Man pages for dyerlab/gstudio
Tools Related to the Spatial Analysis of Genetic Marker Data

AAllelic Diversity
AeEffective Allelic Diversity
aflp_arapatAFLP Arapat data
allele_countsReturns counts of alleles at a locus by population
allelesReturns the alleles in a 'locus' object
arapatData for Araptus attenuatus genind to normal data.frame with 'locus' objects locus to a data frame
as.list.locusConverts locus to a list
as.locusAs operator for locus
bad_parentsDetermines of the indicated parent can possibly be the parent...
c.locusConcatinate 'locus' objects
column_classFind columns of data in a data.frame for a type of class
cornusCornus adult data
cornus_floridaCornus mom/offspring data set
cov2distConverts covariance matrix to distance one.
create_resistancesEstimates resistance rasters from binary feature raster.
data_2_columnTwo Column Example Data
data_aflpAFLP example data set
data_separatedSeparated Example Data
data_snpSNP Example Data
data_zymelikeZyme-like Example Data
DestEstimation Joost's Dest parameter
dist2covConverts distance matrix to covarance one.
dist_amovaEstimation of amova distance
distance_to_covarianceTakes distance matrix and turns it into a covariance matrix
dist_brayEstimation of jaccard distance
dist_cavalliEstimation of Bray-Curtis distance
dist_cgdEstimation of conditional genetic distance
dist_euclideanEstimation of euclidean distance
dist_jaccardEstimation of jaccard distance
dist_neiEstimation of Bray-Curtis distance
dist_ssEstimation of SS distance
exclusion_probabilityPaternity exclusion probability
FisEstimate simple inbreeding from frequencies
frequenciesGet allele frequencies
frequency_matrixCreate a matrix of allele frequencies for a single locus...
FstEstimation Wright's Fst parameter
genetic_autocorrelationPerforms 'Autocorrelation Analysis
genetic_distanceEstimate genetic distances among strata in a ,
genetic_diversityEstimate genetic diversity among strata in a Population,
genetic_relatednessEstimates pair-wise relatedness
genetic_structureEstimation of , genetic structure statistics.
genotype_countsReturns the number of non-missing genotypes per stratum
genotype_frequenciesGenotype Frequencies
geom_frequenciesPlot allele frequencies
geom_locusTranslate a vector of 'locus' objects into a 'gemo_bars'...
geom_strataReturns ggplot layer for population data
geom_strata_labelReturns ggplot layer for population data with labels
geom_surfaceTranslate raster into ggplot object
grid.csvCDPop Data
GstEstimation Nei's Gst parameter
Gst_primeEstimation Nei's Gst parameter with Hedrick's correction for...
gstudio-packageRoutines used in spatial analysis of genetic marker data
harmonic_meanThis is a quick and dirty harmonic mean calculation
HeEstimate expected heterozygosity
HesEstimate expected heterozygosity Returns the general expected...
HoEstimate observed heterozygosity Returns the general observed...
HosEstimate observed heterozygosity corrected for sample size...
HtEstimate expected heterozygosity Returns the general expected...
hweTests for Hardy-Weinberg Equilibrium
indicesReturns quickly indices for a matrix of size N
is_frequencyIs-A function for Allele Frequencies
is_heterozygoteDetermine heterozygosity
is.locusAn 'is-a' operator for 'locus' if 'locus' is NA
kronecker_deltaThis function returns the kronecker operator for two loci.
lag_matrixReturns matrix only with values within a particular bin...
locusGeneral constructor for locus object
locus-operator-indexOverload '[' for vectors of 'locus' objects
locus-operator-minusOverload '-' operator for pairs of 'locus' objects
locus-operator-plusOverload '+' operator for pairs of 'locus' objects
make_lociMake loci
make_populationMakes a random population
mateProduces offspring
maximum_allele_sizeReturns the max digits of all loci passed.
migrateThis function returns a data frame that has moved migrants
minus_momSubtracts maternal component to offspring genotypes
mixed_matingProduce the next generation but allow for some level of...
multilocus_assignmentReturns multilocus assignment probability
multilocus_diversityReturns multilocus diversity
optimal_samplingEstimate optimal sampling allocation
parent_finderThis function finds a set of potential parents from an...
partitionSubdivide a 'data.frame' of genetic information, into a list...
paternityEstimates fractional paternity probability
PePolymorphic index for loci
permute_ciPermute for confidence interval
permute_matrixPermutes rows and corresponding cols of a matrix.
pies_on_mapCreate a pie chart map of allele frequencies on google maps.
ploidyReturns the number of alleles in a 'locus' object
plot.locusOverload plot function
plot_populationsPlotting the locations of a 'population'
population_mapRetrieve a map for a set of populations.
print.locusOverload of 'print' function for 'locus' objects
rarefactionDoes allelic diversity rarefaction
read_populationRead a raw text file in and translate appropriate columns...
rel_lynchThis estimates the Lynch & Ritland (1999)
rel_nasonThis estimates the Fij statistic from Nason allele-wise or...
rel_quellerThis estimates the Queller & Goodnight (1989)
rel_ritlandThis estimates the relatedness statistic from Ritland (1996)
rep.locusReplicate a locus
riceRice Canopy
snp_prob.csvSNP probability data
spiderplot_dataTranslate paternity output into segments for geom_segments
strata_coordinatesGrab coordinates for strata
strata_distanceReturn distances between strats
summary.locusProvides a summary of the 'locus' object
to_dfdistConvert to DFDist format
to_fixed_locusreturns string representation of locus for output like...
to_genepopTranslates a 'data.frame'
to_mvReturns the passed items as multivariate data
to_mv_freqReturns mv frequencies for stratum in long format
to_structureTranslates a 'data.frame' with loci into a textual STRUCTURE...
transition_probabilityReturns transition probability for offspring given one or...
write_populationWrites data frame with genotypes and other data to a file
dyerlab/gstudio documentation built on Sept. 1, 2018, 1:13 a.m.