Profile pairs

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.

Side Effects

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

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.)

References

Bates and Watts (1988). Nonlinear Regression Analysis and Its Applications. Wiley. doi:10.1002/9780470316757 .

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")
#> <environment: namespace:MASS>
   
 graphics::pairs(Pur.prof)