seriate_refine: Refine CA-based Seriation

In kairos: Analysis of Chronological Patterns from Archaeological Count Data

Refine CA-based Seriation

Description

Refine CA-based Seriation

Usage

seriate_refine(object, ...)

## S4 method for signature 'AveragePermutationOrder'
seriate_refine(object, cutoff, margin = 1, axes = 1, n = 30, ...)

## S4 method for signature 'BootstrapCA'
seriate_refine(object, cutoff, margin = 1, axes = 1, ...)

Arguments

object	A PermutationOrder object (typically returned by seriate_average()).
...	Further arguments to be passed to internal methods.
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.

Details

seriate_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."

Value

A RefinePermutationOrder object.

Author(s)

N. Frerebeau

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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.jas.2012.04.040")}.

See Also

Other seriation methods: permute(), seriate_average(), seriate_rank()

kairos documentation built on Nov. 27, 2023, 5:08 p.m.