在 R 中规范化系统发育树
当在 R 中处理系统发育树数据时（特别是在处理“phylo”或“phylo4”对象时），标准化分支长度会很有用，这样某些分类单元（进化得更快的分类单元）不会贡献不成比例的分支长度到树上。这在计算 UniFrac 值中似乎很常见，可以在此处的讨论中找到：http:// bmf2.colorado.edu/unifrac/help.psp。 （但是，我需要的不仅仅是 UniFrac 值）。
但是，我找不到执行此标准化步骤的函数。我查看了 ape、picante、adephylo 和 phylobase。有人可以指导我找到包含此函数的包，或者使编写此类函数变得简单的包吗？
When working with phylogenetic tree data in R (specifically when working with "phylo" or "phylo4" objects) it would be useful to normalize branch lengths so that certain taxa (the ones that evolve faster) do not contribute a disproportionate amount of branch length to the tree. This seems to be common in computing UniFrac values, as can be found in the discussion here: http://bmf2.colorado.edu/unifrac/help.psp. (I need more than just UniFrac values, however).
However, I cannot find a function that performs this normalization step. I have looked in ape, picante, adephylo, and phylobase. Could someone direct me to a package that includes this function, or a package that makes writing this kind of function straightforward?
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您是否正在寻找一个仅缩放树的分支长度的函数？如果是这样，ape 中的compute.brlen() 将会执行此操作。 Grafen 的 rho 和 all = 1 有内置选项。您也可以提供自己的函数。
我不知道 UniFrac 是否会进行其他类型的分支长度缩放。但如果是这样，您可以编写函数并传递它。
Are you looking for a function to just scale the branch lengths of a tree? If so,
compute.brlen()in ape will do it. There are built in options for Grafen's rho and all = 1. You can also supply your own function.I don't know if UniFrac does some other kind of branch length scaling. But if so, you could write your function and pass it.