compare: Compare proxies across two data sets

In analogue: Analogue and Weighted Averaging Methods for Palaeoecology

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, ...)

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

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.

Details

ToDo

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.

Author(s)

Gavin L. Simpson

Examples

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

analogue documentation built on June 21, 2021, 1:08 a.m.