GSP                     Example Genomic Simulation Pedigree, GSP, with
                        13 members
GSP_opts                A list of tibbles specifying the pedigrees
                        available from 'createGSP()'
Geno                    Genotype matrix of 78 individuals and 100 SNP
                        markers
I_meta                  Metadata for 78 individuals
M_meta                  Metadata for 100 molecular markers
RecRates                Recombination rate data for many roughly 1 Mb
                        bins
RepPop1                 A simple example of a reppop table
RepPop4                 Another simple example of a reppop table
check_chrom_lengths     check that the chromosome lengths are
                        acceptable given recombination rates
check_gsp_for_validity_and_saturation
                        Check that GSP does not reuse genetic material
                        and yet uses all of it
check_pedigree_for_inbreeding
                        Check the a GSP (in prepped list format) for
                        inbreeding loops
computeQs_from_segments
                        return the admixture fractions of sampled
                        individuals
create_GSP              Create a GSP from user inputs about what type
                        of hybrids from which populations to create
                        hybrids
drop_segs_down_gsp      High level function for dropping segments down
                        a GSP
example_chrom_lengths   Lengths of the three chromosomes used in the
                        example data set
example_segments        Example of a segments tibble
gscramble2newhybrids    Convert 'gscramble' output to newhybrids format
gscramble2plink         Write 'gscramble' I_meta, M_meta, and Geno to a
                        plink file
gsp2dot                 Write a dot file to represent a genome
                        simulation pedigree
gsp3                    Tibble holding specification for a 5 member
                        genomic permutation pedigree.
gsp4                    Tibble holding specification for a 7 member
                        genomic permutation pedigree.
mat_scramble            Scramble a matrix of genotype data
perm_gs_by_pops         Take the output of rearrange_genos and permute
                        everyone by population
plink2gscramble         read plink-formatted .map and .ped files into
                        'gscramble' format
plink_map2rec_rates     Convert a PLINK map file to 'gscramble'
                        RecRates bins in a tibble
plot_simulated_chromomsome_segments
                        Plot the simulated chromosomes of an individual
prep_gsp_for_hap_dropping
                        Take a gsp in tibble form and make a list
                        suitable for gene dropping
rearrange_genos         rearrange genotypes into separate columns for
                        each haplotype.
recomb_point            Randomly sample the positions of recombinations
                        on a chromosome
renumber_GSP            Renumber GSP members by adding a constant to
                        each
seg2tib                 Takes a gamete in segment format and returns a
                        tibble with Pop and indiv_index
segments2markers        Map alleles from scrambled founders to the
                        sampled segments from a GSP.
segregate               Segregate segments down genomic simulation
                        pedigrees
sim_level_founder_haplos
                        computes the simulation-level founder haplotype
                        index for each founder haplo
xover                   internal function to do crossovers and create
                        recombinations
