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Last data update: 2014.03.03

R: Variables dendrogram

dendro.variables

R Documentation

Variables dendrogram

Description

Get dendrogram for variables of mixed types

Usage

dendro.variables(data, dist.variables.method = c("associationMeasures", "ClustOfVar"), 
  associationFun = association, check.psd = TRUE)

Arguments

`data`	data frame with variables of interest
`dist.variables.method`	If `"associationMeasures"`, similarities between variables are assessed by combination of appropriate measures of association for different pairs of data types. Then a dendrogram is derived by standard hierarchical clustering (`hclust` with default options). If `"ClustOfVar"`, variables are clustered by the `ClustOfVar{ClustOfVar}` approach.
`associationFun`	By default, appropriate association measures are chosen for each pair of variables, see `association` for details. But the user can also define a function that for any two variables calculates a similarity measure. Ignored if `dist.variables.method = "ClustOfVar"`
`check.psd`	If `TRUE`, it is checked if the variable's similarity matrix S is positive semi-definite (p.s.d.), and if not it is transformed to a p.s.d. one by `nearPD`, see `dist.variables` for details. Ignored if `dist.variables.method = "ClustOfVar"`

Details

Clustering of variables can either be done similarity-based or by the ClustOfVar approach, which uses principal components analysis for mixed data.

Value

An object of class dendrogram

Author(s)

Manuela Hummel

References

Chavent M, Kuentz-Simonet V, Liquet B, Saracco J (2012). ClustOfVar: An R Package for the Clustering of Variables. Journal of Statistical Software, 50:1-16.

Examples

data(mixdata)

dend <- dendro.variables(mixdata)
plot(dend)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(CluMix)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/CluMix/dendro.variables.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dendro.variables
> ### Title: Variables dendrogram
> ### Aliases: dendro.variables
> ### Keywords: cluster
> 
> ### ** Examples
> 
> data(mixdata)
> 
> dend <- dendro.variables(mixdata)
> plot(dend)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>