Revision a53065a09c3fce65a63e137deb5bccb6162e6cff authored by Matthias Templ on 18 November 2020, 20:10:02 UTC, committed by cran-robot on 18 November 2020, 20:10:02 UTC
1 parent 9ae1e67
clustCoDa.Rd
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/clustCoDa.R
\name{clustCoDa}
\alias{clustCoDa}
\alias{plot.clustCoDa}
\title{Cluster analysis for compositional data}
\usage{
clustCoDa(
x,
k = NULL,
method = "Mclust",
scale = "robust",
transformation = "pivotCoord",
distMethod = NULL,
iter.max = 100,
vals = TRUE,
alt = NULL,
bic = NULL,
verbose = TRUE
)
\method{plot}{clustCoDa}(
x,
y,
...,
normalized = FALSE,
which.plot = "clusterMeans",
measure = "silwidths"
)
}
\arguments{
\item{x}{compositional data represented as a data.frame}
\item{k}{number of clusters}
\item{method}{clustering method. One of Mclust, cmeans, kmeansHartigan,
cmeansUfcl, pam, clara, fanny, ward.D2, single, hclustComplete,
average, mcquitty, median, centroid}
\item{scale}{if orthonormal coordinates should be normalized.}
\item{transformation}{default are the isometric logratio coordinates. Can only used when distMethod
is not Aitchison.}
\item{distMethod}{Distance measure to be used. If \dQuote{Aitchison}, then transformation should be \dQuote{identity}.}
\item{iter.max}{parameter if kmeans is chosen. The maximum number of iterations allowed}
\item{vals}{if cluster validity measures should be calculated}
\item{alt}{a known partitioning can be provided (for special cluster validity measures)}
\item{bic}{if TRUE then the BIC criteria is evaluated for each single cluster as validity measure}
\item{verbose}{if TRUE additional print output is provided}
\item{y}{the y coordinates of points in the plot, optional if x is an appropriate structure.}
\item{...}{additional parameters for print method passed through}
\item{normalized}{results gets normalized before plotting. Normalization is done by z-transformation
applied on each variable.}
\item{which.plot}{currently the only plot. Plot of cluster centers.}
\item{measure}{cluster validity measure to be considered for which.plot equals \dQuote{partMeans}}
}
\value{
all relevant information such as cluster centers, cluster memberships, and
cluster statistics.
}
\description{
Clustering in orthonormal coordinates or by using the Aitchison distance
}
\details{
The compositional data set is either internally represented by orthonormal coordiantes
before a cluster algorithm is applied, or - depending on the
choice of parameters - the Aitchison distance is used.
}
\examples{
data(expenditures)
x <- expenditures
rr <- clustCoDa(x, k=6, scale = "robust", transformation = "pivotCoord")
rr2 <- clustCoDa(x, k=6, distMethod = "Aitchison", scale = "none",
transformation = "identity")
rr3 <- clustCoDa(x, k=6, distMethod = "Aitchison", method = "single",
transformation = "identity", scale = "none")
\dontrun{
require(reshape2)
plot(rr)
plot(rr, normalized = TRUE)
plot(rr, normalized = TRUE, which.plot = "partMeans")
}
}
\references{
M. Templ, P. Filzmoser, C. Reimann.
Cluster analysis applied to regional geochemical data: Problems and possibilities.
\emph{Applied Geochemistry}, \strong{23} (8), 2198--2213, 2008
Templ, M., Filzmoser, P., Reimann, C. (2008)
\emph{Cluster analysis applied to regional geochemical data: Problems and possibilities},
Applied Geochemistry, 23 (2008), pages 2198 - 2213.
}
\author{
Matthias Templ (accessing the basic features of hclust, Mclust, kmeans, etc. that
are all written by others)
}
\keyword{multivariate}
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