cordillera2 {stops}R Documentation

Calculates the Optics cordillera

Description

Calculates the OPTICS cordillera as (Rusch et al., 2015). Needs ELKI >0.6.0 - Only tested with the ubuntu binaries. This is the old version that relied on optics; since there is now an R package for optics, the code has been refactored.

Usage

cordillera2(confs, q = 1, minpts = 2, epsilon, rang = NULL, digits = 10,
  path = getwd(), plot = FALSE, ylim, scale = TRUE, ...)

Arguments

confs

numeric matrix or data frame. This should probably be scaled to have mean=0 and variance=1.

q

the norm of the cordillera. Defaults to 1.

minpts

the minpts argument to elki. Defaults to 2.

epsilon

The epsilon parameter for OPTICS. Defaults to 2 times the range of x.

rang

A range of values that makes up dmax (dmax=max-min). If used for comparions this should be supplied. If no value is supplied, it is NULL (default). Then dmax is taken from the data as the difference between the largest reachability and the smallest reachability. In the latter case the cordillera is a "goodness-of-clusteredness" given the data, in the former case it also takes into account that the gaps between certain points may be larger which stands for more structure.

digits

round the raw corrdilrra and the norm factor to these digits. Defaults to 10.

path

the path for storing the temporary files I/O files for optics. Defaults to the current working directory.

plot

plot the reachability and the raw cordillera

ylim

The borders for the cordillera plot

scale

Should the confs be scaled to mean 0 and sd 1? Defaults to TRUE

...

Additional arguments to be passed to optics

Value

A list with the elements

Warning

It may happen that the (normed) cordillera cannot be calculated properly (e.g. division by zero, inifnite raw cordillera, q value to high etc.). A warning will be printed and the normed cordillera is either 0, 1 (if infinity is involved) or NA. In that case one needs to check one or more of the following reachability values returned from optics, minpts, eps, the raw cordillera, dmax or the normalization factor.


[Package stops version 0.0-40 Index]