procrustes(vegan)
procrustes()所属R语言包：vegan
Procrustes Rotation of Two Configurations and PROTEST
两种配置和抗议的Procrustes旋转
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function procrustes rotates a configuration to maximum similarity with another configuration. Function protest tests the non-randomness ("significance") between two configurations.
函数procrustes旋转最大相似度与另一配置的结构。功能protest测试两种配置之间的非随机性（意义）。
用法----------Usage----------
procrustes(X, Y, scale = TRUE, symmetric = FALSE, scores = "sites", ...)
## S3 method for class 'procrustes'
summary(object, digits = getOption("digits"), ...)
## S3 method for class 'procrustes'
plot(x, kind=1, choices=c(1,2), to.target = TRUE,
type = "p", xlab, ylab, main, ar.col = "blue", len=0.05,
cex = 0.7, ...)
## S3 method for class 'procrustes'
points(x, display = c("target", "rotated"), ...)
## S3 method for class 'procrustes'
text(x, display = c("target", "rotated"), labels, ...)
## S3 method for class 'procrustes'
lines(x, type = c("segments", "arrows"), choices = c(1, 2), ...)
## S3 method for class 'procrustes'
residuals(object, ...)
## S3 method for class 'procrustes'
fitted(object, truemean = TRUE, ...)
## S3 method for class 'procrustes'
predict(object, newdata, truemean = TRUE, ...)
protest(X, Y, scores = "sites", permutations = 999, strata, ...)
参数----------Arguments----------
参数：X
Target matrix
目标矩阵
参数：Y
Matrix to be rotated.
旋转的矩阵。
参数：scale
Allow scaling of axes of Y.
允许缩放轴Y。
参数：symmetric
Use symmetric Procrustes statistic (the rotation will still be non-symmetric).
使用对称的Procrustes统计量（旋转仍然会非对称）。
参数：scores
Kind of scores used. This is the display argument used with the corresponding scores function: see scores, scores.cca and scores.cca for alternatives.
一种用分数。这是display使用相应的scores函数的参数：见scores，scores.cca和scores.cca的替代品。
参数：x, object
An object of class procrustes.
对象的类procrustes。
参数：digits
Number of digits in the output.
输出中的数字位数。
参数：kind
For plot function, the kind of plot produced: kind = 1 plots shifts in two configurations, kind = 0 draws a corresponding empty plot, and kind = 2 plots an impulse diagram of residuals.
plot函数，产生什么样的图：kind = 1图两种配置中移动，kind = 0绘制了相应的空图，和kind = 2图的冲动残差图。
参数：choices
Axes (dimensions) plotted.
轴（尺寸）绘制。
参数：xlab, ylab
Axis labels, if defaults unacceptable.
轴标签，如果默认不可接受的。
参数：main
Plot title, if default unacceptable.
图标题，默认情况下不能接受的。
参数：display
Show only the "target" or "rotated" matrix as points.
只显示"target"或"rotated"点矩阵。
参数：to.target
Draw arrows to point to target.
绘制箭头指向目标。
参数：type
The type of plot drawn. In plot, the type can be "points" or "text" to select the marker for the tail of the arrow, or "none" for drawing an empty plot. In lines the type selects either arrows or line segments to connect target and rotated configuration.
绘制的类型图。在plot，type能"points"或"text"选择标记的箭头尾部，或"none"画一个空的图。在linestype选择是arrows或segments连接目标和旋转结构。“
参数：truemean
Use the original range of target matrix instead of centring the fitted values. Function plot.procrustes needs truemean = FALSE.
使用原有的各种目标矩阵，而不是为中心的拟合值。功能plot.procrustes需要truemean = FALSE的。
参数：newdata
Matrix of coordinates to be rotated and translated to the target.
旋转矩阵的坐标，并翻译成目标。
参数：permutations
Number of permutation to assess the significance of the symmetric Procrustes statistic.
数排列对称的Procrustes统计评估的意义。
参数：strata
An integer vector or factor specifying the strata for permutation. If supplied, observations are permuted only within the specified strata.
