Diversitree: comparative phylogenetic analyses of diversification in R
Diversitree: comparative phylogenetic analyses of diversification in R
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DOI：
10.1111/j.2041-210x.2012.00234.x
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发表时间：
2012-12-01
影响因子：
6.6
通讯作者：
FitzJohn, Richard G.
中科院分区：
文献类型：
--
作者：
FitzJohn, Richard G.
1. R包多样性树包含许多经典和当代的比较系统发育方法。主要包括BiSSE（二态物种形成和灭绝），MuSSE（BiSSE的多态扩展）和MISSSE（定量状态物种形成和灭绝）。多样性树还包括分析性状进化和独立估计物种形成/灭绝率的方法。2.在这篇文章中，我描述了功能，并演示了使用该软件包，使用一种新的方法，MuSSE（多态物种形成和灭绝），以检查两个性状对物种形成的联合影响。3.通过模拟，我发现MuSSE可以可靠地检测到一个影响物种形成率的二元特征，同时考虑到其他对物种形成率没有影响的特征。4. Diversitree是一个开源软件，可以在Comprehensive R Archive Network（cran）上找到。教程和工作示例可以从http://www.zoology.ubc.ca/prog/diversitree下载。
1. The R package diversitree contains a number of classical and contemporary comparative phylogenetic methods. Key included methods are BiSSE (binary state speciation and extinction), MuSSE (a multistate extension of BiSSE), and QuaSSE (quantitative state speciation and extinction). Diversitree also includes methods for analysing trait evolution and estimating speciation/extinction rates independently. 2. In this note, I describe the features and demonstrate use of the package, using a new method, MuSSE (multistate speciation and extinction), to examine the joint effects of two traits on speciation. 3. Using simulations, I found that MuSSE could reliably detect that a binary trait that affected speciation rates when simultaneously accounting for additional thats that had no effect on speciation rates. 4. Diversitree is an open source and available on the Comprehensive R Archive Network (cran). A tutorial and worked examples can be downloaded from http://www.zoology.ubc.ca/prog/diversitree.