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

Arguments

data frame; training set samples to compare against

data frame; passive or core samples

env

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

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.

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
sumMissingnumeric; abundance sum for species missing from the training set x.
sumPoorOptnumeric; abundance sum for species with potentially poorly estimated optima.
closestSampnumeric; minimum dissimilarity to a sample in the training data x.
residLennumeric; 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.
inTrainlogical; simple indicator of whether a species in y is present in the training data x.
n2numeric; Hill's N2 for each species in y.
n2Trainnumeric; as for n2 but computed from the training data x.
maxnumeric; the maximum abundance of each species computed using y.
maxTrainnumeric; as for max but computed using the training data x.

Details

ToDo

Examples

Run this code

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

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