cma {analogue} | R Documentation |
Extracts and formats close modern analogue samples from a modern reference set that are closer than a defined cut off threshold.
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")
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. |
The plot method is simply a wrapper to stripchart
.
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. |
Currently, only objects of class analog
are supported.
The plot method invisibly returns a list with the following components:
distances
object
.groups
Gavin L. Simpson
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.
analog
, stripchart
, or
boxplot
for an alternative representation.
## 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)