betadiver(vegan)
betadiver()所属R语言包：vegan
Indices of beta Diversity
β多样性指数
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The function estimates any of the 24 indices of beta diversity reviewed by Koleff et al. (2003). Alternatively, it finds the co-occurrence frequencies for triangular plots (Koleff et al. 2003).
该函数估计的Koleff等24个指标的β多样性的评论。 （2003年）。另外，也发现了三角形图（Koleff等，2003）共现的频率。
用法----------Usage----------
betadiver(x, method = NA, order = FALSE, help = FALSE, ...)
## S3 method for class 'betadiver'
plot(x, ...)
## S3 method for class 'betadiver'
scores(x, triangular = TRUE, ...)
参数----------Arguments----------
参数：x
Community data matrix, or the betadiver result for plot and scores functions.
社区数据矩阵或betadiverplot和scores函数的结果。
参数：method
The index of beta diversity as defined in Koleff et al. (2003), Table 1. You can use either the subscript of β or the number of the index. See argument help below.
该指数的β多样性中定义的Koleff等。 （2003），表1中。您可以使用β或索引数的下标。请参阅参数help下面。
参数：order
Order sites by increasing number of species. This will influence the configuration in the triangular plot and non-symmetric indices.
越来越多的物种订购网站。这将影响的三角图中的配置和非对称指数。
参数：help
Show the numbers, subscript names and the defining equations of the indices and exit.
显示的数字，标名和公式的指标和出口。
参数：triangular
Return scores suitable for triangular plotting of proportions. If FALSE, returns a 3-column matrix of raw counts.
返回适用于三角形的绘制比例的分数。如果FALSE，返回3列矩阵的原始计数。
参数：...
Other arguments to functions.
其他函数的参数。
Details
详细信息----------Details----------
The most commonly used index of beta diversity is β_w = S/α - 1, where S is the total number of species, and α is the average number of species per site (Whittaker 1960). A drawback of this model is that S increases with sample size, but the expectation of α remains constant, and so the beta diversity increases with sample size. A solution to this problem is to study the beta diversity of pairs of sites. If we denote the number of species shared between two sites as a and the numbers of unique species (not shared) as b and c, then S = a + b + c and α = (2 a + b + c)/2 so that β_w = (b+c)/(2 a + b + c). This is the S酶rensen dissimilarity as defined in vegan function vegdist with argument binary = TRUE. Many other indices are dissimilarity indices as well.
最常用的β多样性指数β_w = S/α - 1，其中S是总种数，α是每个站点物种的平均数量（惠特克1960年）。这种模式的缺点是，S与样本量增加，但期望α保持不变，所以beta多样性随样本量。这个问题的一个解决方案是对网站的beta多样性的研究。如果我们a和b，那么c和<X表示作为S = a + b + c两个站点之间的和独特的物种共享的物种的数量（不共享） >，这样α = (2 a + b + c)/2。这是索伦森相异的定义在β_w = (b+c)/(2 a + b + c)函数vegan的参数vegdist。许多其他指标的差异性指数，以及。
Function betadiver finds all indices reviewed by Koleff et al. (2003). All these indices could be found with function designdist which uses different notation, but the current function provides a conventional shortcut. The function only finds the indices. The proper analysis must be done with functions such as betadisper, adonis or mantel.
功能betadiver发现所有审阅Koleff等指标。 （2003年）。所有这些指标可以发现与功能designdist使用不同的符号，但目前的功能提供了一个常规的捷径。该功能只发现指数。必须做适当的分析功能，如betadisper，adonis或mantel。
The indices are directly taken from Table 1 of Koleff et al. (2003), and they can be selected either by the index number or the subscript name used by Koleff et al. The numbers, names and defining equations can be seen using betadiver(help = TRUE). In all cases where there are two alternative forms, the one with the term -1 is used. There are several duplicate indices, and the number of distinct alternatives is much lower than 24 formally provided. The formulations used in functions differ occasionally from those in Koleff et al. (2003), but they are still mathematically equivalent. With method = NA, no index is calculated, but instead an object of class betadiver is returned. This is a list of elements a, b and c. Function plot can be used to display the proportions of these elements in triangular plot as suggested by Koleff et al. (2003), and scores extracts the triangular coordinates or the raw scores. Function plot returns invisibly the triangular coordinates as an "ordiplot" object.
