betadisper(vegan)
betadisper()所属R语言包：vegan
Multivariate homogeneity of groups dispersions (variances)
多因素同质性的群体分散体（方差）
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Implements Marti Anderson's PERMDISP2 procedure for the analysis of multivariate homogeneity of group dispersions (variances). betadisper is a multivariate analogue of Levene's test for homogeneity of variances. Non-euclidean distances between objects and group centroids are handled by reducing the original distances to principal coordinates. This procedure has latterly been used as a means of assessing beta diversity. There are anova, scores, plot and boxplot methods.
实现马蒂·安德森PERMDISP2程序的多元组的均匀性，分散体（差异）分析。 betadisper Levene检验方差齐性是一个多变量的模拟。非欧几里德的处理对象和组质心之间的距离，减少了原来的主坐标的距离。此程序，其后为被用作评估beta多样性的一种手段。有anova，scores，plot和boxplot方法。
TukeyHSD.betadisper creates a set of confidence intervals on the differences between the mean distance-to-centroid of the levels of the grouping factor with the specified family-wise probability of coverage. The intervals are based on the Studentized range statistic, Tukey's 'Honest Significant Difference' method.
TukeyHSD.betadisper创建一个置信区间的组之间的平均距离重心分组因子的水平的与指定的覆盖家庭明智的概率上的差异。的时间间隔是基于学生化的范围统计，杜克的“公正显着差异的方法。
用法----------Usage----------
betadisper(d, group, type = c("median","centroid"), bias.adjust = FALSE)
## S3 method for class 'betadisper'
anova(object, ...)
## S3 method for class 'betadisper'
scores(x, display = c("sites", "centroids"),
choices = c(1,2), ...)
## S3 method for class 'betadisper'
plot(x, axes = c(1,2), cex = 0.7, hull = TRUE,
ylab, xlab, main, sub, ...)
## S3 method for class 'betadisper'
boxplot(x, ylab = "Distance to centroid", ...)
## S3 method for class 'betadisper'
TukeyHSD(x, which = "group", ordered = FALSE,
conf.level = 0.95, ...)
参数----------Arguments----------
参数：d
a distance structure such as that returned by dist, betadiver or vegdist.
距离结构，如返回dist，betadiver或vegdist。
参数：group
vector describing the group structure, usually a factor or an object that can be coerced to a factor using as.factor. Can consist of a factor with a single level (i.e.~one group).
向量组的结构，通常一个因素或对象可以强制转换的一个因素as.factor描述。可以由一个单一的电平（即一组）的一个因素。
参数：type
the type of analysis to perform. Use the spatial median or the group centroid? The spatial median is now the default.
执行的分析的类型。使用的空间中位数或质心？现在的空间中位数是默认值。
参数：bias.adjust
logical: adjust for small sample bias in beta diversity estimates?
调整的逻辑：在beta多样性估计的小样本偏误？
参数：display
character; partial match to access scores for "sites" or "species".
部分字符的匹配分数为"sites"或"species"访问。
参数：object, x
an object of class "betadisper", the result of a call to betadisper.
类的一个对象"betadisper"，结果，调用betadisper。
参数：choices, axes
the principal coordinate axes wanted.
主坐标轴所需要的。
参数：hull
logical; should the convex hull for each group be plotted?
逻辑，绘制各组的凸包吗？
参数：cex, ylab, xlab, main, sub
graphical parameters. For details, see plot.default.
图形参数。有关详细信息，请参阅plot.default。
参数：which
A character vector listing terms in the fitted model for which the intervals should be calculated. Defaults to the grouping factor.
字符向量上市的时间间隔应计算在合适的模型。默认的分组因素。
参数：ordered
Logical; see TukeyHSD.
逻辑; TukeyHSD。
参数：conf.level
A numeric value between zero and one giving the family-wise confidence level to use.
给家庭明智的置信水平，使用零和一之间的数值。
参数：...
arguments, including graphical parameters (for plot.betadisper and boxplot.betadisper), passed to other methods.
