Package index • dartR

All functions
`bandicoot.gl`	A genlight object created via the read.dart functions
`cbind(<dartR>)`	adjust cbind for dartR
`gi2gl()`	Converts a genind object into a genlight object
`gl.He()`	Estimates expected Heterozygosity
`gl.Ho()`	Estimates observed Heterozygosity
`gl.LDNe()`	Estimates effective population size using the Linkage Disequilibrium method based on NeEstimator (V2)
`gl.alf()`	Calculates allele frequency of the first and second allele for each loci A very simple function to report allele frequencies
`gl.allele.freq()`	Generates percentage allele frequencies by locus and population
`gl.amova()`	Performs AMOVA using genlight data
`gl.assign.grm()`	Population assignment using grm
`gl.assign.mahalanobis()`	Assign an individual of unknown provenance to population based on Mahalanobis Distance
`gl.assign.pa()`	Eliminates populations as possible source populations for an individual of unknown provenance, using private alleles
`gl.assign.pca()`	Assign an individual of unknown provenance to population based on PCA
`gl.basic.stats()`	Calculates basic statistics for each loci (Hs, Ho, Fis etc.)
`gl.blast()`	Aligns nucleotides sequences against those present in a target database using blastn
`gl.check.verbosity()`	Checks the current global verbosity
`gl.check.wd()`	Checks the global working directory
`gl.collapse()`	Collapses a distance matrix by amalgamating populations with pairwise fixed difference count less that a threshold
`gl.colors()`	This is a helper function that supports the creation of color palettes for all plotting functions.
`gl.compliance.check()`	Checks a genlight object to see if it complies with dartR expectations and amends it to comply if necessary
`gl.costdistances()`	Calculates cost distances for a given landscape (resistance matrix)
`gl.define.pop()`	Defines a new population in a genlight object for specified individuals
`gl.diagnostics.hwe()`	Provides descriptive stats and plots to diagnose potential problems with Hardy-Weinberg proportions
`gl.diagnostics.sim()`	Comparing simulations against theoretical expectations
`gl.dist.ind()`	Calculates a distance matrix for individuals defined in a genlight object
`gl.dist.pop()`	Calculates a distance matrix for populations with SNP genotypes in a genlight object
`gl.drop.ind()`	Removes specified individuals from a dartR genlight object
`gl.drop.loc()`	Removes specified loci from a dartR genlight object
`gl.drop.pop()`	Removes specified populations from a dartR genlight object
`gl.edit.recode.ind()`	Creates or edits individual (=specimen) names, creates a recode_ind file and applies the changes to a genlight object
`gl.edit.recode.pop()`	Creates or edits and applies a population re-assignment table
`gl.evanno()`	Creates an Evanno plot from a STRUCTURE run object
`gl.fdsim()`	Estimates the rate of false positives in a fixed difference analysis
`gl.filter.allna()`	Filters loci that are all NA across individuals and/or populations with all NA across loci
`gl.filter.callrate()`	Filters loci or specimens in a genlight {adegenet} object based on call rate
`gl.filter.hamming()`	Filters loci based on pairwise Hamming distance between sequence tags
`gl.filter.heterozygosity()`	Filters individuals with average heterozygosity greater than a specified upper threshold or less than a specified lower threshold
`gl.filter.hwe()`	Filters loci that show significant departure from Hardy-Weinberg Equilibrium
`gl.filter.locmetric()`	Filters loci on the basis of numeric information stored in other$loc.metrics in a genlight {adegenet} object
`gl.filter.maf()`	Filters loci on the basis of minor allele frequency (MAF) in a genlight `adegenet` object
`gl.filter.monomorphs()`	Filters monomorphic loci, including those with all NAs
`gl.filter.overshoot()`	Filters loci for which the SNP has been trimmed from the sequence tag along with the adaptor
`gl.filter.pa()`	Filters loci that contain private (and fixed alleles) between two populations
`gl.filter.parent.offspring()`	Filters putative parent offspring within a population
`gl.filter.rdepth()`	Filters loci based on counts of sequence tags scored at a locus (read depth)
`gl.filter.reproducibility()`	Filters loci in a genlight {adegenet} object based on average repeatability of alleles at a locus
`gl.filter.secondaries()`	Filters loci that represent secondary SNPs in a genlight object
`gl.filter.sexlinked()`	Filters loci that are sex linked
`gl.filter.taglength()`	Filters loci in a genlight {adegenet} object based on sequence tag length
`gl.fixed.diff()`	Generates a matrix of fixed differences and associated statistics for populations taken pairwise
`gl.fst.pop()`	Calculates a pairwise Fst values for populations in a genlight object
