Function extracts eigenvalues from an object that has them. Many multivariate methods return such objects.
eigenvals(x, ...)
# S3 method for cca
eigenvals(x, model = c("all", "unconstrained", "constrained"),
constrained = NULL, ...)
# S3 method for decorana
eigenvals(x, kind = c("additive", "axiswise", "decorana"),
...)
# S3 method for eigenvals
summary(object, ...)An object of class "eigenvals", which is a vector of
eigenvalues.
The summary method returns an object of class
"summary.eigenvals", which is a matrix.
An object from which to extract eigenvalues.
An eigenvals result object.
Which eigenvalues to return for objects that inherit from class
"cca" only.
Return only constrained eigenvalues. Deprecated as of vegan
2.5-0. Use model instead.
Kind of eigenvalues returned for decorana. Only
"additive" eigenvalues can be used for reporting importances
of components in summary. "axiswise" gives the
non-additive eigenvalues, and "decorana" the decorana values
(see decorana for details).
Other arguments to the functions (usually ignored)
Jari Oksanen.
This is a generic function that has methods for cca,
wcmdscale, pcnm, prcomp,
princomp, dudi (of ade4), and
pca and pco (of
labdsv) result objects. The default method also
extracts eigenvalues if the result looks like being from
eigen or svd. Functions
prcomp and princomp contain square roots
of eigenvalues that all called standard deviations, but
eigenvals function returns their squares. Function
svd contains singular values, but function
eigenvals returns their squares. For constrained ordination
methods cca, rda and
capscale the function returns the both constrained and
unconstrained eigenvalues concatenated in one vector, but the partial
component will be ignored. However, with argument
constrained = TRUE only constrained eigenvalues are returned.
The summary of eigenvals result returns eigenvalues,
proportion explained and cumulative proportion explained. The result
object can have some negative eigenvalues (wcmdscale,
dbrda, pcnm) which correspond to
imaginary axes of Euclidean mapping of non-Euclidean distances
(Gower 1985). In these case real axes (corresponding to positive
eigenvalues) will "explain" proportion >1 of total variation, and
negative eigenvalues bring the cumulative proportion to
1. capscale will only find the positive eigenvalues
and only these are used in finding proportions. For
decorana the importances and cumulative proportions
are only reported for kind = "additive", because other
alternatives do not add up to total inertia of the input data.
Gower, J. C. (1985). Properties of Euclidean and non-Euclidean distance matrices. Linear Algebra and its Applications 67, 81--97.
data(varespec)
data(varechem)
mod <- cca(varespec ~ Al + P + K, varechem)
ev <- eigenvals(mod)
ev
summary(ev)
## choose which eignevalues to return
eigenvals(mod, model = "unconstrained")
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