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