[R] Plotting confidence intervals for lme

Spencer Graves spencer.graves at pdf.com
Wed Jul 6 18:44:29 CEST 2005

	  Consider the following extension of an example in "?lme":

fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)
int <- intervals(fm2)
kf <- dim(int$fixed)[1]
plot(int$fixed[,2], kf:1,
      xlab="x", ylab="", xlim=range(int$fixed),
axis(2, kf:1, dimnames(int$fixed)[[1]])
segments(int$fixed[,1], kf:1,
          int$fixed[,3], kf:1)

	  However, we are mixing units, i.e., the units for the intercept are 
"distance", while for "age" are "distance/time", and the interpretation 
of the coefficient of a factor like Sex depends on contrasts used. 
Thus, I don't know how much sense it makes to prepare plots like this.

	  For similar plots that make more sense, see Pinheiro and Bates (2000 
Mixed-Effects Models in S and S-PLUS (Springer).

	  spencer graves

Ghislain Vieilledent wrote:

> Hello and sorry to disturb.
> I'm trying to plot the confidence intervals for the fixed effects of a lme.
> I want to obtain graphically, if it is possible, a bar with Estimate, upper 
> and lower CI for each level of the factors.
> I know how to do for a lm model but for a lme one, I tried with 
> plot(intervals(...)) and plot(ci(...)) from the gmodels package but it 
> doesn't work well.
> Thanks for you help and have a good day.

Spencer Graves, PhD
Senior Development Engineer
PDF Solutions, Inc.
333 West San Carlos Street Suite 700
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spencer.graves at pdf.com
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