refine: Refine CA-based Seriation

Description

Refine CA-based Seriation

Usage

refine(object, ...)
# S4 method for AveragePermutationOrder
refine(object, cutoff, margin = 1, axes = 1, n = 30, ...)
# S4 method for BootstrapCA
refine(object, cutoff, margin = 1, axes = 1, ...)

Value

A list with the following elements:

length: A numeric vector giving the convex hull maximum dimension length.
cutoff: A numeric value giving the cutoff value for samples selection.
exclude: An integer vector giving the subscript of the observations to be removed.
margin: A numeric value specifying the dimension along which the refinement procedure has been applied: 1 indicates rows, 2 indicates columns.

Arguments

object: A PermutationOrder object (typically returned by seriate_average()) or a dimensio::BootstrapCA object (typically returned by dimensio::bootstrap()).
...: Currently not used.
cutoff: A function that takes a numeric vector as argument and returns a single numeric value (see below).
margin: A length-one numeric vector giving the subscripts which the refinement will be applied over: 1 indicates rows, 2 indicates columns.
axes: An integer vector giving the subscripts of the CA axes to be used.
n: A non-negative integer giving the number of bootstrap replications.

Author

N. Frerebeau

Details

refine() allows to identify samples that are subject to sampling error or samples that have underlying structural relationships and might be influencing the ordering along the CA space.

This relies on a partial bootstrap approach to CA-based seriation where each sample is replicated n times. The maximum dimension length of the convex hull around the sample point cloud allows to remove samples for a given cutoff value.

According to Peebles and Schachner (2012), "[this] point removal procedure [results in] a reduced dataset where the position of individuals within the CA are highly stable and which produces an ordering consistent with the assumptions of frequency seriation."

See vignette("seriation").

References

Peeples, M. A., & Schachner, G. (2012). Refining correspondence analysis-based ceramic seriation of regional data sets. Journal of Archaeological Science, 39(8), 2818-2827. tools:::Rd_expr_doi("10.1016/j.jas.2012.04.040").