Mathematica notebook with simulation methods

This notebook includes the simulation model for the paper "Introgression makes waves in inferred histories of effectivepopulation size". In the present state, the key elements of the simulations are expressed in functions, with the simulation of population structure with gene flow or introgression in the function "funkycoalescence". These functions are insufficiently commented as they stand, and comments need to be added. The function incorporates the coalescence approach as described by Hudson (1990), with mutation (added as "rate") and migration (or instantaneous separation into subpopulations).

本Notebook包含了论文《Introgression makes waves in inferred histories of effective population size》（《渐渗在有效种群大小推断历史中掀起波澜》）所搭载的模拟模型。就当前版本而言，模拟的核心要素均以函数形式实现，其中针对带有基因流或渐渗的种群结构模拟被封装于`funkycoalescence`函数内。目前这些函数的注释仍不够完备，有待补充完善。该函数采用了Hudson（1990）所描述的溯祖方法，并集成了以"rate"参数表征的突变模型，以及迁移（或瞬时分离为亚种群）模型。