`gl.genleastcost()`	Performs least-cost path analysis based on a friction matrix
`gl.grm()`	Calculates an identity by descent matrix
`gl.grm.network()`	Represents a genomic relationship matrix (GRM) as a network
`gl.hwe.pop()`	Performs Hardy-Weinberg tests over loci and populations
`gl.ibd()`	Performs isolation by distance analysis
`gl.impute()`	Imputates missing data
`gl.install.vanilla.dartR()`	Installs all required packages for using all functions available in dartR
`gl.join()`	Combines two genlight objects
`gl.keep.ind()`	Removes all but the specified individuals from a dartR genlight object
`gl.keep.loc()`	Removes all but the specified loci from a genlight object
`gl.keep.pop()`	Removes all but the specified populations from a dartR genlight object
`gl.ld.distance()`	Plots linkage disequilibrium against distance by population disequilibrium patterns
`gl.ld.haplotype()`	Visualize patterns of linkage disequilibrium and identification of haplotypes
`gl.list.reports()`	Prints dartR reports saved in tempdir
`gl.load()`	Loads an object from compressed binary format produced by gl.save()
`gl.make.recode.ind()`	Creates a proforma recode_ind file for reassigning individual (=specimen) names
`gl.make.recode.pop()`	Creates a proforma recode_pop_table file for reassigning population names
`gl.map.interactive()`	Creates an interactive map (based on latlon) from a genlight object
`gl.map.structure()`	Maps a STRUCTURE plot using a genlight object
`gl.merge.pop()`	Merges two or more populations in a genlight object into one population
`gl.nhybrids()`	Creates an input file for the program NewHybrids and runs it if NewHybrids is installed
`gl.outflank()`	Identifies loci under selection per population using the outflank method of Whitlock and Lotterhos (2015)
`gl.pcoa()`	Ordination applied to genotypes in a genlight object (PCA), in an fd object, or to a distance matrix (PCoA)
`gl.pcoa.plot()`	Bivariate or trivariate plot of the results of an ordination generated using gl.pcoa()
`gl.percent.freq()`	Generates percentage allele frequencies by locus and population
`gl.play.history()`	Replays the history and applies it to a genlight object
`gl.plot.faststructure()`	Plots fastStructure analysis results (Q-matrix)
`gl.plot.heatmap()`	Represents a distance matrix as a heatmap
`gl.plot.network()`	Represents a distance or dissimilarity matrix as a network
`gl.plot.structure()`	Plots STRUCTURE analysis results (Q-matrix)
`gl.print.history()`	Prints history of a genlight object
`gl.print.reports()`	Prints dartR reports saved in tempdir
`gl.propShared()`	Calculates a similarity (distance) matrix for individuals on the proportion of shared alleles
`gl.random.snp()`	Randomly changes the allocation of 0's and 2's in a genlight object
`gl.read.csv()`	Reads SNP data from a csv file into a genlight object
`gl.read.dart()`	Imports DArT data into dartR and converts it into a dartR genlight object
`gl.read.fasta()`	Reads FASTA files and converts them to genlight object
`gl.read.silicodart()`	Imports presence/absence data from SilicoDArT to genlight {agegenet} format (ploidy=1)
`gl.read.vcf()`	Converts a vcf file into a genlight object
`gl.reassign.pop()`	Assigns an individual metric as pop in a genlight {adegenet} object
`gl.recalc.metrics()`	Recalculates locus metrics when individuals or populations are deleted from a genlight {adegenet} object
`gl.recode.ind()`	Recodes individual (=specimen = sample) labels in a genlight object
`gl.recode.pop()`	Recodes population assignments in a genlight object
`gl.rename.pop()`	Renames a population in a genlight object
`gl.report.bases()`	Reports summary of base pair frequencies
`gl.report.callrate()`	Reports summary of Call Rate for loci or individuals
`gl.report.diversity()`	Calculates diversity indexes for SNPs
`gl.report.fstat()`	Reports various statistics of genetic differentiation between populations with confident intervals
`gl.report.hamming()`	Calculates the pairwise Hamming distance between DArT trimmed DNA sequences
`gl.report.heterozygosity()`	Reports observed, expected and unbiased heterozygosities and FIS (inbreeding coefficient) by population or by individual from SNP data
`gl.report.hwe()`	Reports departure from Hardy-Weinberg proportions
`gl.report.ld.map()`	Calculates pairwise linkage disequilibrium by population
`gl.report.locmetric()`	Reports summary of the slot $other$loc.metrics
`gl.report.maf()`	Reports minor allele frequency (MAF) for each locus in a SNP dataset
`gl.report.monomorphs()`	Reports monomorphic loci
`gl.report.overshoot()`	Reports loci for which the SNP has been trimmed from the sequence tag along with the adaptor
`gl.report.pa()`	Reports private alleles (and fixed alleles) per pair of populations
