file 13 - R code for simulated bottleneck in the N=10 x5 population with variance in individual IBD retained

This code runs a simulation of the bottleneck and subsequent pedigree used for the N=10 x5 population. Variance in individual IBD generated during the bottleneck retained through the pedigree. This method takes linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates as well as number of alleles per locus. This code links to the following files, which must be in the working directory: files 16 – 17, files 24 – 26 and file 28.