Calculates allele frequency of the first and second allele for each loci
A very simple function to report allele frequencies
Estimates effective population size using the Linkage Disequilibrium
method based on NeEstimator (V2)
A genlight object created via the read.dart functions
Estimates observed Heterozygosity
Assign an individual of unknown provenance to population based on
Mahalanobis Distance
adjust cbind for dartR
Population assignment using grm
Performs AMOVA using genlight data
Estimates expected Heterozygosity
Converts a genind object into a genlight object
Checks a genlight object to see if it complies with dartR
expectations and amends it to comply if necessary
Calculates cost distances for a given landscape (resistance matrix)
Eliminates populations as possible source populations for an
individual of unknown provenance, using private alleles
Aligns nucleotides sequences against those present in a target database
using blastn
Calculates basic statistics for each loci (Hs, Ho, Fis etc.)
Checks the current global verbosity
Defines a new population in a genlight object for specified
individuals
Provides descriptive stats and plots to diagnose potential problems
with Hardy-Weinberg proportions
Collapses a distance matrix by amalgamating populations with pairwise
fixed difference count less that a threshold
Assign an individual of unknown provenance to population based on PCA
Comparing simulations against theoretical expectations
Creates or edits individual (=specimen) names, creates a recode_ind
file and applies the changes to a genlight object
Creates or edits a population re-assignment table
Calculates a distance matrix for populations with SNP genotypes in a
genlight object
Removes specified individuals from a genlight object
Creates an Evanno plot from a STRUCTURE run object
Calculates a distance matrix for individuals defined in a genlight object
Removes specified loci from a genlight object
Estimates the rate of false positives in a fixed difference analysis
Removes specified populations from a genlight object
Filters loci that are all NA across individuals and/or populations
with all NA across loci
Filters monomorphic loci, including those with all NAs
Filters loci for which the SNP has been trimmed from the sequence tag
along with the adaptor
Filters loci that show significant departure from Hardy-Weinberg
Equilibrium
Filters loci or specimens in a genlight {adegenet} object based on
call rate
Filters loci based on pairwise Hamming distance between sequence tags
Filters individuals with average heterozygosity greater than a
specified upper threshold or less than a specified lower threshold
Filters loci based on linkage disequilibrium (LD)
Filters loci in a genlight {adegenet} object based on sequence tag
length
Filters loci on the basis of numeric information stored in
other$loc.metrics in a genlight {adegenet} object
Filters loci on the basis of minor allele frequency (MAF) in a
genlight
adegenet object
Filters loci that represent secondary SNPs in a genlight object
Filters loci that are sex linked
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
Calculates a pairwise Fst values for populations in a genlight object
Generates a matrix of fixed differences and associated statistics for
populations taken pairwise
Performs least-cost path analysis based on a friction matrix
Removes all but the specified loci from a genlight object
Filters loci that contain private (and fixed alleles) between two populations
gl.filter.parent.offspring
Filters putative parent offspring within a population
Installs all required packages for using all functions
available in dartR
Combines two genlight objects
Imputates missing data
Removes all but the specified individuals from a genlight object
Performs Hardy-Weinberg tests over loci and populations
Removes all but the specified populations from a genlight object
Performs isolation by distance analysis
Calculates an identity by descent matrix
Represents a genomic relationship matrix (GRM) as a network
Plots linkage disequilibrium against distance by population
disequilibrium patterns
Maps a STRUCTURE plot using a genlight object
Creates a proforma recode_ind file for reassigning individual
(=specimen) names
Loads an object from compressed binary format produced by gl.save()
Prints dartR reports saved in tempdir
Creates a proforma recode_pop_table file for reassigning population
names
Merges two or more populations in a genlight object into one population
Creates an interactive map (based on latlon) from a genlight object
Creates an input file for the program NewHybrids and runs it if
NewHybrids is installed
Visualize patterns of linkage disequilibrium and identification of
haplotypes
Plots STRUCTURE analysis results (Q-matrix)
Represents a distance matrix as a heatmap
Replays the history and applies it to a genlight object
Bivariate or trivariate plot of the results of an ordination generated
using gl.pcoa()
Generates percentage allele frequencies by locus and population
Represents a distance or dissimilarity matrix as a network
Prints dartR reports saved in tempdir
Ordination applied to genotypes in a genlight object (PCA), in an fd
object, or to a distance matrix (PCoA)
Identifies loci under selection per population using the outflank
method of Whitlock and Lotterhos (2015)
Prints history of a genlight object
Reads FASTA files and converts them to genlight object
Imports DArT data into dartR and converts it into a genlight object
Calculates a similarity (distance) matrix for individuals on the proportion of
shared alleles
Reads SNP data from a csv file into a genlight object
Assigns an individual metric as pop in a genlight {adegenet} object
Recodes individual (=specimen = sample) labels in a genlight object
Randomly changes the allocation of 0's and 2's in a genlight object
Converts a vcf file into a genlight object
Recalculates locus metrics when individuals or populations are deleted from a
genlight {adegenet} object
Imports presence/absence data from SilicoDArT to genlight {agegenet}
format (ploidy=1)
Calculates diversity indexes for SNPs
Reports observed, expected and unbiased heterozygosities and FIS
(inbreeding coefficient) by population or by individual from SNP data
Reports departure from Hardy-Weinberg proportions
Reports summary of base pair frequencies
Calculates the pairwise Hamming distance between DArT trimmed DNA
sequences
Calculates pairwise population based Linkage Disequilibrium across all loci
using the specified number of cores
Renames a population in a genlight object
Recodes population assignments in a genlight object
Calculates pairwise linkage disequilibrium by population
Reports summary of Call Rate for loci or individuals
Reports monomorphic loci
Reports loci containing secondary SNPs in sequence tags and calculates
number of invariant sites
Identifies loci that are sex linked
Reports summary of Read Depth for each locus
Reports loci for which the SNP has been trimmed from the sequence tag
along with the adaptor
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)
Reports minor allele frequency (MAF) for each locus in a SNP dataset
Reports summary of the slot $other$loc.metrics
Reports summary of sequence tag length across loci
Sets the default verbosity level
Selects colors from one of several palettes and output as a vector
Reports private alleles (and fixed alleles) per pair of populations
gl.report.parent.offspring
Identifies putative parent offspring within a population
Selects shapes from the base R shape palette and outputs as a vector
Samples individuals from populations
Runs Wright-Fisher simulations
Creates the reference table for running gl.sim.WF.run
Saves an object in compressed binary format for later rapid retrieval
Creates a site frequency spectrum based on a dartR or genlight object
Runs a STRUCTURE analysis using a genlight object
Simulates mutations within a genlight object
re-sorts genlight objects
Subsamples n loci from a genlight object and return it as a genlight object
Simulates a specified number of offspring based on alleles provided by
potential father(s) and mother(s)
Smear plot of SNP or presence/absence (SilicoDArT) data
Creates a dispersal file as input for the function gl.sim.WF.run
Simulates emigration between populations
Spatial autocorrelation following Smouse and Peakall 1999
Simulates individuals based on the allele frequencies provided via a genlight
object.
