Package: strataG 2.5.01

Eric Archer

strataG: Summaries and Population Structure Analyses of Genetic Data

A toolkit for analyzing stratified population genetic data. Functions are provided for summarizing and checking loci (haploid, diploid, and polyploid), single stranded DNA sequences, calculating most population subdivision metrics, and running external programs such as structure and fastsimcoal. The package is further described in Archer et al (2016) <doi:10.1111/1755-0998.12559>.

Authors:Eric Archer [aut, cre], Paula Adams [aut], Brita Schneiders [aut], Sarina Fernandez [aut], Warren Asfazadour [aut]

strataG_2.5.01.tar.gz

strataG_2.5.01.tar.gz(r-4.4-noble)
strataG.pdf |strataG.html✨
strataG/json (API)

# Install 'strataG' in R:

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

Bug tracker:https://github.com/ericarcher/stratag/issues

Uses libs:

c++– GNU Standard C++ Library v3
jags– Just Another Gibbs Sampler for Bayesian MCMC

Datasets:

bowhead.snp.position - Bowhead Whale SNP Genotype Groups
bowhead.snps - Bowhead Whale SNP Genotypes
dloop.g - Dolphin dLoop gtypes Object
dolph.haps - Dolphin mtDNA Haplotype Sequences
dolph.msats - Dolphin Microsatellite Genotypes
dolph.seqs - Dolphin mtDNA D-loop Sequences
dolph.strata - Dolphin Genetic Stratification and Haplotypes
msats.g - Dolphin Microsatellite gtypes Object

On CRAN:

dna-sequences genetics locus-summaries microsatellites population-genetics population-genomics population-structure snp-data snps

149 exports 24 stars 2.14 score 128 dependencies 58 downloads

Last updated 2 months agofrom:f38fd47ced

Exports:alleleFreqs alleleSplit allelicRichness arlequinRead arlequinWrite arp2gtypes as.data.frame as.matrix as.multidna baseFreqs clumpp createConsensus df2gtypes dupGenotypes evanno expandHaplotypes expectedNumAlleles fixedDifferences fixedSites freq2GenData fsc2gtypes fscBlock_dna fscBlock_freq fscBlock_microsat fscBlock_snp fscBlock_standard fscCleanup fscDeme fscEstParam fscEvent fscReadArp fscReadParamEst fscReadSFS fscRun fscSettingsDef fscSettingsDemes fscSettingsEst fscSettingsEvents fscSettingsGenetics fscSettingsMigration fscTutorial fscWrite fstToNm fusFs gelato gelatoPlot genepop genepopWrite genind2gtypes genlight2gtypes getAlleleNames getDescription getIndNames getLociNames getNumInd getNumLoci getNumStrata getOther getPloidy getSchemes getSequences getStrata getStrataNames gtypes2genind gtypes2genlight gtypes2loci gtypes2phyDat heterozygosity hweTest is.gtypes isTi isTv iupacCode iupacMat jackHWE jackInfluential labelHaplotypes landscape2df landscape2gtypes LDgenepop ldNe loci2gtypes lowFreqSubs maf mafft maverickRun mostDistantSequences mostRepresentativeSequences mRatio neiDa nucleotideDivergence nucleotideDiversity numAlleles numGenotyped numGensEq numMissing overallTest pairwiseMatrix pairwiseSummary pairwiseTest permuteStrata phase phaseFilter phasePosterior phaseReadPair phaseReadSample phaseWrite phyDat2gtypes privateAlleles propSharedLoci propUniqueAlleles read.arlequin read.fasta read.mega readGenData removeUnusedSequences sequence2gtypes sequenceLikelihoods setDescription<-setOther<-setSchemes<-setStrata<-sfs sharedAlleles simGammaHaps strataSplit stratify structurePlot structureRead structureRun structureWrite subType summarizeAll summarizeInds summarizeLoci summarizeSeqs summary tajimasD theta TiTvRatio trimNs validIupacCodes variableSites wrightFst write.arlequin write.fasta write.mega write.nexus.snapp writeGtypes

