taxondive(vegan)
taxondive()所属R语言包：vegan
Indices of Taxonomic Diversity and Distinctness
分类多样性和独特性指数
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function finds indices of taxonomic diversity and distinctness, which are averaged taxonomic distances among species or individuals in the community (Clarke & Warwick 1998, 2001)
功能发现指数的遗传多样性和独特性，这是物种或个人在社区（克拉克和华威1998年，2001年的平均分类之间的距离）
用法----------Usage----------
taxondive(comm, dis, match.force = FALSE)
taxa2dist(x, varstep = FALSE, check = TRUE, labels)
参数----------Arguments----------
参数：comm
Community data.
社区数据。
参数：dis
Taxonomic distances among taxa in comm. This should be a dist object or a symmetric square matrix.
分类的距离物种间在comm。这应该是一个dist对象或对称的方形矩阵。
参数：match.force
Force matching of column names in comm and labels in dis. 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dis。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：x
Classification table with a row for each species or other basic taxon, and columns for identifiers of its classification at higher levels.
分类表一排，每个物种或其他基本类群，并对其进行分类的标识符列在较高的水平。
参数：varstep
Vary step lengths between successive levels relative to proportional loss of the number of distinct classes.
改变步长之间的连续的水平相对于不同的类的数量比例损失。
参数：check
If TRUE, remove all redundant levels which are different for all rows or constant for all rows and regard each row as a different basal taxon (species). If FALSE all levels are retained and basal taxa (species) also must be coded as variables (columns). You will get a warning if species are not coded, but you can ignore this if that was your intention.
如果TRUE，删除所有冗余的水平是不同的所有行或常量的所有行，并把每一行作为一个不同的基部类群（种）。如果FALSE各级保留基部类群（种）也必须被编码为变量（列）。你会得到一个警告，如果种不编码，但是你可以忽略这一点，如果是你的意图。
参数：labels
The labels attribute of taxonomic distances. Row names will be used if this is not given. Species will be matched by these labels in comm and dis in taxondive if these have different dimensions.
labels属性分类的距离。如果没有给出，将用于行名称。物种将这些标签在comm和distaxondive，如果这些不同的尺寸相匹配。
Details
详细信息----------Details----------
Clarke & Warwick (1998, 2001) suggested several alternative indices of taxonomic diversity or distinctness. Two basic indices are called taxonomic diversity (Δ) and distinctness (Δ^*):
克拉克和华威大学（1998年，2001年）提出了几种可供选择的指数的遗传多样性和明显。两个基本指标被称为遗传多样性（Δ）和独特性（Δ^*）：
The equations give the index value for a single site, and summation goes over species i and j. Here ω are taxonomic distances among taxa, and x are species abundances, and n is the total abundance for a site. With presence/absence data both indices reduce to the same index Δ^+, and for this index Clarke & Warwick (1998) also have an estimate of its standard deviation. Clarke & Warwick (2001) presented two new indices: sΔ^+ is the product of species richness and Δ^+, and index of variation in taxonomic distinctness (Λ^+) defined as
方程给出一个站点的索引值，总和超过种i和j。这是ω是分类物种间的距离，x是物种丰度，n是一个网站的总丰度。与存在/不存在数据两个指数降低到相同的索引Δ^+，与此指数克拉克和华威大学（1998年）也有其标准差的估计。克拉克和华威大学（2001年）提出了两个新的指标：sΔ^+是物种丰富度和产品的Δ^+，和分类差异变异指数（Λ^+）定义为
The dis argument must be species dissimilarities. These must be similar to dissimilarities produced by dist. It is customary to have integer steps of taxonomic hierarchies, but other kind of dissimilarities can be used, such as those from phylogenetic trees or genetic differences. Further, the dis need not be taxonomic, but other species classifications can be used.
dis参数必须是物种的不同点。这些都必须相似，相异的dist。这是习惯上有整数的步骤的分类层次结构，但可以使用其他种相异，如那些从进化树或遗传差异。另外，dis不需要的分类，但可用于其他物种分类。
Function taxa2dist can produce a suitable dist object from a classification table. Each species (or basic taxon) corresponds to a row of the classification table, and columns give the classification at different levels. With varstep = FALSE the successive levels will be separated by equal steps, and with varstep = TRUE the step length is relative to the proportional decrease in the number of classes (Clarke & Warwick 1999). With check = TRUE, the function removes classes which are distinct for all species or which combine all species into one class, and assumes that each row presents a distinct basic taxon. The function scales the distances so that longest path length between taxa is 100 (not necessarily when check = FALSE).
函数taxa2dist可以产生一个合适的dist对象的分类表。每个物种（或基本分类单元）对应的分类表的行和列，在不同级别给分类。 varstep = FALSE连续的水平将分离等于步骤，和varstep = TRUE步长是相对比例减少类的数量（克拉克和华威1999年）。 check = TRUE，功能删除类的所有物种是不同的，或结合到一个类中的所有物种，并假设每一行提供了一个独特的基本类群。的功能尺度的距离，使物种间的路径长度，最长的为100（时没有必要check = FALSE）。
Function plot.taxondive plots Δ^+ against Number of species, together with expectation and its approximate 2*sd limits. Function summary.taxondive finds the z values and their significances from Normal distribution for Δ^+.
函数plot.taxondive图Δ^+对物种数量，，连同期望和大约2 * SD限制。功能summary.taxondive发现z价值和意义正态分布为Δ^+。
值----------Value----------
Function returns an object of class taxondive with following items:
函数返回一个对象的类taxondive的以下项目：
参数：Species
Number of species for each site.
为每个站点的物种数。
参数：D, Dstar, Dplus, SDplus, Lambda
Δ, Δ^*, Δ^+, sΔ^+ and Λ^+ for each site.
Δ，Δ^*，Δ^+，sΔ^+和Λ^+为每个站点。
参数：sd.Dplus
Standard deviation of Δ^+.
标准偏差的Δ^+。
参数：ED, EDstar, EDplus
Expected values of corresponding statistics.
相应的统计数据的预期值。
Function taxa2dist returns an object of class "dist", with an attribute "steps" for the step lengths between successive levels.
功能taxa2dist返回一个类的对象"dist"属性"steps"步长之间的水平。
注意----------Note----------
The function is still preliminary and may change. The scaling of taxonomic dissimilarities influences the results. If you multiply taxonomic distances (or step lengths) by a constant, the values of all Deltas will be multiplied with the same constant, and the value of Λ^+ by the square of the constant.
功能仍是初步的，可能会改变。分类相异的缩放比例影响的结果。如果乘以生物分类由一个恒定的距离（或步长），将所有德尔塔值乘以具有相同的常数，和的值Λ^+的常数的平方。
（作者）----------Author(s)----------
Jari Oksanen
参考文献----------References----------
its statistical properties. Journal of Applied Ecology 35, 523–531.
of biodiversity: weighting of step lengths between hierarchical levels. Marine Ecology Progress Series 184: 21–29.
applicable to species lists: variation in taxonomic distinctness. Marine Ecology Progress Series 216, 265–278.
参见----------See Also----------
diversity.
diversity。
实例----------Examples----------
## Preliminary: needs better data and some support functions[＃初赛：需要更好的数据和一些支持功能]
data(dune)
data(dune.taxon)
# Taxonomic distances from a classification table with variable step lengths.[分类的分类表的变步长的距离。]
taxdis <- taxa2dist(dune.taxon, varstep=TRUE)
plot(hclust(taxdis), hang = -1)
# Indices[指数]
mod <- taxondive(dune, taxdis)
mod
summary(mod)
plot(mod)
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。
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发表于 2012-10-1 15:14:04
