GeneticStudio packages for R.


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Documentation for package ‘gstudio’ version 0.2

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gstudio-package Spatial analysis of genetic marker data
$ Accessing data column within a Population object
$-method Accessing data column within a Population object
$<- Accessing data column within a Population object
$<--method Accessing data column within a Population object
allele.frequencies Returns a 'Frequencies' object (or objects)
allele.frequencies-method Returns a 'Frequencies' object (or objects)
araptus_attenuatus An example data set for co-dominant loci
as.character Overload of 'as.character' function
as.character-method Overload of 'as.character' function
as.vector Overload of 'as.vector'
as.vector-method Overload of 'as.vector'
column.names Returns data names for specific kind of class
column.names-method Returns data names for specific kind of class
dim Dimensions of the 'Population'
dim-method Dimensions of the 'Population'
Frequencies Constructor function for 'Frequencies' objects
Frequencies-class Class 'Frequencies'
genetic.distance Main function for estimating genetic distances
genetic.diversity Estimates rarefied genetic diversity
genetic.structure Main function for estimating genetic structure parameters
genotype.counts Returns tally of genotypes
genotype.counts-method Returns tally of genotypes
get.frequencies Gets allele frequencies from pop
get.frequencies-method Gets allele frequencies from pop
google.pie.chart Get Google Pie Chart URL
great.circle.distance Get the "great circle" distance (in km) between two points
he Gets expected heterozygosity
he-method Gets expected heterozygosity
ho Gets observed heterozygosity
ho-method Gets observed heterozygosity
indices Returns the numeric indices of data column names
indices-method Returns the numeric indices of data column names
is.heterozygote Is a locus a heterozygote
is.heterozygote-method Is a locus a heterozygote
is.na Overload of 'is.na'
is.na-method Overload of 'is.na'
length Overload of 'length'
length-method Overload of 'length'
Locus Constructor function for 'Locus' objects
Locus-class Class 'Locus'
multivariate.loci Returns multivariate genotypes for all loci
multivariate.loci-method Returns multivariate genotypes for all loci
names Data column names in 'Population' a locus object
names-method Data column names in 'Population' a locus object
partition Returns a list of 'Population' objects
partition-method Returns a list of 'Population' objects
pies.on.map Creates google map with pie charts for allele frequencies.
plot.genetic.diversity Plots out results of genetic diversity
plot.genetic.structure Plots out results of genetic structure
popgraph.on.map Creates google map with pie charts for allele frequencies.
Population Constructor function for 'Population' objects
Population-class Class 'Population'
population.graph Create a Population Graph from a data set
print Printing a locus object
print-method Printing a locus object
print.genetic.diversity Prints out results of genetic diversity
print.genetic.structure Prints out results of genetic structure
print.summary.gstudio Printing of a summary.Locus object
read.population Loads a population from a *.csv file
row.names Overload row.names function for 'Population'
row.names-method Overload row.names function for 'Population'
show Showing a locus object
show-method Showing a locus object
stratum.distance Calucluate pair-wise distance between stratum
summary Overload of 'summary'
summary-method Overload of 'summary'
validate_gstudio_tests Verify test conditions for package components
[-Locus-method Accessing elements within a locus object
[-method Accessing elements within a locus object
[-method Accessing data column within a Population object
[-Population-accessors Accessing data column within a Population object
[<--Locus-method Accessing elements within a locus object
[<--method Accessing elements within a locus object
[<--method Accessing data column within a Population object
[<--Population-accessors Accessing data column within a Population object
[[-method Accessing data column within a Population object
[[-Population-accessors Accessing data column within a Population object