cma {analogue}R Documentation

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, ...)

## Default S3 method:
cma(object, ...)

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

## S3 method for class 'cma':
plot(x, method = c("overplot", "jitter", "stack"),
   jitter = 0.1, vertical = FALSE,
   draw.quant = TRUE, xlab = NULL, ylab = "",
   main = "", cex.axis = NULL, ...,
   col.quant = "red", lty.quant= "dashed")

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$train is NULL, in which case "cutoff" must be supplied.
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 or additional arguments passed to stripchart.
x an object of class "cma".
method the method to be used to separate coincident points. The default method
"overplot" causes such points to be overplotted, but it is also possible to specify "jitter" to jitter the points, or "stack" have coincident points stacked. The last method only makes sense for very granular data.
jitter when method="jitter" is used, jitter gives the amount of jittering applied.
vertical when vertical is TRUE the plots are drawn vertically rather than the default horizontal.
draw.quant logical; should the quantiles be drawn on the stripchart?
xlab,ylab,main Graphical parameters
cex.axis The magnification to be used for axis annotation relative to the current setting of cex. See par.
col.quant,lty.quant colour and line type in which to drawn the quantile lines.

Details

The plot method is simply a wrapper to stripchart.

Value

For the plot method, a plot on the current device. Invisibly the plotted data are returned; see Note for further details.
A list of class "cma" with the following components:

close a 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.
call the matched call.
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.

Note

Currently, only objects of class analog are supported.

The plot method invisibly returns a list with the following components:

Author(s)

Gavin L. Simpson

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, stripchart, or boxplot for an alternative representation.

Examples

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

## select only the preindustrial reference condition samples
## from the RLGH core
rlgh.ref <- rlgh[25:37, ]

## analog matching between SWAP and RLGH reference samples
swap.ana <- analog(swapdiat, rlgh.ref, method = "chord")
swap.ana

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

## plot the results
plot(swap.cma)

[Package analogue version 0.6-6 Index]