cdt | R Documentation |
Compute the centered default transform of a (data set of) compositions or amounts (or its inverse).
cdt(x,...)
## Default S3 method:
cdt( x ,...)
## S3 method for class 'acomp'
cdt( x ,...)
## S3 method for class 'rcomp'
cdt( x ,...)
## S3 method for class 'aplus'
cdt( x ,...)
## S3 method for class 'rplus'
cdt( x ,...)
## S3 method for class 'rmult'
cdt( x ,...)
## S3 method for class 'ccomp'
cdt( x ,...)
## S3 method for class 'factor'
cdt( x ,...)
## S3 method for class 'data.frame'
cdt( x ,...)
cdtInv(x,orig=gsi.orig(x),...)
## Default S3 method:
cdtInv( x ,orig=gsi.orig(x),...)
## S3 method for class 'acomp'
cdtInv( x ,orig=gsi.orig(x),...)
## S3 method for class 'rcomp'
cdtInv( x ,orig=gsi.orig(x),...)
## S3 method for class 'aplus'
cdtInv( x ,orig=gsi.orig(x),...)
## S3 method for class 'rplus'
cdtInv( x ,orig=gsi.orig(x),...)
## S3 method for class 'rmult'
cdtInv( x ,orig=gsi.orig(x),...)
## S3 method for class 'ccomp'
cdtInv( x ,orig=gsi.orig(x),...)
## S3 method for class 'factor'
cdtInv( x ,orig=gsi.orig(x),...)
## S3 method for class 'data.frame'
cdtInv( x ,orig=gsi.orig(x),...)
x |
a classed (matrix of) amount or composition, to be transformed with its
centered default transform, or its inverse; in case of the method for |
... |
generic arguments past to underlying functions. |
orig |
a compositional object which should be mimicked
by the inverse transformation. It is used to determine the
backtransform to be used and eventually to
reconstruct the names of the parts. It is the generic
argument. Typically this argument is extracted from |
The general idea of this package is to analyse the same data with
different geometric concepts, in a fashion as similar as possible. For each of the
four concepts there exists a unique transform expressing the geometry
in a linear subspace, keeping the relation to the variables. This
unique transformation is computed by cdt
. For
acomp
the transform is clr
, for
rcomp
it is cpt
, for
aplus
it is ilt
, and for
rplus
it is iit
. Each component of the result
is identified with a unit vector in the direction of the corresponding
component of the original composition or amount. Keep in mind that the
transform is not necessarily surjective and thus variances in the
image space might be singular.
A corresponding matrix or vector containing the transforms. (Exception: cdt.data.frame can return a data.frame if the input has no "origClass"-attribute)
R. Tolosana-Delgado, K.Gerald v.d. Boogaart http://www.stat.boogaart.de
van den Boogaart, K.G. and R. Tolosana-Delgado (2008) "compositions": a unified R package to analyze Compositional Data, Computers & Geosciences, 34 (4), pages 320-338, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.cageo.2006.11.017")}.
backtransform
, idt
, clr
, cpt
, ilt
, iit
## Not run:
# the cdt is defined by
cdt <- function(x) UseMethod("cdt",x)
cdt.default <- function(x) x
cdt.acomp <- clr
cdt.rcomp <- cpt
cdt.aplus <- ilt
cdt.rplus <- iit
## End(Not run)
x <- acomp(1:5)
(ds <- cdt(x))
cdtInv(ds,x)
(ds <- cdt(rcomp(1:5)))
cdtInv(ds,rcomp(x))
data(Hydrochem)
x = Hydrochem[,c("Na","K","Mg","Ca")]
y = acomp(x)
z = cdt(y)
y2 = cdtInv(z,y)
par(mfrow=c(2,2))
for(i in 1:4){plot(y[,i],y2[,i])}
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