一个整数向量或因素确定地层的置换。如果提供，观测置换仅在指定的阶层。
参数：ar.col
Arrow colour.
箭头的颜色。
参数：len
Width of the arrow head.
箭头头的宽度。
参数：labels
Character vector of text labels. Rownames of the result object are used as default.
字符向量的文本标签。结果对象的行名作为缺省值。
参数：cex
Character expansion for points or text.
点或文字的字符扩展。
参数：...
Other parameters passed to functions. In procrustes and protest parameters are passed to scores, in graphical functions to underlying graphical functions.
其他参数传递给函数。在procrustes和protest参数被传递到scores，底层图形功能的图形功能。
Details
详细信息----------Details----------
Procrustes rotation rotates a matrix to maximum similarity with a target matrix minimizing sum of squared differences. Procrustes rotation is typically used in comparison of ordination results. It is particularly useful in comparing alternative solutions in multidimensional scaling. If scale=FALSE, the function only rotates matrix Y. If scale=TRUE, it scales linearly configuration Y for maximum similarity. Since Y is scaled to fit X, the scaling is non-symmetric. However, with symmetric=TRUE, the configurations are scaled to equal dispersions and a symmetric version of the Procrustes statistic is computed.
普鲁克旋转旋转矩阵的最大相似性，与差的平方和最小化的目标矩阵。普鲁克旋转通常用于协调结果的比较。这是特别有用多维尺度比较不同的解决方案。如果scale=FALSE，该功能只旋转矩阵Y。如果scale=TRUE，线性扩展配置Y最大的相似性。由于Y进行缩放以适合X，非对称的缩放。然而，symmetric=TRUE，的配置比例等于分散体和对称的版本的普鲁克统计，计算。
Instead of matrix, X and Y can be results from an ordination from which scores can extract results. Function procrustes passes extra arguments to scores, scores.cca etc. so that you can specify arguments such as scaling.
相反的矩阵，X和Y可以从一个协调结果scores可以提取结果。功能procrustes额外的参数传递到scores，scores.cca等，让您可以指定参数，如scaling。
Function plot plots a procrustes object and returns invisibly an ordiplot object so that function identify.ordiplot can be used for identifying points. The items in the ordiplot object are called heads and points with kind=1 (ordination diagram) and sites with kind=2 (residuals). In ordination diagrams, the arrow heads point to the target configuration if to.target = TRUE, and to rotated configuration if to.target = FALSE. Target and original rotated axes are shown as cross hairs in two-dimensional Procrustes analysis, and with a higher number of dimensions, the rotated axes are projected onto plot with their scaled and centred range. Function plot passes parameters to underlying plotting functions. For full control of plots, you can draw the axes using plot with kind = 0, and then add items with points or lines. These functions pass all parameters to the underlying functions so that you can select the plotting characters, their size, colours etc., or you can select the width, colour and type of line segments or arrows, or you can select the orientation and head width of arrows.
函数plot绘制procrustes对象，并返回不可见的ordiplot对象，使函数identify.ordiplot可用于识别点。 ordiplot对象中的项目被称为heads和pointskind=1（统筹图）和sites与kind=2（残值）。在统筹图，箭头头指向的目标配置如果to.target = TRUE如果to.target = FALSE，并旋转结构。目标和原始的旋转轴被示为在两维的Procrustes分析的十字准线，并具有较高的维数，旋转轴投影到积用自己的缩放和居中的范围。函数plot参数传递给潜在的绘图功能。图的完全控制，可以得出轴plot与kind = 0，然后添加项目points或lines。这些函数传递参数的基本功能，让您可以选择绘图字符，它们的大小，颜色等，或者你可以选择的宽度，颜色和类型segments或箭头，或者您也可以选择方向和头宽的arrows。
Function residuals returns the pointwise residuals, and fitted the fitted values, either centred to zero mean (if truemean=FALSE) or with the original scale (these hardly make sense if symmetric = TRUE). In addition, there are summary and print methods.
