pairs.profile: Profile pairs

In ellipse: Functions for Drawing Ellipses and Ellipse-Like Confidence Regions

Profile pairs

Description

This function produces pairwise plots of profile traces, profile sketches, and ellipse approximations to confidence intervals.

Usage

pairs_profile(x, labels = c(names(x), "Profile tau"), panel = lines, invert = TRUE, 
    plot.tau = TRUE, plot.trace = TRUE, plot.sketch = TRUE, 
	plot.ellipse = FALSE, level = 0.95, ...)
	
# Deprecated generic function.  Use graphics::pairs instead.
pairs(x, ...)

Arguments

x	An object of class profile, generally the result of the profile() function.
labels	The labels to use for each variable. These default to the variable names.
panel	The function to use to draw the sketch in each panel.
invert	Whether to swap the axes so things look better.
plot.tau	Whether to do the profile tau (profile t) plots.
plot.trace	Whether to do the profile trace plots.
plot.sketch	Whether to do the profile sketch plots.
plot.ellipse	Whether to do the ellipse approximations.
level	The nominal confidence level for the profile sketches and ellipses.
...	Other plotting parameters.

Details

This function implements the plots used in Bates and Watts (1988) for nonlinear regression diagnostics.

Prior to ellipse version 0.5, the pairs_profile function was a profile method for the pairs generic. This caused various conflicts, because graphics also exports a pairs generic, and package MASS exported a profile method for graphics::pairs. As of R version 4.4.0, the MASS method will be in stats instead.

If x is a profile object then pairs_profile(x) will call the function from this package. If you'd rather use the MASS/stats method, then make sure the appropriate package is loaded, and call pairs(x). (Prior to ellipse 0.5, there were complicated rules to determine what pairs(x) would do; those should still work for now, but ellipse::pairs will disappear in a future release.)

Side Effects

Produces a plot on the current device for each pair of variables in the profile object.

References

Bates and Watts (1988). Nonlinear Regression Analysis and Its Applications. Wiley. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/9780470316757")}.

See Also

pairs, profile, ellipse.profile, ellipse.nls

Examples

 # Plot everything for the Puromycin data
 data(Puromycin)
 Purboth <- nls(formula = rate ~ ((Vm + delV * (state == "treated"))
   * conc)/(K + conc), data = Puromycin,
   start = list(Vm = 160, delV = 40, K = 0.05))
 Pur.prof <- profile(Purboth)
 pairs_profile(Pur.prof, plot.ellipse = TRUE)
 
 # Show the corresponding plot from MASS/stats:
 if (getRversion() < "4.4.0") {
   loadNamespace("MASS")
 } else
   loadNamespace("stats")
   
 graphics::pairs(Pur.prof)

ellipse documentation built on July 26, 2023, 6:10 p.m.