compare | R Documentation |
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.
compare(x, ...)
## Default S3 method:
compare(x, y, env,
by = c("sites", "species"),
ordination = "rda",
method = "chord",
transform = NULL,
n2limit = 5L,
...)
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 |
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
|
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 |
... |
arguments passed to other methods. |
ToDo
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 |
sumPoorOpt |
numeric; abundance sum for species with potentially poorly estimated optima. |
closestSamp |
numeric; minimum dissimilarity to a sample
in the training data |
residLen |
numeric; the squared residual length for each
sample in |
inTrain |
logical; simple indicator of whether a species
in |
n2 |
numeric; Hill's N2 for each species in |
n2Train |
numeric; as for |
max |
numeric; the maximum abundance of each species
computed using |
maxTrain |
numeric; as for |
Gavin L. Simpson
data(ImbrieKipp, V12.122, SumSST)
compare(ImbrieKipp, V12.122, env = SumSST, ordination = "rda",
method = "chord")
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