| % File src/library/stats/man/cophenetic.Rd |
| % Part of the R package, https://www.R-project.org |
| % Copyright 1995-2014 R Core Team |
| % Distributed under GPL 2 or later |
| |
| \name{cophenetic} |
| \alias{cophenetic} |
| \alias{cophenetic.default} |
| \alias{cophenetic.dendrogram} |
| \title{Cophenetic Distances for a Hierarchical Clustering} |
| \description{ |
| Computes the cophenetic distances for a hierarchical clustering. |
| } |
| \usage{ |
| cophenetic(x) |
| \method{cophenetic}{default}(x) |
| \method{cophenetic}{dendrogram}(x) |
| } |
| \arguments{ |
| \item{x}{an R object representing a hierarchical clustering. |
| For the default method, an object of class \code{"\link{hclust}"} or |
| with a method for \code{\link{as.hclust}()} such as |
| \code{"\link[cluster]{agnes}"} in package \CRANpkg{cluster}.} |
| } |
| \details{ |
| The cophenetic distance between two observations that have been |
| clustered is defined to be the intergroup dissimilarity at which the |
| two observations are first combined into a single cluster. |
| Note that this distance has many ties and restrictions. |
| |
| It can be argued that a dendrogram is an appropriate summary of some |
| data if the correlation between the original distances and the |
| cophenetic distances is high. Otherwise, it should simply be viewed as |
| the description of the output of the clustering algorithm. |
| |
| \code{cophenetic} is a generic function. Support for classes which |
| represent hierarchical clusterings (total indexed hierarchies) can be |
| added by providing an \code{\link{as.hclust}()} or, more directly, a |
| \code{cophenetic()} method for such a class. |
| |
| The method for objects of class \code{"\link{dendrogram}"} requires |
| that all leaves of the dendrogram object have non-null labels. |
| } |
| \value{ |
| An object of class \code{"dist"}. |
| } |
| \references{ |
| Sneath, P.H.A. and Sokal, R.R. (1973) |
| \emph{Numerical Taxonomy: The Principles and Practice of Numerical |
| Classification}, p.\sspace{}278 ff; |
| Freeman, San Francisco. |
| } |
| \author{Robert Gentleman} |
| \seealso{ |
| \code{\link{dist}}, |
| \code{\link{hclust}} |
| } |
| \examples{ |
| require(graphics) |
| |
| d1 <- dist(USArrests) |
| hc <- hclust(d1, "ave") |
| d2 <- cophenetic(hc) |
| cor(d1, d2) # 0.7659 |
| |
| ## Example from Sneath & Sokal, Fig. 5-29, p.279 |
| d0 <- c(1,3.8,4.4,5.1, 4,4.2,5, 2.6,5.3, 5.4) |
| attributes(d0) <- list(Size = 5, diag = TRUE) |
| class(d0) <- "dist" |
| names(d0) <- letters[1:5] |
| d0 |
| utils::str(upgma <- hclust(d0, method = "average")) |
| plot(upgma, hang = -1) |
| # |
| (d.coph <- cophenetic(upgma)) |
| cor(d0, d.coph) # 0.9911 |
| } |
| \keyword{cluster} |
| \keyword{multivariate} |