treedive(vegan)
treedive()所属R语言包：vegan
Functional Diversity estimated from a Species Dendrogram
功能多样性的估计从一个物种树状图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Functional diversity is defined as the total branch length in a trait dendrogram connecting all species, but excluding the unnecessary root segments of the tree (Petchey and Gaston 2006).
功能的多样性被定义为连接所有物种的性状聚类分析的总分支长度，但不包括不必要的树的根段（周三前瞻2006年和Gaston）。
用法----------Usage----------
treedive(comm, tree, match.force = FALSE)
treeheight(tree)
treedist(x, tree, relative = TRUE, ...)
参数----------Arguments----------
参数：comm, x
Community data frame or matrix.
社区数据框或矩阵。
参数：tree
A dendrogram which for treedive must be for species (columns).
treedive必须的物种（列）进行的聚类分析。
参数：match.force
Force matching of column names in comm and labels in tree. If FALSE, matching only happens when dimensions differ, and in that case the species must be in identical order in both.
强制匹配列名comm和标签tree。如果FALSE，匹配只发生在尺寸不同，在这种情况下，物种必须在两个顺序相同。
参数：relative
Use distances relative to the height of combined tree.
使用联合树的高度的距离相对。
参数：...
Other arguments passed to functions (ignored).
其他参数传递给函数（忽略）。
Details
详细信息----------Details----------
Function treeheight finds the sum of lengths of connecting segments in a dendrogram produced by hclust, or other dendrogram that can be coerced to a correct type using as.hclust. When applied to a clustering of species traits, this is a measure of functional diversity (Petchey and Gaston 2002, 2006).
函数treeheight发现在一个树状的hclust，或其他聚类分析的，可以强制转换为正确的类型使用as.hclust，连接段长度的总和。当应用到物种性状的聚类功能的多样性（周三前瞻和Gaston 2002年，2006年），这是一个措施。
Function treedive finds the treeheight for each site (row) of a community matrix. The function uses a subset of dendrogram for those species that occur in each site, and excludes the tree root if that is not needed to connect the species (Petchey and Gaston 2006). The subset of the dendrogram is found by first calculating cophenetic distances from the input dendrogram, then reconstructing the dendrogram for the subset of the cophenetic distance matrix for species occurring in each site. Diversity is 0 for one spcies, and NA for empty communities.
功能treedive发现treeheight社区矩阵的每个站点（行）。该函数使用的一个子集的聚类分析这些物种中出现的每个站点，但不包括树根，并不需要连接的物种（周三前瞻2006年和Gaston）。树状图的子集被发现通过首先计算cophenetic从输入树状图的距离，然后重建发生在每个站点中的物种的cophenetic距离矩阵的子集的树形图。多样性是一个物种绝灭，NA空的社区。
Function treedist finds the dissimilarities among trees. Pairwise dissimilarity of two trees is found by combining species in a common tree and seeing how much of the tree height is shared and how much is unique. With relative = FALSE the dissimilarity is defined as 2AB - A - B, where A and B are heights of component trees and AB is the height of the combined tree. With relative = TRUE the dissimilarity is (2AB - A - B)/(AB). Although the latter formula is similar to Jaccard dissimilarity (see vegdist, designdist), it is not in the range 0 … 1, since combined tree can add a new root. When two zero-height trees are combined into a tree of above zero height, the relative index attains its maximum value 2. The dissimilarity is zero from a combined zero-height tree.
函数treedist发现树木之间的异同。两两相异的两棵树相结合，种在一个共同的树，看到多少树高是共享的，多少是独一无二的。用relative = FALSE的差异性被定义为2AB - A - B，其中A和，B是组件树的高度和AB是合并后的树的高度。随着relative = TRUE的的相异是(2AB - A - B)/(AB)。虽然后者的公式是类似的Jaccard相异（见vegdist，designdist），它是在范围0 … 1，因为结合树可以添加新的根。当被组合成两个高度为零，树的树的上述零高度，相对折射率达到其最大值2。相异从合并的高度为零，树是零。
The functions need a dendrogram of species traits as an input. If species traits contain factor or ordered factor variables, it is recommended to use Gower distances for mixed data (function daisy in package cluster), and usually the recommended clustering method is UPGMA (method = "average" in function hclust) (Podani and Schmera 2006).
功能需要一个树状的物种特征作为输入。如果物种特性包含factor或ordered的因子变量，它是建议使用高尔距离，混合数据（函数daisy在包cluster），而且通常推荐的聚类方法UPGMA（method = "average"的功能hclust）（Podani和Schmera 2006年）。
It is possible to analyse the non-randomness of functional diversity using oecosimu. This needs specifying an adequate Null model, and the results will change with this choice.
是可能的在使用oecosimu分析功能多样性非随机性。这需要指定一个适当的空模型，其结果将改变这样的选择。
值----------Value----------
A vector of diversity values or a single tree height, or a dissimilarity structure that inherits from dist and can be used similarly.
一个向量的多样性值或一个单一的树高，或相异继承自dist，可以使用同样的结构。
（作者）----------Author(s)----------
Jari Oksanen
参考文献----------References----------
for comparing microbial communities. Applied and Environmental Microbiology 71, 8228–8235.
richness and community composition. Ecology Letters 5, 402–411.
basics and looking forward. Ecology Letters 9, 741–758.
functional diversity. Oikos 115, 179–185.
参见----------See Also----------
taxondive is something very similar from
taxondive是非常类似的东西从
实例----------Examples----------
## There is no data set on species properties yet, and therefore[＃有没有数据集物种物业，并因此]
## the example uses taxonomy [＃示例使用分类的]
data(dune)
data(dune.taxon)
d <- taxa2dist(dune.taxon, varstep=TRUE)
cl <- hclust(d, "aver")
treedive(dune, cl)
## Significance test using Null model communities.[显着性检验使用Null示范社区。]
## The current choice fixes only site totals.[＃当前选择修复唯一的网站总数。]
oecosimu(dune, treedive, "r0", tree = cl)
## Clustering of tree distances[＃聚类树的距离]
dtree <- treedist(dune, cl)
plot(hclust(dtree, "aver"))
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。
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发表于 2012-10-1 15:14:18