该指数是直接拍摄从表1的Koleff等。 （2003），它们可以被选择的索引号或下标使用的名称由Koleff等。的号码，姓名和定义方程可以看出使用betadiver(help = TRUE)。在所有情况下，有两种可供选择的形式，一个与术语-1使用。有几个重复的指数，和数量的不同的替代品是远低于24正式提供。功能中使用的制剂不同偶尔从那些在Koleff等。 （2003年），但他们仍然是数学上是等价的。随着method = NA，没有指数的计算方法，而是一个对象的类betadiver的返回。这是一个列表的元素a，b和c。函数plot可以用来显示在这些元素的比例由Koleff等人的建议，三角图。 （2003年），和scores提取的的三角坐标或原始分数。功能plot返回看不见的三角坐标系作为"ordiplot"对象。
值----------Value----------
With method = NA, the function returns an object of class "betadisper" with elements a, b, and c. If method is specified, the function returns a "dist" object which can be used in any function analysing dissimilarities. For beta diversity, particularly useful functions are betadisper to study the betadiversity in groups, adonis for any model, and mantel to compare beta diversities to other dissimilarities or distances (including geographical distances). Although betadiver returns a "dist" object, some indices are similarities and cannot be used as such in place of dissimilarities, but that is a severe user error. Functions 10 ("j") and 11 ("sor") are two such similarity indices.
随着method = NA，该函数返回一个类的对象"betadisper"的元素a，b和c。如果method指定，该函数返回一个"dist"对象，它可以用在任何功能分析异同。对于β多样性，特别有用的功能是betadisper研究组betadiversity的，adonis对任何模型，和mantel比较测试的多样性上有所不同距离（包括GEO上的距离）。虽然betadiver返回一个"dist"对象，一些指标相似性和不能被用作这样代替的异同，但是这是一个严重的用户错误。功能10（"j"）和11（"sor"）有两个这样的相似性指数。
警告----------Warning ----------
Some indices return similarities instead of dissimilarities.
一些指数返回的相似性，而不是相异。
注意----------Note----------
The argument method was called index in older versions of the function (upto vegan version 1.17-11). Argument index is deprecated, but still recognized
参数method被称为index在旧版本的功能（高达vegan的的版本1.17-11）。参数index已过时，但仍然承认
（作者）----------Author(s)----------
Jari Oksanen
参考文献----------References----------
components of beta diversity. Global Ecology and Biogeography 19, 134–143.
diversity for presence-absence data. Journal of Animal Ecology 72, 367–382.
California. Ecological Monographs 30, 279–338.
参见----------See Also----------
designdist for an alternative to implement all these functions, vegdist for some canned alternatives, and betadisper, adonis, mantel for analysing beta diversity objects. Functions nestedbetasor and nestedbetajac implement decomposition beta diversity measures (S酶rensen and Jaccard) into turnover and nestedness components following Baselga (2010).
designdist实现所有这些功能的替代，vegdist一些罐装的替代品，和betadisper，adonis，mantelβ多样性分析对象。功能nestedbetasor和nestedbetajac实现营业额和嵌套性成分巴塞尔加（2010）的分解β多样性的措施（索伦森和Jaccard）。
实例----------Examples----------
## Raw data and plotting[＃原始数据和绘制]
data(sipoo)
m <- betadiver(sipoo)
plot(m)
## The indices[＃指数]
betadiver(help=TRUE)
## The basic Whittaker index[＃基本Whittaker指数]
d <- betadiver(sipoo, "w")
## This should be equal to Sorensen index (binary Bray-Curtis in[＃这应该是平等的Sorensen指数（二进制的Bray-Curtis的]
## vegan)[＃素食主义者）]
range(d - vegdist(sipoo, binary=TRUE))
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 2012-10-1 15:03:44
