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), ...)
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. |
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-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-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. |
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.
Currently, only objects of class analog
are supported.
The number of rows in the returned matrices is equal to the maximum
number of close modern analogues identified for an individual fossil
sample. If no close modern analogues exist for an individual fossil
sample, then the relevant column in "distances"
will contain all
missing values and in "samples"
the string "none"
. Rows
of individual columns will be padded with missing values if the number
of close modern analogues for that sample is less than the maximum
number of close modern analogues identified for a single sample.
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.
## 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)