cma: Close modern analogues

Description

Extracts and formats close modern analogue samples from a modern reference set that are closer than a defined cut off threshold.

Usage

cma(object, ...)
## S3 method for class 'default':
cma(object, \dots)
## S3 method for class 'analog':
cma(object, cutoff, prob = c(0.01, 0.025, 0.05), ...)

Arguments

object

an object for which close modern analogues are to be returned. Currently only for objects of class analog.

cutoff

numeric; critical value determining level below which samples from the modern reference set are defined as close modern analogues. May be missing, in which case the 2.5% quantile of the training set dissimilarities is used unless object$

prob

numeric vector of probabilities with values in [0,1], for which quantiles of the distribution of training set dissimilarities will be calculated. See quantile.

...

arguments to be passed to other cma methods.

Value

A list of class "cma" with the following components:
closea named list of named vectors of close modern analogues and their dissimilarities. The names of the list components are the names of the fossil samples. The named vector in each component of close is the distances for the close modern analogues from the training set that are as close as cutoff, or closer, to the fossil sample.
callthe matched call.
cutoffthe cutoff threshold used to define close modern analogues.
quantnumeric vector of the requested quantiles.
probsthe probabilities of the requested quantiles.
methodcharacter; the dissimilarity coefficient used
n.analogsnumeric vector of the number of analogues per fossil sample.

References

Flower, R.J., Juggins, S. and Battarbee, R.W. (1997) Matching diatom assemblages in lake sediment cores and modern surface sediment samples: the implications for lake conservation and restoration with special reference to acidified systems. Hydrobiologia 344; 27--40.

Simpson, G.L., Shilland, E.M., Winterbottom, J. M. and Keay, J. (2005) Defining reference conditions for acidified waters using a modern analogue approach. Environmental Pollution 137; 119--133.

Examples

Run this code

## continue the RLGH example from ?join
example(join)

## analog matching between SWAP and RLGH core
swap.analog <- analog(swapdiat, rlgh, method = "chord")
swap.analog
summary(swap.analog)

## close modern analogues
swap.cma <- cma(swap.analog)
swap.cma
summary(swap.cma)