功能residuals返回逐点残差和fitted的拟合值，要么为中心，以零的意思（如果truemean=FALSE）或与原来的规模（这很难意义，如果symmetric = TRUE ）。此外，有summary和print方法。
If matrix X has a lower number of columns than matrix Y, then matrix X will be filled with zero columns to match dimensions. This means that the function can be used to rotate an ordination configuration to an environmental variable (most practically extracting the result with the fitted function). Function predict can be used to add new rotated coordinates to the target. The predict function will always translate coordinates to the original non-centred matrix. The function canot be used with newdata for symmetric analysis.
如果矩阵X具有较低的列数比矩阵Y，然后矩阵X将充满了零列，以符合尺寸。这意味着该函数可以被用来旋转协调配置环境变量（最实际提取的结果与fitted函数）。功能predict可以用来添加新的旋转坐标的目标。 predict函数将总是翻译的原非中心矩阵的坐标。的功能canot使用newdatasymmetric分析。
Function protest calls procrustes(..., symmetric = TRUE) repeatedly to estimate the "significance" of the Procrustes statistic. Function protest uses a correlation-like statistic derived from the symmetric Procrustes sum of squares ss as r =√{(1-ss)}, and sometimes called m_{12}. Function protest has own print method, but otherwise uses procrustes methods. Thus plot with a protest object yields a &ldquo rocrustean superimposition plot.”
功能protest调用procrustes(..., symmetric = TRUE)反复的普鲁克统计估计的“意义”。函数protest使用了相关的统计数据来自对称的Procrustes的平方ssr =√{(1-ss)}，有时也被称为m_{12}。功能protest有自己的print方法，但以其他方式使用procrustes方法。因此plot与protest对象产生一个“削足适履叠加图”。
值----------Value----------
Function procrustes returns an object of class procrustes with items. Function protest inherits from procrustes, but amends that with some new items:
功能procrustes返回的对象的类procrustes的项目。功能protest继承自procrustes，但修订了一些新的项目：
参数：Yrot
Rotated matrix Y.
旋转矩阵Y。
参数：X
Target matrix.
目标矩阵。
参数：ss
Sum of squared differences between X and Yrot.
之间的差异X和Yrot的平方和。
参数：rotation
Orthogonal rotation matrix.
正交旋转矩阵。
参数：translation
Translation of the origin.
翻译的由来。
参数：scale
Scaling factor.
比例因子。
参数：xmean
The centroid of the target.
目标的质心。
参数：symmetric
Type of ss statistic.
类型ss统计。
参数：call
Function call.
函数调用。
参数：t0
This and the following items are only in class protest: Procrustes correlation from non-permuted solution.
这与下列项目只在类protest：Procrustes从非置换解决方案的相关性。
参数：t
Procrustes correlations from permutations.
Procrustes上的相关性排列。
参数：signif
"Significance" of t
意义的t
参数：permutations
Number of permutations.
的排列数目。
参数：strata
The name of the stratifying variable.
的分层的变量的名称。
参数：stratum.values
Values of the stratifying variable.
分层变量的值。
注意----------Note----------
The function protest follows Peres-Neto & Jackson (2001), but the implementation is still after Mardia et al.
的功能protest佩雷斯如下：内托和杰克逊（2001），但实施后仍然Mardia等。
（作者）----------Author(s)----------
Jari Oksanen
参考文献----------References----------
J.M. (1979). Multivariate Analysis. Academic Press.
data sets match? The advantages of a Procrustean superimposition approach over the Mantel test. Oecologia 129: 169-178.
参见----------See Also----------
monoMDS, for obtaining objects for procrustes, and mantel for an
monoMDS获得对象procrustes和mantel的，
实例----------Examples----------
data(varespec)
vare.dist <- vegdist(wisconsin(varespec))
mds.null <- monoMDS(vare.dist, y = cmdscale(vare.dist))
mds.alt <- monoMDS(vare.dist)
vare.proc <- procrustes(mds.alt, mds.null)
vare.proc
summary(vare.proc)
plot(vare.proc)
plot(vare.proc, kind=2)
residuals(vare.proc)
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。
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发表于 2012-10-1 15:11:38
