[R] plot of all.effects object

[John Fox]

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/