R: Variablewise statistics for clusters

cluster.varstats {fpc} | R Documentation

## Variablewise statistics for clusters

### Description

This function gives some helpful variable-wise information for cluster interpretation, given a clustering and a data set. The output object contains some tables. For categorical variables, tables compare clusterwise distributions with overall distributions. Continuous variables are categorised for this.

If desired, tables, histograms, some standard statistics of continuous variables and validation plots as available through `discrproj` (Hennig 2004) are given out on the fly.

### Usage

    cluster.varstats(clustering,vardata,contdata=vardata,
                                 clusterwise=TRUE,
                                tablevar=NULL,catvar=NULL,
                                 quantvar=NULL, catvarcats=10,
                                 proportions=FALSE,
                                projmethod="none",minsize=ncol(contdata)+2,
                              ask=TRUE,rangefactor=1)

    ## S3 method for class 'varwisetables'
    print(x,digits=3,...)

### Arguments

`clustering` | vector of integers. Clustering (needs to be in standard coding, 1,2,...).
`vardata` | data matrix or data frame of which variables are summarised.
`contdata` | variable matrix or data frame, normally all or some variables from `vardata`, on which cluster visualisation by projection methods is performed unless `projmethod="none"`. It should make sense to interpret these variables in a quantitative (interval-scaled) way.
`clusterwise` | logical. If `FALSE`, only the output tables are computed but no more detail and graphs are given on the fly.
`tablevar` | vector of integers. Numbers of variables treated as categorical (i.e., no histograms and statistics, just tables) if `clusterwise=TRUE`. Note that an error will be produced by factor type variables unless they are declared as categorical here.
`catvar` | vector of integers. Numbers of variables to be categorised by proportional quantiles for table computation. Recommended for all continuous variables.
`quantvar` | vector of integers. Variables for which means, standard deviations and quantiles should be given out if `clusterwise=TRUE`.
`catvarcats` | integer. Number of categories used for categorisation of variables specified in `quantvar`.
`proportions` | logical. If `TRUE`, output tables contain proportions, otherwise numbers of observations.
`projmethod` | one of `"none"`, `"dc"`, `"bc"`, `"vbc"`, `"mvdc"`, `"adc"`, `"awc"` (recommended if not `"none"`), `"arc"`, `"nc"`, `"wnc"`, `"anc"`. Cluster validation projection method introduced in Hennig (2004), passed on as `method` argument in `discrproj`.
`minsize` | integer. Projection is not carried out for clusters with fewer points than this. (If this is chosen smaller, it may lead to errors with some projection methods.)
`ask` | logical. If `TRUE`, `par(ask=TRUE)` is set in the beginning to prompt the user before plots and `par(ask=FALSE)` in the end.
`rangefactor` | numeric. Factor by which to multiply the range for projection plot ranges.
`x` | an object of class `"varwisetables"`, output object of `cluster.varstats`.
`digits` | integer. Number of digits after the decimal point to print out.
`...` | not used.

### Value

An object of class `"varwisetables"`, which is a list with a table for each variable, giving (categorised) marginal distributions by cluster.

### Author(s)

Christian Hennig c.hennig@ucl.ac.uk http://www.homepages.ucl.ac.uk/~ucakche

### References

Hennig, C. (2004) Asymmetric linear dimension reduction for classification. Journal of Computational and Graphical Statistics 13, 930-945 .

### Examples

      set.seed(112233)
      options(digits=3)
      require(MASS)
      require(flexmix)
      data(Cars93)
      Cars934 <- Cars93[,c(3,5,8,10)]
      cc <-
        discrete.recode(Cars934,xvarsorted=FALSE,continuous=c(2,3),discrete=c(1,4))
      fcc <- flexmix(cc$data~1,k=2,
      model=lcmixed(continuous=2,discrete=2,ppdim=c(6,3),diagonal=TRUE))
      cv <-
        cluster.varstats(fcc@cluster,Cars934, contdata=Cars934[,c(2,3)],
        tablevar=c(1,4),catvar=c(2,3),quantvar=c(2,3),projmethod="awc",
        ask=FALSE)
      print(cv)

[Package fpc version 2.1-10 Index]