Man pages for MarianaLag/Mlag
Tools Related to the Spatial Analysis of Genetic Marker Data
| A | Allelic Diversity |
| Ae | Effective Allelic Diversity |
| aflp_arapat | AFLP Arapat data |
| allele_counts | Returns counts of alleles at a locus by population |
| alleles | Returns the alleles in a 'locus' object |
| arapat | Data for Araptus attenuatus |
| as.data.frame.genind | Converts genind to normal data.frame with 'locus' objects |
| 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... |
| c.locus | Concatinate 'locus' objects |
| column_class | Find columns of data in a data.frame for a type of class |
| cornus | Cornus adult data |
| cornus_florida | Cornus mom/offspring data set |
| cov2dist | Converts covariance matrix to distance one. |
| create_resistances | Estimates resistance rasters from binary feature raster. |
| 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 |
| dist2cov | Converts distance matrix to covarance one. |
| dist_amova | Estimation of amova distance |
| distance_to_covariance | Takes distance matrix and turns it into a covariance matrix |
| 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 |
| frequency_matrix | Create a matrix of allele frequencies for a single locus... |
| Fst | Estimation Wright's Fst parameter |
| genetic_autocorrelation | Performs 'Autocorrelation Analysis |
| 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_counts | Returns the number of non-missing genotypes per stratum |
| genotype_frequencies | Genotype Frequencies |
| geom_frequencies | Plot allele frequencies |
| geom_locus | Translate a vector of 'locus' objects into a 'gemo_bars'... |
| geom_strata | Returns ggplot layer for population data |
| geom_strata_label | Returns ggplot layer for population data with labels |
| 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... |
| gstudio-package | Routines used in spatial analysis of genetic marker data |
| harmonic_mean | This is a quick and dirty harmonic mean calculation |
| He | Estimate expected heterozygosity |
| Hes | Estimate expected heterozygosity Returns the general expected... |
| Ho | Estimate observed heterozygosity Returns the general observed... |
| Hos | Estimate observed heterozygosity corrected for sample size... |
| Ht | Estimate expected heterozygosity Returns the general expected... |
| hwe | Tests for Hardy-Weinberg Equilibrium |
| indices | Returns quickly indices for a matrix of size N |
| is_frequency | Is-A function for Allele Frequencies |
| is_heterozygote | Determine heterozygosity |
| is.locus | An 'is-a' operator for 'locus' |
| is.na.locus | Determines if 'locus' is NA |
| kronecker_delta | This function returns the kronecker operator for two loci. |
| lag_matrix | Returns matrix only with values within a particular bin... |
| locus | General constructor for locus object |
| locus-operator-index | Overload '[' for vectors of 'locus' objects |
| locus-operator-minus | Overload '-' operator for pairs of 'locus' objects |
| locus-operator-plus | Overload '+' operator for pairs of 'locus' objects |
| make_loci | Make loci |
| make_population | Makes a random population |
| mate | Produces offspring |
| maximum_allele_size | Returns the max digits of all loci passed. |
| migrate | This function returns a data frame that has moved migrants |
| minus_mom | Subtracts maternal component to offspring genotypes |
| mixed_mating | Produce the next generation but allow for some level of... |
| multilocus_assignment | Returns multilocus assignment probability |
| multilocus_diversity | Returns multilocus diversity |
| optimal_sampling | Estimate optimal sampling allocation |
| parent_finder | This function finds a set of potential parents from an... |
| partition | Subdivide a 'data.frame' of genetic information, into a list... |
| paternity | Estimates fractional paternity probability |
| Pe | Polymorphic index for loci |
| permute_ci | Permute for confidence interval |
| permute_matrix | Permutes rows and corresponding cols of a matrix. |
| ploidy | Returns the number of alleles in a 'locus' object |
| plot.locus | Overload plot function |
| plot_populations | Plotting the locations of a 'population' |
| population_graph | Convience function to create population graph object from... |
| 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... |
| rel_lynch | This estimates the Lynch & Ritland (1999) |
| rel_nason | This estimates the Fij statistic from Nason allele-wise or... |
| rel_queller | This estimates the Queller & Goodnight (1989) |
| rel_ritland | This estimates the relatedness statistic from Ritland (1996) |
| rep.locus | Replicate a locus |
| rice | Rice Canopy |
| 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 |
| subsample_loci | Generate subset of data with random sample of loci. |
| summary.locus | Provides a summary of the 'locus' object |
| to_dfdist | Convert to DFDist format |
| to_fixed_locus | returns string representation of locus for output like... |
| to_genepop | Translates a 'data.frame' |
| to_mv | Returns the passed items 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... |
| transition_probability | Returns transition probability for offspring given one or... |
| write_population | Writes data frame with genotypes and other data to a file |
