residuals.prcurve: Residuals of a principal curve fit.
In gavinsimpson/analogue: Analogue and Weighted Averaging Methods for Palaeoecology

Description Usage Arguments Details Value Author(s) See Also Examples

Returns various representations of the residuals of a principal curve fit.

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## S3 method for class 'prcurve'
residuals(object, which = c("distance", "raw", "smooths", "pca"),
          ...)

`object`	an object of class `"prcurve"`, the result of a call to `prcurve`.
`which`	character; the type of residuals to return. See Details.
`...`	arguments passed to other methods. See Details.

Various types of residual are available for the principal curve. In a departure from the usual convention, which residuals are returned is controlled via the which argument. This is to allow users to pass a type argument to the residuals method for the function used to fit the individual smooth functions when which = "smooths".

The types of residuals available are

"distance": the default residual for a principal curve. This residual is taken as the Euclidean distance between each observations and the point on the principal curve to which it projects, in full multivariate space.
"raw": raw residuals are the basis for "distance" residuals, and are the difference between the observed and fitted values (position on the curve) for each observation in terms of each variable in the data set. These residuals are in the form of a matrix with number of observation rows and number of variables cols.
"smooths": these residuals are the result of calling residuals() on each of the smooth models fitted to the individual variables. See below for further details. A matrix of the same dimensions as for which = "raw" is returned.
"pca": similar to the raw residuals, but expressed in terms of the principal components of the input data. Hence these residuals are the difference between each observation's location in PCA space and their corresponding location on the curve.

For "smooths" residuals, what is returned is governed by the residuals method available for the smooth model fitted to the individual variables. For principal curves fitted using the smoothSpline plugin, see smooth.spline. For principal curves fitted via the smoothGAM plugin, see residuals.gam.

... can be used to pass additional arguments to these residuals methods. In particular, the type argument is commonly used to choose which type of residual is returned by the specific methods.

In the case of principal curves fitted using the plugin smoothSpline, residuals for which = "smooths" are only available if the the additional argument keep.data was specified during fitting via prcurve. See the examples for an illustration of this usage.

A vector of residual distances (which = "distance") or a matrix of residuals (for the other options).

Gavin L. Simpson

prcurve for fitting a principal curve.

  
  ## Load Abernethy Forest data set
  data(abernethy)

  ## Remove the Depth and Age variables
  abernethy2 <- abernethy[, -(37:38)]
  
  ## Fit the principal curve, preserving the data in the smooth.spline
  ## smooth functions fitted via keep.data = TRUE
  aber.pc <- prcurve(abernethy2, method = "ca", keep.data = TRUE)

  ## default "distance" residuals
  res <- resid(aber.pc)
  head(res)

  ## residuals from the underlying smooth models, also illustrates
  ## how to select specific types of residual from the individual
  ## method using argument 'type'
  res <- resid(aber.pc, which = "smooths", type = "deviance")
  dim(res)
  head(res[, 1:5])		# just show a few species residuals