validationplot: Validation Plots

In pls: Partial Least Squares and Principal Component Regression

Validation Plots

Description

Functions to plot validation statistics, such as RMSEP or R^2, as a function of the number of components.

Usage

validationplot(
  object,
  val.type = c("RMSEP", "MSEP", "R2"),
  estimate,
  newdata,
  ncomp,
  comps,
  intercept,
  ...
)

## S3 method for class 'mvrVal'
plot(
  x,
  nCols,
  nRows,
  type = "l",
  lty = 1:nEst,
  lwd = par("lwd"),
  pch = 1:nEst,
  cex = 1,
  col = 1:nEst,
  legendpos,
  xlab = "number of components",
  ylab = x$type,
  main,
  ask = nRows * nCols < nResp && dev.interactive(),
  ...
)

Arguments

object	an mvr object.
val.type	character. What type of validation statistic to plot.
estimate	character. Which estimates of the statistic to calculate. See RMSEP.
newdata	data frame. Optional new data used to calculate statistic.
ncomp, comps	integer vector. The model sizes to compute the statistic for. See RMSEP.
intercept	logical. Whether estimates for a model with zero components should be calculated as well.
...	Further arguments sent to underlying plot functions.
x	an mvrVal object. Usually the result of a RMSEP, MSEP or R2 call.
nCols, nRows	integers. The number of coloumns and rows the plots will be laid out in. If not specified, plot.mvrVal tries to be intelligent.
type	character. What type of plots to create. Defaults to "l" (lines). Alternative types include "p" (points) and "b" (both). See plot for a complete list of types.
lty	vector of line types (recycled as neccessary). Line types can be specified as integers or character strings (see par for the details).
lwd	vector of positive numbers (recycled as neccessary), giving the width of the lines.
pch	plot character. A character string or a vector of single characters or integers (recycled as neccessary). See points for all alternatives.
cex	numeric vector of character expansion sizes (recycled as neccessary) for the plotted symbols.
col	character or integer vector of colors for plotted lines and symbols (recycled as neccessary). See par for the details.
legendpos	Legend position. Optional. If present, a legend is drawn at the given position. The position can be specified symbolically (e.g., legendpos = "topright"). This requires >= 2.1.0. Alternatively, the position can be specified explicitly (legendpos = t(c(x,y))) or interactively (legendpos = locator()). This only works well for plots of single-response models.
xlab, ylab	titles for x and y axes. Typically character strings, but can be expressions (e.g., expression(R^2) or lists. See title for details.
main	optional main title for the plot. See Details.
ask	logical. Whether to ask the user before each page of a plot.

Details

validationplot calls the proper validation function (currently MSEP, RMSEP or R2) and plots the results with plot.mvrVal. validationplot can be called through the mvr plot method, by specifying plottype = "validation".

plot.mvrVal creates one plot for each response variable in the model, laid out in a rectangle. It uses matplot for performing the actual plotting. If legendpos is given, a legend is drawn at the given position.

The argument main can be used to specify the main title of the plot. It is handled in a non-standard way. If there is only on (sub) plot, main will be used as the main title of the plot. If there is more than one (sub) plot, however, the presence of main will produce a corresponding ‘global’ title on the page. Any graphical parametres, e.g., cex.main, supplied to coefplot will only affect the ‘ordinary’ plot titles, not the ‘global’ one. Its appearance can be changed by setting the parameters with par, which will affect both titles. (To have different settings for the two titles, one can override the par settings with arguments to the plot function.)

Note

legend has many options. If you want greater control over the appearance of the legend, omit the legendpos argument and call legend manually.

Author(s)

Ron Wehrens and Bjørn-Helge Mevik

See Also

mvr, plot.mvr, RMSEP, MSEP, R2, matplot, legend

Examples

data(oliveoil)
mod <- plsr(sensory ~ chemical, data = oliveoil, validation = "LOO")
## Not run: 
## These three are equivalent:
validationplot(mod, estimate = "all")
plot(mod, "validation", estimate = "all")
plot(RMSEP(mod, estimate = "all"))
## Plot R2:
plot(mod, "validation", val.type = "R2")
## Plot R2, with a legend:
plot(mod, "validation", val.type = "MSEP", legendpos = "top") # R >= 2.1.0

## End(Not run)

pls documentation built on Sept. 16, 2024, 1:07 a.m.