`gl.report.parent.offspring()`	Identifies putative parent offspring within a population
`gl.report.rdepth()`	Reports summary of Read Depth for each locus
`gl.report.replicates()`	Identify replicated individuals
`gl.report.reproducibility()`	Reports summary of RepAvg (repeatability averaged over both alleles for each locus) or reproducibility (repeatability of the scores for fragment presence/absence)
`gl.report.secondaries()`	Reports loci containing secondary SNPs in sequence tags and calculates number of invariant sites
`gl.report.sexlinked()`	Identifies loci that are sex linked
`gl.report.taglength()`	Reports summary of sequence tag length across loci
`gl.run.faststructure()`	Runs a faststructure analysis using a genlight object
`gl.run.structure()`	Runs a STRUCTURE analysis using a genlight object
`gl.sample()`	Samples individuals from populations
`gl.save()`	Saves an object in compressed binary format for later rapid retrieval
`gl.select.colors()`	Selects colors from one of several palettes and output as a vector
`gl.select.shapes()`	Selects shapes from the base R shape palette and outputs as a vector
`gl.set.verbosity()`	Sets the default verbosity level
`gl.sfs()`	Creates a site frequency spectrum based on a dartR or genlight object
`gl.sim.WF.run()`	Runs Wright-Fisher simulations
`gl.sim.WF.table()`	Creates the reference table for running gl.sim.WF.run
`gl.sim.create_dispersal()`	Creates a dispersal file as input for the function gl.sim.WF.run
`gl.sim.emigration()`	Simulates emigration between populations
`gl.sim.ind()`	Simulates individuals based on the allele frequencies provided via a genlight object.
`gl.sim.mutate()`	Simulates mutations within a genlight object
`gl.sim.offspring()`	Simulates a specified number of offspring based on alleles provided by potential father(s) and mother(s)
`gl.smearplot()`	Smear plot of SNP or presence/absence (SilicoDArT) data
`gl.sort()`	re-sorts genlight objects
`gl.spatial.autoCorr()`	Spatial autocorrelation following Smouse and Peakall 1999
`gl.subsample.loci()`	Subsamples n loci from a genlight object and return it as a genlight object
`gl.test.heterozygosity()`	Tests the difference in heterozygosity between populations taken pairwise
`gl.tree.nj()`	Outputs an nj tree to summarize genetic similarity among populations
`gl.write.csv()`	Writes out data from a genlight object to csv file
`gl2bayescan()`	Converts a genlight object into a format suitable for input to Bayescan
`gl2bpp()`	Converts a genlight object into a format suitable for input to the BPP program
`gl2dartR()`	Convert a genlight object to a dartR object
`gl2demerelate()`	Creates a dataframe suitable for input to package {Demerelate} from a genlight {adegenet} object
`gl2eigenstrat()`	Converts a genlight object into eigenstrat format
`gl2fasta()`	Concatenates DArT trimmed sequences and outputs a FASTA file
`gl2faststructure()`	Converts a genlight object into faststructure format (to run faststructure elsewhere)
`gl2gds()`	Converts a genlight object into gds format
`gl2genalex()`	Converts a genlight object into a format suitable for input to genalex
`gl2genepop()`	Converts a genlight object into genepop format (and file)
`gl2geno()`	Converts a genlight object to geno format from package LEA
`gl2gi()`	Converts a genlight object to genind object
`gl2hiphop()`	Converts a genlight objects into hiphop format
`gl2phylip()`	Creates a Phylip input distance matrix from a genlight (SNP) {adegenet} object
`gl2plink()`	Converts a genlight object into PLINK format
`gl2related()`	Converts a genlight object to format suitable to be run with Coancestry
`gl2sa()`	Converts genlight objects to the format used in the SNPassoc package
`gl2sfs()`	Converts a genlight object into a sfs input file
`gl2shp()`	Converts a genlight object to ESRI shapefiles or kml files
`gl2snapp()`	Converts a genlight object to nexus format suitable for phylogenetic analysis by SNAPP (via BEAUti)
`gl2structure()`	Converts a genlight object to STRUCTURE formatted files
`gl2svdquartets()`	Converts a genlight object to nexus format PAUP SVDquartets
`gl2treemix()`	Converts a genlight object to a treemix input file
`gl2vcf()`	Converts a genlight object into vcf format
`interactive_reference()`	Shiny app for the input of the reference table for the simulations
`interactive_sim_run()`	Shiny app for the input of the simulations variables
`is.fixed()`	Tests if two populations are fixed at a given locus
`platy`	Example data set as text file to be imported into a genlight object
`possums.gl`	A simulated genlight object created to run a landscape genetic example
`rbind(<dartR>)`	adjust rbind for dartR
`[`(<dartR>,<ANY>,<ANY>,<ANY>)	indexing dartR objects correctly...
