R语言 hopach包 correlationordering()函数中文帮助文档(中英文对照)

loveR

correlationordering(hopach)
correlationordering()所属R语言包：hopach

                                        function to compute empirical correlation between distance in a list and distance by a metric
                                         函数来计算之间的距离在列表和距离度量的经验关系

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Given a matrix of pair wise distances based on a choice of distance metric, correlationordering computes the empirical correlation (over all pairs of elements) between the distance apart in the rows/columns of the matrix and the distance according to the metric. Correlation ordering will be high if elements close to each other in the matrix have small pair wise distances. If the rows/columns of the distance matrix are ordered according to a clustering of the elements, then correlation ordering should be large compared to a matrix with randomly ordered rows/columns.
鉴于成对距离的基础上，选择距离度量矩阵，correlationordering计算矩阵中的行/列的距离和距离之间的经验关系（以上所有元素对）根据度量。矩阵中的元素彼此接近，如果有小成对距离，相关订货会很高。如果距离矩阵的行/列排序，根据元素的聚类，那么相关的顺序应该是比较大随机排列的行/列的矩阵。


用法----------Usage----------


correlationordering(dist)

improveordering(dist,echo=FALSE)



参数----------Arguments----------

参数：dist
matrix of all pair wise distances between a set of 'p' elements,  as produced, for example, by the distancematrix function.  The value in row 'j' and column 'i' is the distance between element 'i' and element 'j'. The matrix must be symmetric. The ordering of the rows/ columns is compared to the values in the matrix.
矩阵成对一套p的元素，如生产，例如distancematrix函数之间的距离。行“J”和列值我元素i和元素J之间的距离。矩阵必须是对称的。行/列的顺序比较矩阵的值。


参数：echo
indicator of whether the value of correlation ordering before and after rearranging the ordering should be printed.
是否应印有相关的价值顺序重新排列顺序前后的指标。


Details

详情----------Details----------

Correlation ordering is defined as the empirical correlation between distance in a list and distance according to some other metric. The value in row 'i' and column 'j' of dist is compared to 'j-i'. The function correlationordering computes the correlation ordering for a matrix dist, whereas the function improveordering swaps the ordering of elements in dist until doing so no longer improves correlation ordering. The algorithm for improveordering is not optimized, so that the function can be quite slow for more than 50 elements. These functions are used by the hopach clustering function to sensibly order the clusters in the first level of the hierarchical tree, and can also be used to order elements within clusters when the number of elements is not too large.
相关排序是根据其他一些度量定义列表和距离之间的距离的经验关系。行i和列Jdist价值相比，J-。功能correlationordering计算相关矩阵dist订购，而功能improveordering掉dist直到做所以不再提高相关排序元素的顺序。在算法improveordering“不优化，使功能可以超过50个元素是相当缓慢的。 hopach聚类功能明智地下令在聚类的层次树的第一级使用这些功能，也可用于聚类内订购的元素时，元素的数目不算太大。


值----------Value----------

For correlationordering, a number between -1 and 1, as returned by the cor function, equal to the correlation ordering for the matrix dist.
correlationordering，，cor函数返回-1和1之间的数，等于相关矩阵dist的订货。

For improveordering, a vector of length 'p' containing the row indices for the new ordering of the rows/columns of dist, so that dist[improveordering(dist)] now has higher correlation ordering.
improveordering，矢量长度P包含dist，使区[improveordering（区）]现在已经较高的相关性排序的行/列新订购的排指数。


警告----------Warning ----------

The function improveordering can be very slow for more than about 50 elements. The method employed is a greedy, step-wise algorithm, in which sequentially swaps all pairs of elements and accepts any swap that improves correlation ordering.
函数improveordering可能会很慢了约50个元素。采用的方法是一个贪婪，分步进行算法，对所有元素，并在其中依次互换接受任何交换，提高相关排序。


作者（S）----------Author(s)----------


Katherine S. Pollard <kpollard@gladstone.ucsf.edu> and Mark J. van der Laan <laan@stat.berkeley.edu>



参考文献----------References----------




参见----------See Also----------

distancematrix, hopach
distancematrix，hopach


举例----------Examples----------


mydata<-matrix(rnorm(50),nrow=10)
mydist<-distancematrix(mydata,d="euclid")
image(as.matrix(mydist))
correlationordering(mydist)
neword<-improveordering(mydist,echo=TRUE)
correlationordering(mydist[neword,neword])
image(as.matrix(mydist[neword,neword]))

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。