[R] glm and plot.effects

[John Fox]

Dear Michael,

Look more closely at the two plots: With rescale.axis=TRUE (the default),
the vertical axis is on the scale of the linear predictor (i.e., the logit
scale), but the tick marks are labelled in the scale of the response (i.e.,
the probability scale); this preserves the linear structure of the model.
With rescale.axis=FALSE, the vertical axis is on the scale of the response
(directly on the probability scale). 

If you want the vertical axis labelled on the scale of the linear predictor,
specify type="link" (the default is "response").

I hope this helps,
 John

--------------------------------
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox 
-------------------------------- 

> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Michael Kubovy
> Sent: Friday, October 06, 2006 7:19 AM
> To: R list
> Subject: [R] glm and plot.effects
> 
> Dear R-helpers,
> 
> I don't see a difference between the following two plots of 
> effect objects, which I understand should be different. What 
> am I missing?
> 
> require(doBy)
> require(effects)
> data(budworm)
> m1 <- glm(ndead/20 ~ sex + log(dose), data=budworm, weight=ntotal,
> family=binomial)
> m1.eff <- all.effects(m1)
> plot(m1.eff, rescale.axis = FALSE, selection = 2, main = 
> 'rescale = F') plot(m1.eff, rescale.axis = TRUE, selection = 
> 2, main = 'rescale = T')
> 
> *********************************
> R version 2.4.0 (2006-10-03)
> powerpc-apple-darwin8.7.0
> 
> locale:
> C
> 
> attached base packages:
> [1] "grid"      "tools"     "splines"   "methods"   "utils"
> [6] "stats"     "graphics"  "grDevices" "datasets"  "base"
> 
> other attached packages:
>     effects       doBy      Hmisc      chron     weaver  codetools
>     "1.0-9"      "0.8"    "3.1-1"    "2.3-8"    "1.0.0"    "0.0-3"
>      digest   proptest   survival       lme4     Matrix        JGR
>     "0.2.2"    "0.1-1"     "2.29" "0.9975-0" "0.9975-1"   "1.4-11"
>      iplots     JavaGD      rJava       MASS    lattice
>     "1.0-4"    "0.3-5"   "0.4-10"   "7.2-29"   "0.14-9"
> 
> _____________________________
> Professor Michael Kubovy
> University of Virginia
> Department of Psychology
> USPS:     P.O.Box 400400    Charlottesville, VA 22904-4400
> Parcels:    Room 102        Gilmer Hall
>          McCormick Road    Charlottesville, VA 22903
> Office:    B011    +1-434-982-4729
> Lab:        B019    +1-434-982-4751
> Fax:        +1-434-982-4766
> WWW:    http://www.people.virginia.edu/~mk9y/
> 
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