read.nexus(ape)
read.nexus()所属R语言包：ape
Read Tree File in Nexus Format
阅读在Nexus格式的文件树
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function reads one or several trees in a NEXUS file.
这个函数读取一个NEXUS文件中的一个或多个树。
用法----------Usage----------
read.nexus(file, tree.names = NULL)
参数----------Arguments----------
参数：file
a file name specified by either a variable of mode character, or a double-quoted string.
是一个变量的模式字符，或一个双引号字符串中指定的文件名。
参数：tree.names
if there are several trees to be read, a vector of mode character that gives names to the individual trees.
如果有多个要读取的树木，一个向量的模式字符赋予名称的单独的树。
Details
详细信息----------Details----------
The present implementation tries to follow as much as possible the NEXUS standard (but see the restriction below on TRANSLATION tables). Only the block “TREES” is read; the other data can be read with other functions (e.g., read.dna, read.table, ...). A trace of the original data is kept with the attribute "origin" (see below).
本实施细则试图遵循尽可能多的Nexus标准的（但请参见下面的限制转换表）。只有块“树”被读取，可以读取其他数据与其他功能（例如，read.dna，read.table，...）。一丝丝的原始数据保存的属性"origin"（见下文）。
If a TRANSLATION table is present it is assumed that only the tip labels are translated and they are all translated with integers without gap. Consequently, if nodes have labels in the tree(s) they are read as they are and not looked for in the translation table. The logic behind this is that in the vast majority of cases, node labels will be support values rather than proper taxa names. This is consistent with write.nexus which translates only the tip labels.
如果转换表是目前被认为仅仅是冰山的标签翻译，他们都翻译与无间隙的整数。因此，如果节点在树中的标签（），他们都读，因为他们并没有看着的对照表。这背后的逻辑是，在绝大多数情况下，将支持节点标签值，而不是适当的分类单元名称。这是符合write.nexus这只是冰山标签转换。
"read.nexus" tries to represent correctly trees with a badly represented root edge (i.e. with an extra pair of parentheses). For instance, the tree "((A:1,B:1):10);" will be read like "(A:1,B:1):10;" but a warning message will be issued in the former case as this is apparently not a valid Newick format. If there are two root edges (e.g., "(((A:1,B:1):10):10);"), then the tree is not read and an error message is issued.
“read.nexus”尝试一具代表性的根缘（即一对额外的括号）表示正确树。例如，树“（（A：1，B：1）：10）;”将念想“（A：1，B：1）：10”，但会发出一个警告消息在前者的情况下，这显然是不有效Newick格式。如果有两个根边缘（例如，“（（（A：1，B：1）：10）：10）;”），然后在树不阅读并发出错误信息。
值----------Value----------
an object of class "phylo" with the following components:
一个对象类"phylo"与以下组件：
参数：edge
a two-column matrix of mode character where each row represents an edge of the tree; the nodes and the tips are symbolized with numbers (these numbers are not treated as numeric, hence the mode character); the nodes are represented with negative numbers (the root being "-1"), and the tips are represented with positive numbers. For each row, the first column gives the ancestor. This representation allows an easy manipulation of the tree, particularly if it is rooted.
一个两列的矩阵，其中每一行模式字符表示的树的边缘;节点和提示符号与数字（这些数字不被视为数值，因此模式字符）;节点用负数表示（根"-1"），并提示用正数表示。对于每一行，第一列给出的祖先。这表示允许的树，特别是如果它是植根于一个简单的操作。
参数：edge.length
a numeric vector giving the lengths of the branches given by edge.
一个数值向量给由edge给出的分支的长度。
参数：tip.label
a vector of mode character giving the names of the tips; the order of the names in this vector corresponds to the (positive) number in edge.
模式字符的向量给予的名称的提示，此向量中的名称的顺序对应的（正）的数量在edge。
参数：node.label
(optional) a vector of mode character giving the names of the nodes (set to NULL if not available in the file).
（可选）的模式字符赋予一个向量的节点名称（NULL如果没有可用的文件）。
参数：root.edge
(optional) a numeric value giving the length of the branch at the root is it exists (NULL otherwise).
（可选）的根分支的长度是一个数值，它的存在（NULL否则）。
If several trees are read in the file, the returned object is of class "multiPhylo", and is a list of objects of class "phylo".
如果几棵树读取该文件，返回的对象是的类"multiPhylo"，是一个类的对象"phylo"。
（作者）----------Author(s)----------
Emmanuel Paradis
参考文献----------References----------
extensible file format for systematic information. Systematic Biology, 46, 590–621.
参见----------See Also----------
read.tree, write.nexus, write.tree, read.nexus.data, write.nexus.data
read.tree，write.nexus，write.tree，read.nexus.data，write.nexus.data
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
|
发表于 2012-9-11 23:21:26
