scores.prcurve: 'scores' method for principal curve objects of class...

In analogue: Analogue and Weighted Averaging Methods for Palaeoecology

scores method for principal curve objects of class "prcurve".

Description

A scores method to extract the position on the curve to which each observation projects (display = "curve") or the coordinates of the curve in the dimensions of the input data (display = "dimensions").

Usage

## S3 method for class 'prcurve'
scores(x, display = c("curve", "dimensions"), ...)

Arguments

x	an object of class "prcurve", usually from a call to prcurve.
display	character; which type of scores to extract. display = "curve" returns the position along the curve onto which each observation projects; this can be used like a PCA axis score. display = "dimensions" returns the coordinates of the curve in the dimensions of the original data.
...	Arguments passed to other methods. Not used.

Value

If display = "curve" a 1-column matrix is returned with a row for each observation in the input data. If display = "dimensions", a matrix of coordinates for the principal curve is returned. The dimensions of this matrix relate to the dimensions of the input data; if there were n samples (rows) and m variables (columns) then the matrix returned by scores.prcurve will have n rows and m columns.

Author(s)

Gavin L. Simpson

See Also

prcurve for fitting principal curves to data.

Examples

## Load the Abernethy Forest data set
data(abernethy)

## Remove the Depth and Age variables
abernethy2 <- abernethy[, -(37:38)]

## Fit the principal curve using varying complexity of smoothers
## for each species
aber.pc <- prcurve(abernethy2, method = "ca", trace = TRUE,
                   vary = TRUE, penalty = 1.4)

## Extract position on the curve
pos <- scores(aber.pc, display = "curve")
head(pos)

## Extract the coordinates of the curve
coord <- scores(aber.pc, display = "dimensions")
dim(coord)
all.equal(dim(coord), dim(abernethy2))

analogue documentation built on Sept. 30, 2024, 9:41 a.m.