Package: poppr 2.9.8

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]

poppr_2.9.8.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
poppr/json (API)

# Install 'poppr' in R:

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

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

Pkgdown/docs site:https://grunwaldlab.github.io

Uses libs:

openmp– GCC OpenMP (GOMP) support library

Datasets:

Aeut - Oomycete root rot pathogen *Aphanomyces euteiches* AFLP data
monpop - Peach brown rot pathogen *Monilinia fructicola*
old_partial_clone - Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance
old_Pinf - Phytophthora infestans data from Mexico and South America.
partial_clone - Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance
Pinf - Phytophthora infestans data from Mexico and South America.
Pram - Phytophthora ramorum data from OR Forests and Nurseries

On CRAN:

clonality genetic-analysis genetic-distances minimum-spanning-networks multilocus-genotypes multilocus-lineages population-genetics populations openmp

10.25 score 72 stars 848 scripts 11k downloads 99 exports 73 dependencies

Last updated from:08eb52554f. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	203
linux-devel-x86_64	OK	219
source / vignettes	OK	287
linux-release-arm64	OK	208
linux-release-x86_64	OK	198
macos-release-arm64	OK	119
macos-release-x86_64	OK	367
macos-oldrel-arm64	OK	139
macos-oldrel-x86_64	OK	338
windows-devel	OK	211
windows-release	OK	188
windows-oldrel	OK	181
wasm-release	OK	145

Exports:%>%aboot as.genambig as.genclone as.snpclone bitwise.dist bitwise.ia boot.ia bootgen2genind bruvo.between bruvo.boot bruvo.dist bruvo.msn clonecorrect cutoff cutoff_predictor cutoff<-diss.dist distalgo distalgo<-distargs distargs<-distenv distenv<-distname distname<-diversity_boot diversity_ci diversity_stats duplicated edwards.dist filter_stats fix_replen genclone2genind genind2genalex genotype_curve getfile greycurve ia imsn incomp info_table informloci is.clone is.genclone is.snpclone jack.ia levels locus_table make_haplotypes missingno mlg mlg.crosspop mlg.filter mlg.filter<-mlg.id mlg.table mlg.vector MLG2df mll mll.custom mll.custom<-mll.levels mll.levels<-mll.reset mll<-nei.dist nmll old2new_genclone pair.ia pgen plot_filter_stats plot_poppr_msn poppr poppr_has_parallel poppr.all poppr.amova poppr.msn popsub prevosti.dist print private_alleles provesti.dist psex read.genalex recode_polyploids resample.ia reynolds.dist rogers.dist rraf rrmlg samp.ia shufflepop test_replen unique upgma visible visible<-win.ia

Dependencies:ade4 adegenet ape base64enc boot bslib cachem cli cluster commonmark cpp11 digest dplyr farver fastmap fontawesome fs generics ggplot2 glue gtable htmltools httpuv igraph isoband jquerylib jsonlite labeling later lattice lifecycle magrittr MASS Matrix memoise mgcv mime nlme otel pegas permute pillar pixmap pkgconfig plyr polysat progressr promises R6 rappdirs RColorBrewer Rcpp RcppArmadillo reshape2 rlang S7 sass scales segmented seqinr shiny sourcetools sp stringi stringr tibble tidyselect utf8 vctrs vegan viridisLite withr xtable

Algorightms and Equations

Rendered fromalgo.Rnwusingknitr::knitr

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

Help page	Topics
The 'poppr' R package	poppr-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 data	Aeut
Create a snpclone object from a genlight object.	as.snpclone as.snpclone,genlight-method
Calculate dissimilarity or Euclidean distance for genlight objects	bitwise.dist
Bootstrap the index of association	boot.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 microsatellites	bruvo.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.filter	cutoff_predictor
Calculate a distance matrix based on relative dissimilarity	diss.dist
Perform a bootstrap analysis on diversity statistics	diversity_boot
Perform bootstrap statistics, calculate, and plot confidence intervals.	diversity_ci
Produce a table of diversity statistics	diversity_stats
Utilize all algorithms of mlg.filter	filter_stats
Find and fix inconsistent repeat lengths	fix_replen
GENclone and SNPclone classes	genclone genclone-class snpclone snpclone-class
Export data from genind objects to genalex formatted \*.csv files.	genind2genalex
Produce a genotype accumulation curve	genotype_curve
Get a file name and path and store them in a list.	getfile
Display a greyscale gradient adjusted to specific parameters	greycurve
Index of Association	ia jack.ia pair.ia resample.ia
Create minimum spanning networks interactively	imsn
Check for samples that are incomparable due to missing data	incomp
Create a table summarizing missing data or ploidy information of a genind or genclone object	info_table
Remove all non-phylogentically informative loci	informloci
Check for validity of a genclone or snpclone object	is.clone is.genclone is.snpclone
Create a table of summary statistics per locus.	locus_table
Split samples from a genind object into pseudo-haplotypes	make_haplotypes make_haplotypes,ANY-method make_haplotypes,genclone-method make_haplotypes,genind-method make_haplotypes,genlight-method make_haplotypes,snpclone-method
Treat missing data	missingno
Create counts, vectors, and matrices of multilocus genotypes.	mlg mlg.crosspop mlg.id mlg.table mlg.vector
MLG definitions based on genetic distance	mlg.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 lineages	mll.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 lineages	mll.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 object	old2new_genclone
Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance	old_partial_clone partial_clone
Genotype Probability	pgen
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 poppr	poppr.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 population	popsub
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 chance	psex
Correcting rare allele frequencies	rare_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 Frequencies	rraf
Round Robin Multilocus Genotypes	rrmlg
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
UPGMA	upgma
Calculate windows of the index of association for genlight objects.	win.ia

Package: poppr 2.9.8

poppr: Genetic Analysis of Populations with Mixed Reproduction

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