`testset.gl`	A genlight object created via the gl.read.dart function
`testset.gs`	A genlight object created via the gl.read.silicodart function
`testset_SNPs_2Row`	Testfile in DArT format (as provided by DArT)
`testset_metadata`	Metadata file. Can be integrated via the dart2genlight function.
`testset_pop_recode`	Recode file to be used with the function.
`theme_dartR()`	dartR theme
`utils.assignment()`	Population assignment probabilities
`utils.assignment_2()`	Population assignment probabilities
`utils.assignment_3()`	Population assignment probabilities
`utils.assignment_4()`	Population assignment probabilities
`utils.basic.stats()`	Calculates mean observed heterozygosity, mean expected heterozygosity and Fis per locus, per population and various population differentiation measures
`utils.check.datatype()`	Utility function to check the class of an object passed to a function
`utils.clumpp()`	Functions from package starmie for merging Q matrices from Structure runs using the CLUMPP algorithms.
`utils.dart2genlight()`	Converts DarT to genlight.
`utils.dist.binary()`	Calculates a distance matrix for individuals defined in a dartR genlight object using binary P/A data (SilicoDArT)
`utils.dist.ind.snp()`	Calculates a distance matrix for individuals defined in a dartR genlight object using SNP data (DArTseq)
`utils.flag.start()`	A utility script to flag the start of a script
`utils.hamming()`	Calculates the Hamming distance between two DArT trimmed DNA sequences
`utils.het.pop()`	Calculates expected mean expected heterozygosity per population
`utils.jackknife()`	Conducts jackknife resampling using a genlight object
`utils.n.var.invariant()`	A utility script to calculate the number of variant and invariant sites by locus
`utils.outflank.MakeDiploidFSTMat()`	Creates OutFLANK input file from individual genotype info.
`utils.outflank()`	OutFLANK: An Fst outlier approach by Mike Whitlock and Katie Lotterhos, University of British Columbia.
`utils.outflank.plotter()`	Plotting functions for Fst distributions after OutFLANK
`utils.plot.save()`	An internal function to save a ggplot object to disk in RDS binary format
`utils.read.dart()`	utility function to read in DArT data
`utils.recalc.avgpic()`	A utility script to recalculate the OneRatioRef, OneRatioSnp, PICRef, PICSnp, and AvgPIC by locus after some individuals or populations have been deleted.
`utils.recalc.callrate()`	A utility script to recalculate the callrate by locus after some populations have been deleted
`utils.recalc.freqhets()`	A utility script to recalculate the frequency of the heterozygous SNPs by locus after some populations have been deleted
`utils.recalc.freqhomref()`	A utility script to recalculate the frequency of the homozygous reference SNP by locus after some populations have been deleted
`utils.recalc.freqhomsnp()`	A utility script to recalculate the frequency of the homozygous alternate SNP by locus after some populations have been deleted
`utils.recalc.maf()`	A utility script to recalculate the minor allele frequency by locus, typically after some populations have been deleted
`utils.reset.flags()`	A utility script to reset to FALSE (or TRUE) the locus metric flags after some individuals or populations have been deleted.
`utils.spautocor()`	Spatial autocorrelation coefficient calculations
`utils.structure.evanno()`	Util function for evanno plots
`utils.structure.genind2gtypes()`	structure util functions
`utils.structure.run()`	Utility function to run Structure
`zzz`	Setting up the package

Reference

All functions