[R] plot of all.effects object

[John Fox]

Dear David,

> -----Original Message-----
> From: David Afshartous [mailto:dafshartous at med.miami.edu]
> Sent: September-11-08 4:48 PM
> To: John Fox
> Cc: r-help at r-project.org
> Subject: Re: [R] plot of all.effects object
> 
> 
> Dear John,
> 
> Thanks and sorry for the typo.
> 
> For the example below, how do I get the time.num variable to correspond to
> the x-axis?  I tried refitting the model with a different order of
supplied
> variables but this didn't do it.

You can specify the x.var argument to the plot() method for eff objects, as
explained in ?plot.eff.

John
 
> 
> Cheers,
> David
> 
> 
> 
> 
> On 9/11/08 4:28 PM, "John Fox" <jfox at mcmaster.ca> wrote:
> 
> > Dear David,
> >
> > You have to spell the name of term correctly:
> >
> >  plot(fm.effects, "time.num:drug:X")
> >
> > (Admittedly, the error message is cryptic: I'll look into that.)
> >
> > A couple of other comments: (1) There is only one high-order term in
> > your model, so it's not necessary to use all.effects(); (2) if you
> > plot(fm.effects) (i.e., without specifying the term to plot) you'll be
> > presented with a menu, in this instance with only one choice.
> >
> > I hope this helps,
> >  John
> >
> > On Thu, 11 Sep 2008 15:54:25 -0400
> >  David Afshartous <dafshartous at med.miami.edu> wrote:
> >>
> >>
> >> All,
> >>
> >> I'm trying to plot an all.effects() object, as shown in the help for
> >> all.effects and also Crawley's R book (p.178, 2007). The data has a
> >> repeated
> >> measures structure, but I'm using all.effects for the simple lm() fit
> >> here.
> >> Below is a reproducible example that yields the error message.
> >>
> >>
> >> fm.ex = lm(dv ~ time.num*drug*X, data = dat.new)
> >> fm.effects = all.effects(fm.ex, xlevels = list(time.num = 1:4))
> >>
> >>> plot(fm.effects, "time.num:Drug:X")
> >> Error in plot.window(...) : need finite 'xlim' values
> >> In addition: Warning messages:
> >> 1: In min(x) : no non-missing arguments to min; returning Inf
> >> 2: In max(x) : no non-missing arguments to max; returning -Inf
> >> 3: In min(x) : no non-missing arguments to min; returning Inf
> >> 4: In max(x) : no non-missing arguments to max; returning -Inf
> >>
> >> Cheers,
> >> David
> >>
> >>
> >>
> >>
> >>
> >> ############################
> >>  sessionInfo()
> >> R version 2.7.1 (2008-06-23)
> >> i386-apple-darwin8.10.1
> >>
> >> locale:
> >> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> >>
> >> attached base packages:
> >> [1] grid      stats     graphics  grDevices utils     datasets
> >>  methods
> >> base
> >>
> >> other attached packages:
> >> [1] effects_1.0-12 lattice_0.17-8
> >>
> >> loaded via a namespace (and not attached):
> >> [1] Matrix_0.999375-11 lme4_0.999375-24   nlme_3.1-89
> >>        tools_2.7.
> >>
> >> set.seed(500)
> >> n.timepoints <- 4
> >> n.subj.per.tx <- 20
> >> sd.d <- 5;
> >> sd.p <- 2;
> >> sd.res <- 1.3
> >> drug <- factor(rep(c("D", "P"), each = n.timepoints, times =
> >> n.subj.per.tx))
> >> drug.baseline <- rep( c(0,5), each=n.timepoints, times=n.subj.per.tx
> >> )
> >> Patient <- rep(1:(n.subj.per.tx*2), each = n.timepoints)
> >> Patient.baseline <- rep( rnorm( n.subj.per.tx*2, sd=c(sd.d, sd.p) ),
> >> each=n.timepoints )
> >> time <- factor(paste("Time-", rep(1:n.timepoints, n.subj.per.tx*2),
> >> sep=""))
> >> time.baseline <-
> >> rep(1:n.timepoints,n.subj.per.tx*2)*as.numeric(drug=="D")
> >> dv <- rnorm( n.subj.per.tx*n.timepoints*2,
> >> mean=time.baseline+Patient.baseline+drug.baseline, sd=sd.res )
> >> dat.new <- data.frame(time, drug, dv, Patient)
> >> dat.new$time.num = rep(1:n.timepoints, n.subj.per.tx*2)
> >> dat.new$X <- rnorm(160) ### to check plot of all.effects info
> >>
> >> ______________________________________________
> >> R-help at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide
> >> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> > --------------------------------
> > John Fox, Professor
> > Department of Sociology
> > McMaster University
> > Hamilton, Ontario, Canada
> > http://socserv.mcmaster.ca/jfox/