Data-set empirical trees

The input file” treebase_input.rda” has the trees cached from TreeBase by the R-package treebase (Sanderson, M.J., Donoghue, M.J., et al. 1994). The file was later treated for specific statistics and compared with simulated trees, as described in out methodology. For that the “processing_treebase.R” R-script was used, being the file “treebaselist_output.RData” the final output. We would like to stress that this is not a complete catalogue of all R-scripts used in our study, especially regarding plotting and investigation of model behavior, once much was simulated with a cluster computer involving multiple outputs, code files and csv parameter tables that changed over time. If you plan to run similar experiments, we strongly encourage the reading of our TreeSimGM R-package help material.

输入文件`treebase_input.rda`存储了由R包`treebase`（Sanderson、M.J.、Donoghue、M.J.等，1994年）从TreeBase中缓存得到的系统发育树。本文件后续按照本研究方法中的描述，完成了特定统计量处理，并与模拟生成的系统发育树进行了比对。本次处理使用了`processing_treebase.R`这一R脚本，最终输出结果存储于`treebaselist_output.RData`文件中。

需要特别说明的是，本文件并未涵盖本研究中使用的全部R脚本，尤其是与绘图及模型行为探究相关的脚本。这是因为本研究的大量模拟实验依托集群计算机完成，期间产生了多份输出结果、代码文件以及随时间迭代更新的csv格式参数表。

若您计划开展类似的实验，我们强烈建议您参阅本研究配套的`TreeSimGM` R包帮助文档。