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Jupyter笔记本包含了论文《基因渐渗（introgression）在有效种群大小（effective population size）推断历史中产生波动》（"Introgression makes waves in inferred histories of effective population size"）所配套的模拟模型。就当前版本而言，模拟流程的核心要素均以函数形式封装，其中针对带有基因流（gene flow）或渐渗事件的种群结构模拟，实现于`funkycoalescence`函数之中。目前这些函数的注释尚不充分，有待补充完善。该函数采用了Hudson（1990）所描述的溯祖（coalescence）分析方法，集成了以"rate"参数形式配置的突变模型，以及迁移（或瞬时分离形成亚种群）相关的模拟逻辑。