Tests the difference in heterozygosity between populations taken
pairwise
Writes out data from a genlight object to csv file
Converts a genlight object into eigenstrat format
Converts a genlight object into a format suitable for input to Bayescan
Outputs an nj tree to summarize genetic similarity among populations
Converts a genlight object into faststructure format (to run faststructure
elsewhere)
Converts a genlight object into gds format
Concatenates DArT trimmed sequences and outputs a FASTA file
Converts a genlight object into a format suitable for input to genalex
Creates a dataframe suitable for input to package {Demerelate} from a
genlight {adegenet} object
Converts a genlight object into a format suitable for input to the BPP
program
Creates a Phylip input distance matrix from a genlight (SNP) {adegenet}
object
Converts a genlight object into a sfs input file
Converts genlight objects to the format used in the SNPassoc package
Converts a genlight object to format suitable to be run with Coancestry
Converts a genlight object to ESRI shapefiles or kml files
Converts a genlight object into genepop format (and file)
Converts a genlight object to genind object
Converts a genlight object to geno format from package LEA
Converts a genlight object into PLINK format
Converts a genlight objects into hiphop format
Converts a genlight object to a treemix input file
Converts a genlight object to nexus format suitable for phylogenetic analysis
by SNAPP (via BEAUti)
Converts a genlight object to nexus format PAUP SVDquartets
A simulated genlight object created to run a landscape genetic example
Converts a genlight object to STRUCTURE formatted files
Shiny app for the input of the reference table for the simulations
Converts a genlight object into vcf format
Shiny app for the input of the simulations variables
Example data set as text file to be imported into a genlight object
Tests if two populations are fixed at a given locus
adjust rbind for dartR
Population assignment probabilities
Testfile in DArT format (as provided by DArT)
A genlight object created via the gl.read.dart function
[,dartR,ANY,ANY,ANY-method
indexing dartR objects correctly...
Recode file to be used with the function.
dartR theme
Population assignment probabilities
Metadata file. Can be integrated via the dart2genlight function.
A genlight object created via the gl.read.silicodart function
Calculates a distance matrix for individuals defined in a dartR
genlight object using binary P/A data (SilicoDArT)
A utility script to flag the start of a script
Utility function to check the class of an object passed to a function
Calculates mean observed heterozygosity, mean expected heterozygosity and Fis
per locus, per population and various population differentiation measures
Calculates a distance matrix for individuals defined in a dartR
genlight object using SNP data (DArTseq)
Calculates expected mean expected heterozygosity per population
Converts DarT to genlight
Population assignment probabilities
Population assignment probabilities
Calculates the Hamming distance between two DArT trimmed DNA sequences
A utility script to recalculate the OneRatioRef, OneRatioSnp, PICRef, PICSnp,
and AvgPIC by locus after some individuals or populations have been deleted.
A utility script to recalculate the frequency of the heterozygous SNPs by
locus after some populations have been deleted
A utility script to recalculate the frequency of the homozygous reference
SNP by locus after some populations have been deleted
Imports DarT data to R
Conducts jackknife resampling using a genlight object
OutFLANK: An Fst outlier approach by Mike Whitlock and Katie Lotterhos,
University of British Columbia.
utils.outflank.MakeDiploidFSTMat
Creates OutFLANK input file from individual genotype info.
A utility script to recalculate the callrate by locus after some populations
have been deleted
A utility script to recalculate the minor allele frequency by locus,
typically after some populations have been deleted
Util function for evanno plots
Plotting functions for Fst distributions after OutFLANK
A utility script to recalculate the frequency of the homozygous alternate
SNP by locus after some populations have been deleted
Setting up the package
Utility function to run Structure
A utility script to calculate the number of variant and invariant sites by
locus
A utility script to reset to FALSE (or TRUE) the locus metric flags after
some individuals or populations have been deleted.
utils.structure.genind2gtypes
structure util functions
Spatial autocorrelation coefficient calculations