Dependencies:abind ade4 adegenet ADGofTest ape apex base64enc boot bslib cachem class classInt cli clue cluster coda colorspace commonmark copula cpp11 crayon data.table DBI deldir digest dplyr e1071 fansi farver fastmap fastmatch fBasics fontawesome fs genepop generics ggplot2 ggrepel glue gridExtra gsl gss gtable gtools HDInterval htmltools httpuv igraph isoband jquerylib jsonlite KernSmooth kknn labeling later lattice lifecycle magrittr MASS Matrix memoise mgcv mime modeest munsell mvtnorm nlme numDeriv pcaPP pegas permute phangorn pillar pixmap pkgconfig plyr polyclip promises proxy pspline purrr quadprog R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppProgress reshape2 rlang rmetasim rmutil rpart runjags s2 sass scales segmented seqinr sf shiny sourcetools sp spatial spatstat.data spatstat.geom spatstat.univar spatstat.utils sprex stable stabledist statip stringi stringr swfscMisc tibble tidyr tidyselect timeDate timeSeries units utf8 vctrs vegan viridisLite withr wk xtable

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
Summaries and population structure analyses of DNA sequence genotypic data	strataG-package strataG
Allele Frequencies	alleleFreqs
Split Alleles For Diploid Data	alleleSplit
Allelic Richness	allelicRichness
Read and Write Arlequin Files	arlequin arlequinRead arlequinWrite arp2gtypes read.arlequin write.arlequin
Convert 'gtypes' to data.frame or matrix	as.data.frame as.data.frame,gtypes-method as.data.frame.gtypes as.matrix as.matrix,gtypes-method as.matrix.gtypes
Convert to multidna	as.multidna
Base Frequencies	baseFreqs
Bowhead Whale SNP Genotype Groups	bowhead.snp.position
Bowhead Whale SNP Genotypes	bowhead.snps
Run CLUMPP	clumpp
Consensus Sequence	createConsensus
Convert a data.frame to gtypes	df2gtypes
Dolphin dLoop gtypes Object	dloop.g
Dolphin mtDNA Haplotype Sequences	dolph.haps
Dolphin Microsatellite Genotypes	dolph.msats
Dolphin mtDNA D-loop Sequences	dolph.seqs
Dolphin Genetic Stratification and Haplotypes	dolph.strata
Duplicate Genotypes	dupGenotypes
Run Evanno Method on STRUCTURE Results	evanno
Expand Haplotypes	expandHaplotypes
Read and Write FASTA	fasta read.fasta write.fasta
Fixed Differences	fixedDifferences
Fixed Sites	fixedSites
Convert Haplotype Frequency Matrices	freq2GenData
Input functions for fastsimcoal parameters	fsc.input fscBlock_dna fscBlock_freq fscBlock_microsat fscBlock_snp fscBlock_standard fscDeme fscEstParam fscEvent fscSettings fscSettingsDef fscSettingsDemes fscSettingsEst fscSettingsEvents fscSettingsGenetics fscSettingsMigration
Read fastsimcoal output	fsc2gtypes fscRead fscReadArp fscReadParamEst fscReadSFS
Run fastsimcoal	fscCleanup fscRun fscTutorial
Write fastsimcoal2 input files	fscWrite
Fu's Fs	fusFs
GELATo - Group ExcLusion and Assignment Test	gelato gelatoPlot
Run GENEPOP	genepop genepopWrite
'gtypes' Class	gtypes gtypes-class