参数，包括图形参数（例如，plot.betadisper和boxplot.betadisper），传递给其他方法。
Details
详细信息----------Details----------
One measure of multivariate dispersion (variance) for a group of samples is to calculate the average distance of group members to the group centroid or spatial median (both referred to as 'centroid' from now on unless stated otherwise) in multivariate space. To test if the dispersions (variances) of one or more groups are different, the distances of group members to the group centroid are subject to ANOVA. This is a multivariate analogue of Levene's test for homogeneity of variances if the distances between group members and group centroids is the Euclidean distance.
多变量离散度（方差）为一组样本的措施之一是计算组成员的平均距离在多变的空间的重心或空间的中位数（简称为“重心”从现在开始，除非另有说明）。如果要测试一个或多个组，分散体（方差）是不同的方差分析，组成员组的质心的距离。这是一个多变量的模拟Levene检验方差齐性，如果组成员和组质心之间的距离是欧氏距离。
However, better measures of distance than the Euclidean distance are available for ecological data. These can be accommodated by reducing the distances produced using any dissimilarity coefficient to principal coordinates, which embeds them within a Euclidean space. The analysis then proceeds by calculating the Euclidean distances between group members and the group centroid on the basis of the principal coordinate axes rather than the original distances.
然而，更好的措施的距离比欧氏距离的生态数据。这些可被容纳的，通过减少主坐标系，其中嵌入了他们的欧几里得空间内使用任何相异系数产生的距离。然后进行分析，通过计算组成员之间的欧几里德距离和基质心的主坐标轴的基础上，而不是原来的距离。
Non-metric dissimilarity coefficients can produce principal coordinate axes that have negative Eigenvalues. These correspond to the imaginary, non-metric part of the distance between objects. If negative Eigenvalues are produced, we must correct for these imaginary distances.
非十进制的相异系数可以产生有负的特征值的主坐标轴。这些对应的假想的，非十进制的对象之间的距离的一部分。如果产生了负的特征值，我们必须纠正这些假想的距离。
The distance to its centroid of a point is
的距离的一个点是它的质心
where Delta^2 is the squared Euclidean distance between u[ij], the principal coordinate for the jth point in the ith group, and c[i], the coordinate of the centroid for the ith group. The super-scripted + and - indicate the real and imaginary parts respectively. This is equation (3) in Anderson (2006). If the imaginary part is greater in magnitude than the real part, then we would be taking the square root of a negative value, resulting in NaN. From vegan 1.12-12 betadisper takes the absolute value of the real distance minus the imaginary distance, before computing the square root. This is in line with the behaviour of Marti Anderson's PERMDISP2 programme.
其中Delta^2是的平方之间的欧几里得距离u[ij]，在jth组的主要ith点坐标，并c[i]，重心坐标为ith组。超级脚本+和-分别表示实部和虚部。这是方程（3），安德森（2006年）。的虚部是更大的幅度比真正的一部分，那么我们将采取平方根的负值，导致NaN的。从vegan1.12-12betadisper需要的实际距离的绝对值减去虚距离之前，计算平方根。这是与马蒂·安德森PERMDISP2程序的行为线。
To test if one or more groups is more variable than the others, ANOVA of the distances to group centroids can be performed and parametric theory used to interpret the significance of F. An alternative is to use a permutation test. permutest.betadisper permutes model residuals to generate a permutation distribution of F under the Null hypothesis of no difference in dispersion between groups.
为了测试，如果一个或多个基团是比其他的更可变的，方差分析组矩心的距离可以执行和使用参数的理论来解释意义F.一种替代方法是使用一个置换试验。 permutest.betadisper置换，模型残差产生置换的F分布的零假设下不分散群体之间的差异。
Pairwise comparisons of group mean dispersions can also be performed using permutest.betadisper. An alternative to the classical comparison of group dispersions, is to calculate Tukey's Honest Significant Differences between groups, via TukeyHSD.betadisper. This is a simple wrapper to TukeyHSD.aov. The user is directed to read the help file for TukeyHSD before using this function. In particular, note the statement about using the function with unbalanced designs.
组的成对比较的意思是分散体也可以执行使用permutest.betadisper。古典组比较分散体的另一种方法，是计算Tukey的诚实组间差异显着，通过TukeyHSD.betadisper。这是一个简单的包装TukeyHSD.aov。用户被定向到TukeyHSD使用此功能前阅读帮助文件。特别要注意的声明与非平衡设计使用的功能。
The results of the analysis can be visualised using the plot and boxplot methods.
