gscramble1.0.1 package

check that the chromosome lengths are acceptable given recombination r...

Check that GSP does not reuse genetic material and yet uses all of it

Check the a GSP (in prepped list format) for inbreeding loops

check to make sure that the recombination rates tibble is formatted pr...

check that the RepPop is formatted correctly

return the admixture fractions of sampled individuals

Create a GSP from user inputs about what type of hybrids from which po...

High level function for dropping segments down a GSP

Example of a segments tibble

Convert 'gscramble' output to newhybrids format

Write 'gscramble' I_meta, M_meta, and Geno to a plink file

Write a dot file to represent a genome simulation pedigree

makes a two-column matrix for subscripting alleles out of a genotype m...

Scramble a matrix of genotype data

Take the output of rearrange_genos and permute everyone by population

Convert a PLINK map file to 'gscramble' RecRates bins in a tibble

read plink-formatted .map and .ped files into 'gscramble' format

Plot the simulated chromosomes of an individual

Take a gsp in tibble form and make a list suitable for gene dropping

rearrange genotypes into separate columns for each haplotype.

Randomly sample the positions of recombinations on a chromosome

Renumber GSP members by adding a constant to each

Segregate haplotypes through a genome simulation pedigree list

Takes a gamete in segment format and returns a tibble with Pop and ind...

Map alleles from scrambled founders to the sampled segments from a GSP...

Segregate segments down genomic simulation pedigrees

computes the simulation-level founder haplotype index for each founder...

takes the waka_waka table and returns a simple tibble with results for...

internal function to do crossovers and create recombinations