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