分析的结果可以可视化使用plot和boxplot的方法。
One additional use of these functions is in assessing beta diversity (Anderson et al 2006). Function betadiver provides some popular dissimilarity measures for this purpose.
一个额外的使用这些功能是在beta多样性的评估（Anderson等，2006）。函数betadiver提供了一些流行的用于此目的的差异性措施。
As noted in passing by Anderson (2001) and in a related context by O'Neill (2000), estimates of dispersion around a central location (median or centroid) that is calculated from the same data will be biased downward. This bias matters most when comparing diversity among treatments with small, unequal numbers of samples. Setting bias.adjust=TRUE when using betadisper imposes a sqrt(n/(n-1)) correction (Stier et al. 2012).
正如路过的安德森（2001年）和奥尼尔（2000年）在相关的上下文，分散的估计，计算出相同的数据将被向下偏置围绕一个中心位置（中位数或质心）。这种偏见最重要的比较时，具有体积小，样品数量不相等，各处理间多样性。设置bias.adjust=TRUE使用时betadisper规定了sqrt(n/(n-1))校正公牛等人（2012年）。
值----------Value----------
The anova method returns an object of class "anova" inheriting from class "data.frame".
anova方法返回一个对象的类"anova"继承类"data.frame"的。
The scores method returns a list with one or both of the components "sites" and "centroids".
scores方法返回一个列表组件"sites"和"centroids"中的一者或两者。
The plot function invisibly returns an object of class "ordiplot", a plotting structure which can be used by identify.ordiplot (to identify the points) or other functions in the ordiplot family.
plot功能不可见的返回类的一个对象"ordiplot"，可以使用绘图结构identify.ordiplot（确定）或等功能于ordiplot家庭。
The boxplot function invisibly returns a list whose components are documented in boxplot.
boxplot函数，无形地返回一个列表，其成分中的boxplot。
TukeyHSD.betadisper returns a list. See TukeyHSD for further details.
TukeyHSD.betadisper返回一个列表。见TukeyHSD进一步的细节。
betadisper returns a list of class "betadisper" with the following components:
betadisper返回一个列表类"betadisper"有以下组件：
参数：eig
numeric; the eigenvalues of the principal coordinates analysis.
数字的特征值的主坐标分析。
参数：vectors
matrix; the eigenvectors of the principal coordinates analysis.
矩阵的特征向量的主坐标分析。
参数：distances
numeric; the Euclidean distances in principal coordinate space between the samples and their respective group centroid.
数字;样品和它们各自的组质心在主坐标空间之间的欧氏距离。
参数：group
factor; vector describing the group structure
系数向量描述的集团架构
参数：centroids
matrix; the locations of the group centroids on the principal coordinates.
矩阵组质心的主坐标的位置。
参数：call
the matched function call.
匹配的函数调用。
警告----------Warning----------
Stewart Schultz noticed that the permutation test for type = "centroid" had the wrong type I error and was anti-conservative. As such, the default for type has been changed to "median", which uses the spatial median as the group centroid. Tests suggests that the permutation test for this type of analysis gives the correct error rates.
斯图尔特·舒尔茨注意到，排列测试type = "centroid"有错误的I型错误和反保守。因此，默认为type已经改变"median"，它使用的空间中位数组的质心。试验表明，这种类型的分析的置换试验给出了正确的错误率。
注意----------Note----------
If group consists of a single level or group, then the anova and permutest methods are not appropriate and if used on such data will stop with an error.
如果group由一个单级或组，然后anova和permutest方法是不恰当的，如果使用这些数据将停止错误。
Missing values in either d or group will be removed prior to performing the analysis.
遗漏值在任一d或group将被删除之前执行分析。
（作者）----------Author(s)----------
Gavin L. Simpson; bias correction by Adrian Stier and Ben Bolker.
参考文献----------References----------
analysis of variance. Austral Ecology <STRONG>26</STRONG>, 32–46.
multivariate dispersions. Biometrics <STRONG>62</STRONG>, 245–253.
dispersion as a measure of beta diversity. Ecology Letters <STRONG>9</STRONG>, 683–693.
Test of Homogeneity of Variance. Australian & New Zealand Journal of Statistics <STRONG>42</STRONG>, 81-鈥 |
发表于 2012-10-1 15:03:36
