refine {kairos} | R Documentation |
Refine CA-based Seriation
Description
Refine CA-based Seriation
Usage
refine(object, ...)
## S4 method for signature 'AveragePermutationOrder'
refine(object, cutoff, margin = 1, axes = 1, n = 30, ...)
## S4 method for signature 'BootstrapCA'
refine(object, cutoff, margin = 1, axes = 1, ...)
Arguments
object |
A |
... |
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 |
axes |
An |
n |
A non-negative |
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")
.
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.
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. doi:10.1016/j.jas.2012.04.040.
See Also
Other seriation methods:
as_seriation()
,
assess()
,
order()
,
permute()
,
seriate_average()
,
seriate_rank()