simulation analysis script

Simulating trees under the GeoSSE model requires the C program SimTreeSDD. A snapshot of the code used for the analyses in the paper is archived by Systematic Biology as a supplemental file to the paper (SimTreeSDD-2009.tar.gz) because its GPL licence is not compatible with Dryad's CC0 requirement. Extensive further development is not planned, but the current version of the package is available from: http://tigger.uic.edu/~eeg/code/code.html. The R package diversitree is also required by this script. See Description for chaparral-analysis.R.

基于GeoSSE模型（GeoSSE model）的系统发育树模拟需使用C语言程序SimTreeSDD。本文分析所用的代码快照已由《系统生物学》（Systematic Biology）期刊作为论文补充文件存档，存档文件名为SimTreeSDD-2009.tar.gz；由于该代码的GPL许可证与Dryad平台的CC0协议要求不兼容，故采用此存档方式。目前暂无对该程序包进行大规模后续开发的计划，但当前版本的程序包可通过以下链接获取：http://tigger.uic.edu/~eeg/code/code.html。本脚本同时依赖R语言程序包diversitree。有关详细说明请参阅chaparral-analysis.R的描述部分。