On Apr 28, 2009, at 12:00 AM, Prew, Paul wrote:
Hello, I am not having success in a simple task. Using the effects
package, I would like to add reference lines at probability values
of 0.1 – 0.6 on a plot of the effects.
I have concerns that you are considering these probabilities. They are
not going to be probabilities. They are effects.
The plot command works, but following up with an abline command
produces the message “plot .new has not been called yet”, and of
course the reference lines were not added.
Looking through past R help lists, there was a similar request for
help --- trying to add an abline but “got the error "plot.new has
not been called yet".
The help list reply was
“ ?abline: "This function adds one or more straight lines through
the
current plot.", i.e. the already existing *current plot*.
So plot your data (e.g. with plot(x, y)) before adding a regression
line.”
I interpreted the above to suggest the following ---
plot(allEffects(Clean.label),ask=FALSE, alternating = TRUE,
ylab="Probability of Rating", xlab="City",main="Cleanliness Ratings
by City",
factor.names=FALSE, ticks=c(0.1,0.2,0.3,0.4,0.5,0.6))
abline(h=c(0.1,0.2,0.3,0.4,0.5,0.6))
I do not know why that is happening and you have not provided a
minimal executable example. The vectorized use of abline does succeed
in a simper example:
> plot(.5,.5)
> abline(h=c(0.1,0.2,0.3,0.4,0.5,0.6))
.... so the problem may lie in how the effects package completes its
plot function for this particular object. You ought to provide at a
minimum the results of str on that object. Perhaps it executes a
device call and then turns off the device? However I loaded the
effects package and ran that abline call after the example:
> mod.cowles <- glm(volunteer ~ sex + neuroticism*extraversion,
+ data=Cowles, family=binomial)
> eff.cowles <- allEffects(mod.cowles, xlevels=list(neuroticism=0:24,
+ extraversion=seq(0, 24, 6)))
> eff.cowles
I did not get what I expected, which would have been a single
horizontal line at 0.4 but rather got four lines roughly at 0.351,
0.378, 0.408, 0.439. Even then, I would have expected one more line
before the upper limits of that plot, which makes me think these four
lines were the results of arguments 0.3 ,0.4, 0.5, 0.6. Most R
plotting is done in the coordinate system rather than with absolute
coordinates, but perhaps the mixture of base graphics with lattice
graphis is ht eproblem
Error in int_abline(a = a, b = b, h = h, v = v, untf = untf, ...) :
plot.new has not been called yet
Less bothersome is the fact that the tick marks weren’t modified to
0.1, 0.2, 0.3, etc.
Further searching brought the panel.abline command to light, but
that didn’t produce any results, not even an error message.
plot(allEffects(Clean.label),ask=FALSE, alternating = TRUE,
+ ylab="Probability of Rating", xlab="City",main="Cleanliness
Ratings by City",
+ factor.names=FALSE, ticks=c(0.1,0.2,0.3,0.4,0.5,0.6))
panel.abline(h=c(0.1,0.2,0.3,0.4,0.5,0.6))
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
sessionInfo()
R version 2.9.0 RC (2009-04-10 r48318)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.
1252;LC_MONETARY=English_United States.
1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] tcltk grid stats graphics grDevices utils
datasets methods
[9] base
other attached packages:
[1] relimp_1.0-1 Rcmdr_1.4-9 car_1.2-13 effects_2.0-4
[5] colorspace_1.0-0 nnet_7.2-46 MASS_7.2-46 lattice_0.17-22
loaded via a namespace (and not attached):
[1] tools_2.9.0
Thank you for any advice.
Paul
Paul Prew ▪ Statistician
651-795-5942 ▪ fax 651-204-7504
Ecolab Research Center ▪ Mail Stop ESC-F4412-A
655 Lone Oak Drive ▪ Eagan, MN 55121-1560
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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