Analyses and functions related to the spatial analysis of genetic marker data.


[Up] [Top]

Documentation for package ‘gstudio’ version 1.3

Help Pages

gstudio-package Routines used in spatial analysis of genetic marker data
+.locus Overload '+' operator for pairs of 'locus' objects
-.locus Overload '-' operator for pairs of 'locus' objects
A Allelic Diversity
Ae Effective Allelic Diversity
alleles Returns the alleles in a 'locus' object
alleles.default Returns the alleles in a 'locus' object
alleles.locus Returns the alleles in a 'locus' object
arapat Data for Araptus attenuatus
as.data.frame.locus Converts locus to a data frame
as.list.locus Converts locus to a list
as.locus As operator for locus
bad_parents Determines of the indicated parent can possibly be the parent of the offspring
c.locus Concatinate 'locus' objects
column_class Find columns of data in a data.frame for a type of class
cornus_florida Cornus mom/offspring data set
data_2_column Two Column Example Data
data_aflp AFLP example data set
data_separated Separated Example Data
data_snp SNP Example Data
data_zymelike Zyme-like Example Data
Dest Estimation Joost's Dest parameter
dist_amova Estimation of amova distance
dist_bray Estimation of jaccard distance
dist_cavalli Estimation of Bray-Curtis distance
dist_cgd Estimation of conditional genetic distance
dist_euclidean Estimation of euclidean distance
dist_jaccard Estimation of jaccard distance
dist_nei Estimation of Bray-Curtis distance
dist_ss Estimation of SS distance
exclusion_probability Paternity exclusion probability
Fis Estimate simple inbreeding from frequencies
frequencies Get allele frequencies
frequencies.data.frame Get allele frequencies
frequencies.default Get allele frequencies
frequencies.locus Get allele frequencies
genetic_distance Estimate genetic distances among strata in a ,
genetic_diversity Estimate genetic diversity among strata in a Population,
genetic_relatedness Estimates pair-wise relatedness
genetic_structure Estimation of , genetic structure statistics.
genotype_frequencies Genotype Frequencies
geom_frequencies Plot allele frequencies
geom_locus Translate a vector of 'locus' objects into a 'gemo_bars' layer
geom_strata Returns ggplot layer for population data
geom_surface Translate raster into ggplot object
grid.csv CDPop Data
Gst Estimation Nei's Gst parameter
Gst_prime Estimation Nei's Gst parameter with Hedrick's correction for allelic diversity
He Estimate expected heterozygosity
Ho Estimate observed heterozygosity
indices Returns quickly indices for a matrix of size N
is.locus An 'is-a' operator for 'locus'
is.na.locus Determines if 'locus' is NA
is_frequency Is-A function for Allele Frequences
is_heterozygote Determine heterozygosity
kronecker_delta This function returns the kronecker operator for two loci.
locus General constructor for locus object
make_population Makes a random population
mate Produces offspring
migrate This function returns a data frame that has moved migrants
minus_mom Subtracts maternal component to offspring genotypes
multilocus_diversity Returns multilocus diversity
optimal_sampling Estimate optimal sampling allocation
parent_finder This function finds a set of potential parents from an offspring.
partition Subdivide , into a list of substrata
paternity Estimates fractional paternity probability
Pe Polymorphic index for loci
permute_ci Permute for confidence interval
pies_on_map Plot overload
ploidy Returns the number of alleles in a 'locus' object
plot.data.frame Plotting the locations of a 'population'
plot.locus Overload plot function
population_map Retrieve a map for a set of populations.
print.locus Overload of 'print' function for 'locus' objects
rarefaction Does allelic diversity rarefaction
read_population Read a raw text file in and translate appropriate columns into genotypes
rel_lynch This estimates the Lynch & Ritland (1999)
rel_nason This estimates the Fij statistic from Nason allele-wise or for a whole locus
rel_queller This estimates the Queller & Goodnight (1989)
rel_ritland This estimates the relatedness statistic from Ritland (1996)
rep.locus Replicate a locus
snp_prob.csv SNP probability data
spiderplot_data Translate paternity output into segments for geom_segments
strata_coordinates Grab coordinates for strata
strata_distance Return distances between strats
summary.locus Provides a summary of the 'locus' object
to_fixed_locus returns string representation of locus for output like genepop/heirfstat
to_genepop Translates a 'data.frame'
to_mv Returns the passed itmes as multivariate data
to_mv.data.frame Returns the passed itmes as multivariate data
to_mv.default Returns the passed itmes as multivariate data
to_mv.locus Returns the passed itmes as multivariate data
to_mv_freq Returns mv frequencies for stratum in long format
to_structure Translates a 'data.frame' with loci into a textual STRUCTURE file.
transition_probability Returns transition probability for offspring given one or more parents.
write_population Writes data frame with genotypes and other data to a file
[.locus Overload '[' for vectors of 'locus' objects