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 |