analogue (version 0.17-7)

compare: Compare proxies across two data sets

Description

compare() compares a proxy dataset with a training set or other data set that is considered to be the master. A range of metrics is returned, currently for samples only.

Usage

compare(x, ...)
# S3 method for default
compare(x, y, env,
        by = c("sites", "species"),
        ordination = "rda",
        method = "chord",
        transform = NULL,
        n2limit = 5L,
        ...)

Value

If by = "species" a data frame of diagnostics for each species (proxy) in y relative to x. If by = "sites", the diagnostics are for each sample (row) in y. Depending on the value of by some of the following columns will be returned

sumMissing

numeric; abundance sum for species missing from the training set x.

sumPoorOpt

numeric; abundance sum for species with potentially poorly estimated optima.

closestSamp

numeric; minimum dissimilarity to a sample in the training data x.

residLen

numeric; the squared residual length for each sample in y. A measure of how well the sample fits into the species-environment relationship of a constrained ordination. See residLen for details. Not given if env is not provided.

inTrain

logical; simple indicator of whether a species in y is present in the training data x.

n2

numeric; Hill's N2 for each species in y.

n2Train

numeric; as for n2 but computed from the training data x.

max

numeric; the maximum abundance of each species computed using y.

maxTrain

numeric; as for max but computed using the training data x.

Arguments

x

data frame; training set samples to compare against

y

data frame; passive or core samples

env

numeric vector of environmental or contraint data for residual length ordination. Ignored if by = "species".

by

character; compare data sets by sites or species (proxies).

ordination

character; which constrained ordination method to use

method

character; which dissimilarity method to use. See distance.

transform

character: should a transformation be applied to the data. Ignored.

n2limit

integer; the criterion for indicating species with potentially poorly estimated optima. The default value of 5L is one suggested by R. Telford.

...

arguments passed to other methods.

Author

Gavin L. Simpson

Details

ToDo

Examples

data(ImbrieKipp, V12.122, SumSST)
compare(ImbrieKipp, V12.122, env = SumSST, ordination = "rda",
        method = "chord")