Calculates the OPTICS cordillera as described in Rusch et al. (2017). Needs 'ELKI' >=0.6.0 - only tested with the Ubuntu binaries. This is an old implementation of the OPTICS Cordillera that relied on an external OPTICS implementation; since there is now an R package with an optics function the code has been re-factored. Only works with data matrices and Euclidean distance - cordillera is more general.
e_cordillera(confs, q = 1, minpts = 2, epsilon, dmax = NULL, rang,
digits = 10, path = tempdir(), plot = FALSE, ylim, scale = 1, ...)A list with the elements
$raw... The raw cordillera
$norm... The normalization constant
$normfac... The normalization factor (the number of times that dmax is taken)
$dmax... The maximum distance used for maximum structure
$normed... The normed cordillera (raw/norm)
$optics... The optics object
numeric matrix or data frame.
the norm of the OPTICS Cordillera. Defaults to 1.
the minpts argument to elki. Defaults to 2.
The epsilon parameter for OPTICS. Defaults to 2 times the range of x.
The winsorization value for the highest allowed reachability. If used for comparisons this should be supplied. If no value is supplied, it is NULL (default), then dmax is taken from the data as minimum of epsilon or the largest reachability.
(old parameter) A range of values for making up dmax. If supplied it overrules the dmax parameter and rang[2]-rang[1] is returned as dmax in the object. If no value is supplied rang is taken to be (0, dmax) taken from the data.
round the raw OPTICS cordillera and the norm factor to these digits. Defaults to 10.
the path for storing the temporary files I/O files for optics. Defaults to tempdir(). In any other case it prompts the user for confirmation.
plot the reachability and the raw OPTICS Cordillera
The borders for the OPTICS Cordillera plot
Should the confs be scaled and/or centered? 0 does nothing, 1 does both, 2 only scales with the root mean square.
Additional arguments to be passed to optics
It may happen that the (normed) cordillera cannot be calculated properly (e.g. division by zero, infinite 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.