eigenvals {vegan} | R Documentation |
Extract Eigenvalues from an Ordination Object
Description
Function extracts eigenvalues from an object that has them. Many multivariate methods return such objects.
Usage
eigenvals(x, ...)
## S3 method for class 'cca'
eigenvals(x, model = c("all", "unconstrained", "constrained"),
constrained = NULL, ...)
## S3 method for class 'decorana'
eigenvals(x, kind = c("additive", "axiswise", "decorana"),
...)
## S3 method for class 'eigenvals'
summary(object, ...)
Arguments
x |
An object from which to extract eigenvalues. |
object |
An |
model |
Which eigenvalues to return for objects that inherit from class
|
constrained |
Return only constrained eigenvalues. Deprecated as of vegan
2.5-0. Use |
kind |
Kind of eigenvalues returned for |
... |
Other arguments to the functions (usually ignored) |
Details
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.
Value
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.
Author(s)
Jari Oksanen.
References
Gower, J. C. (1985). Properties of Euclidean and non-Euclidean distance matrices. Linear Algebra and its Applications 67, 81–97.
See Also
eigen
, svd
, prcomp
,
princomp
, cca
, rda
,
capscale
, wcmdscale
,
cca.object
.
Examples
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")