'gtypes' Accessors	accessors getAlleleNames getAlleleNames,gtypes-method getDescription getDescription,gtypes-method getIndNames getIndNames,gtypes-method getLociNames getLociNames,gtypes-method getNumInd getNumInd,gtypes-method getNumLoci getNumLoci,gtypes-method getNumStrata getNumStrata,gtypes-method getOther getOther,gtypes-method getPloidy getPloidy,gtypes-method getSchemes getSchemes,gtypes-method getSequences getSequences,gtypes-method getStrata getStrata,gtypes-method getStrataNames getStrataNames,gtypes-method gtypes.accessors index setDescription setDescription<- setDescription<-,gtypes-method setOther setOther<- setOther<-,gtypes-method setSchemes setSchemes<- setSchemes<-,gtypes-method setStrata setStrata<- setStrata<-,gtypes-method subset [,gtypes,ANY,ANY,ANY-method
Convert Between 'gtypes' And 'genind' objects.	genind2gtypes gtypes2genind
Convert Between 'gtypes' And 'genlight' objects.	genlight2gtypes gtypes2genlight
Convert Between 'gtypes' And 'loci' objects.	gtypes2loci loci2gtypes
Convert Between 'gtypes' And 'phyDat' objects.	gtypes2phyDat phyDat2gtypes
Heterozygosity	heterozygosity
Hardy-Weinberg Equilibrium	HWE hwe hweTest
'gtypes' Constructor	gtypes.initialize initialize,gtypes-method initialize.gtypes new
Test if object is 'gtypes'	is.gtypes
IUPAC Codes	iupac iupacCode iupacMat validIupacCodes
Find and label haplotypes	labelHaplotypes labelHaplotypes.character labelHaplotypes.default labelHaplotypes.gtypes labelHaplotypes.list
Convert Rmetasim landscape	landscape2df landscape2gtypes
Linkage Disequlibrium	LDgenepop
ldNe	ldNe
Low Frequency Substitutions	lowFreqSubs
Minor Allele Frequencies	maf
MAFFT Alignment	mafft
Run MavericK	maverickRun
Read and Write MEGA	MEGA mega mega, read.mega write.mega
Most Distant Sequences	mostDistantSequences
Representative Sequences	mostRepresentativeSequences
M ratio	mRatio
Dolphin Microsatellite gtypes Object	msats.g
Nei's Da	neiDa
Nucleotide Divergence	dA nucleotideDivergence
Nucleotide Diversity	nucleotideDiversity
Number of Alleles	numAlleles
Number of Individuals Genotyped	numGenotyped
Number Missing Data	numMissing
Permute strata	permuteStrata
PHASE	phase phaseFilter phasePosterior phaseReadPair phaseReadSample phaseWrite
Population Genetics Equations	expectedNumAlleles fstToNm numGensEq popGenEqns wrightFst
Population Structure Tests	overallTest pairwiseMatrix pairwiseSummary pairwiseTest popStructTest
Private Alleles	privateAlleles
Proportion Unique Alleles	propUniqueAlleles
Read Genetic Data	readGenData
Remove Unused Sequences	removeUnusedSequences
Convert Sequences To 'gtypes'	sequence2gtypes
Sequence Likelihoods	sequenceLikelihoods
Site Frequency Spectrum	sfs
Shared Loci	propSharedLoci sharedAlleles sharedLoci
Simulate Haplotypes	simGammaHaps
Split Strata	strataSplit
Stratify gtypes	stratify
STRUCTURE	structure structureRead structureRun structureWrite
Plot STRUCTURE Results	structurePlot
Summarize Genotypes and Sequences	summarizeAll
Individual Summaries	summarizeInds
Locus Summaries	summarizeLoci
Sequence Summaries	summarizeSeqs
Summarize gtypes Object	summary summary,gtypes-method summary.gtypes
Tajima's D	tajimasD
Theta	theta
Transition / Transversion Ratio	isTi isTv subType TiTvRatio
Trim N's From Sequences	trimNs
Variable Sites	variableSites
Write NEXUS File for SNAPP	write.nexus.snapp
Write 'gtypes'	writeGtypes

Package: strataG 2.5.01

strataG: Summaries and Population Structure Analyses of Genetic Data

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