analogue (version 0.3-3)

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:
• distances
  a matrix of distances/dissimilarities. Individual columns contain the ordered close modern analogues for individual fossil samples. Rows of this matrix refer to the $k^{\mathrm{th}}$ closest analogue for each fossil sample. See notes below.
• samples
  a matrix of sample names from the reference set that are close modern analogues for a fossil sample. Individual columns contain the ordered close modern analogues for individual fossil samples. Rows of this matrix refer to the $k^{\mathrm{th}}$ closest analogue for each fossil sample. See notes below.
• cutoff
  the cutoff threshold used to define close modern analogues.
• quant
  numeric vector of the requested quantiles.
• probs
  the probabilities of the requested quantiles.
• method
  character; the dissimilarity coefficient used
• n.analogs
  numeric vector of the number of analogues per fossil sample.

Warning

The matrix representation of the returned objects "distances" and "samples" is used for convenience only. Do not attempt to compare values across rows between columns.

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.

See Also

analog

Examples

## 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)