Internal vegan functions that are not intended to be called directly, but only within other functions.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ordiGetData(call, env)
ordiParseFormula(formula, data, xlev = NULL, na.action = na.fail,
subset = NULL)
ordiTerminfo(d, data)
ordiNAexclude(x, excluded)
ordiNApredict(omit, x)
ordiArgAbsorber(..., shrink, origin, scaling, triangular,
display, choices, const, truemean, FUN)
centroids.cca(x, mf, wt)
getPermuteMatrix(perm, N, strata = NULL)
howHead(x, ...)
pasteCall(call, prefix = "Call:")
veganCovEllipse(cov, center = c(0, 0), scale = 1, npoints = 100)
veganMahatrans(x, s2, tol = 1e-8)
hierParseFormula(formula, data)
|
The description here is only intended for vegan
developers: these functions are not intended for users, but they
only should be used within functions. In general, these functions
are not exported to the namespace, but you must use
get
or :::
to directly call these
functions.
ordiGetData
finds the model frame of constraints and
conditions in constrained ordination in the defined
env
ironment. ordiParseFormula
returns a list of three
matrices (dependent variables, and model.matrix
of
constraints and conditions, possibly NULL
) needed in
constrained ordination. Argument xlev
is passed to
model.frame
. ordiTermInfo
finds the term
information for constrained ordination as described in
cca.object
. ordiNAexclude
implements
na.action = na.exclude
for constrained ordination finding WA
scores of CCA components and site scores of unconstrained component
from excluded
rows of observations. Function
ordiNApredict
pads the result object with these or with
WA scores similarly as napredict
.
ordiArgAbsorber
absorbs arguments of scores
function of vegan so that these do not cause superfluous
warnings in graphical function FUN
. If you implement
scores
functions with new arguments, you should update
ordiArgAbsorber
.
centroids.cca
finds the weighted centroids of variables.
getPermuteMatrix
interprets user input and returns a
permutation matrix where each row gives indices of observations for
a permutation. The input perm
can be a single number for the
number of simple permutations, a result of
how
defining a permutation scheme or a
permutation matrix. Function permuted.index
was used earlier
to generate permutations, but it is now deprecated.
howHead
formats the permutation scheme of
how
for display. The formatting is more
compact than the one used in print
in the permute
package, and shows only non-default choices. This output is normally
used when printing the results of vegan permutations.
pasteCall
prints the function call so that it is nicely wrapped
in Sweave
output.
veganCovEllipse
finds the coordinates for drawing a
covariance ellipse.
veganMahatrans
transforms data matrix so that its Euclidean
distances are Mahalanobis distances. The input data x
must be
a matrix centred by columns, and s2
its covariance matrix. If
s2
is not given, covariance matrix is found from x
within the function.
hierParseFormula
returns a list of one matrix (left hand side)
and a model frame with factors representing hierarchy levels
(right hand side) to be used in adipart
,
multipart
and hiersimu
.
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