Isometric default transform
Compute the isometric default transform of a vector (or dataset) of compositions or amounts in the selected class.
idt(x,...)
## Default S3 method:
idt( x,... )
## S3 method for class 'acomp'
idt( x ,...)
## S3 method for class 'rcomp'
idt( x ,...)
## S3 method for class 'aplus'
idt( x ,...)
## S3 method for class 'rplus'
idt( x ,...)
## S3 method for class 'rmult'
idt( x ,...)
## S3 method for class 'ccomp'
idt( x ,...)
## S3 method for class 'factor'
idt( x ,...)
## S3 method for class 'data.frame'
idt( x ,...)
idtInv(x,orig=gsi.orig(x),...)
## Default S3 method:
idtInv( x ,orig=gsi.orig(x),...)
## S3 method for class 'acomp'
idtInv( x ,orig=gsi.orig(x), V=gsi.getV(x),...)
## S3 method for class 'rcomp'
idtInv( x ,orig=gsi.orig(x), V=gsi.getV(x),...)
## S3 method for class 'aplus'
idtInv( x ,orig=gsi.orig(x),...)
## S3 method for class 'rplus'
idtInv( x ,orig=gsi.orig(x),...)
## S3 method for class 'ccomp'
idtInv( x ,orig=gsi.orig(x),...)
## S3 method for class 'rmult'
idtInv( x ,orig=gsi.orig(x),...)
## S3 method for class 'factor'
idtInv( x ,orig=gsi.orig(x), V=gsi.getV(x),...)
## S3 method for class 'data.frame'
idtInv( x , orig=gsi.orig(x), ...)x |
a classed amount or composition, to be transformed with its
isometric 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 the generic
argument. Typically the |
V |
matrix of (transposed, inverted) logcontrasts;
together with |
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 an isometric transform expressing the geometry
in a full-rank euclidean vector space. Such a transformation is computed
by idt. For acomp the transform is ilr, for
rcomp it is ipt, for
aplus it is ilt, and for
rplus it is iit. Keep in mind that the
transform does not keep the variable names, since there is no guaranteed
one-to-one relation between the original parts and each transformed
variable.
The inverse idtInv is intended to allow for an "easy" and automatic
back-transformation, without intervention of the user. The argument orig
(the one determining the behaviour of idtInv as a generic function)
tells the function which back-transformation should be applied, and
gives the column names of orig to the back-transformed
values of x. Therefore, it is very conventient to give the original classed
data set used in the analysis as orig.
A corresponding matrix of row-vectors containing the transforms. (Exception: idt.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, doi: 10.1016/j.cageo.2006.11.017.
## Not run:
# the idt is defined by
idt <- function(x) UseMethod("idt",x)
idt.default <- function(x) x
idt.acomp <- function(x) ilr(x)
idt.rcomp <- function(x) ipt(x)
idt.aplus <- ilt
idt.rplus <- iit
## End(Not run)
idt(acomp(1:5))
idt(rcomp(1:5))
data(Hydrochem)
x = Hydrochem[,c("Na","K","Mg","Ca")]
y = acomp(x)
z = idt(y)
y2 = idtInv(z,y)
par(mfrow=c(2,2))
for(i in 1:4){plot(y[,i],y2[,i])}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.