reset,snpclone-method
Peach brown rot pathogen *Monilinia fructicola*monpop
Calculate Genetic Distance for a genind or genclone object.edwards.dist nei.dist prevosti.dist provesti.dist reynolds.dist rogers.dist
Convert an old genclone object to a new genclone objectold2new_genclone
Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distanceold_partial_clone partial_clone
Genotype Probabilitypgen
Phytophthora infestans data from Mexico and South America.old_Pinf Pinf
Plot minimum spanning networks produced in poppr.plot_poppr_msn
Produce a basic summary table for population genetic analyses.poppr
Determines whether openMP is support on this system.poppr_has_parallel
Process a list of files with popprpoppr.all
Perform Analysis of Molecular Variance (AMOVA) on genind or genclone objects.amova poppr.amova
Create a minimum spanning network of selected populations using a distance matrix.msn.poppr poppr.msn
Subset data by populationpopsub
Phytophthora ramorum data from OR Forests and Nurseries (OR and CA)Pram
Tabulate alleles the occur in only one population.private_alleles
Probability of encountering a genotype more than once by chancepsex
Correcting rare allele frequenciesrare_allele_correction
Importing data from genalex formatted \*.csv files.read.genalex
Recode polyploid microsatellite data for use in frequency based statistics.recode_polyploids
Round Robin Allele Frequenciesrraf
Round Robin Multilocus Genotypesrrmlg
Calculate random samples of the index of association for genlight objects.samp.ia
Shuffle individuals in a 'genclone' or 'genind' object independently over each locus.shufflepop
Test repeat length consistency.test_replen
UPGMAupgma
Calculate windows of the index of association for genlight objects.win.ia