# [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)
class(int\$fixed)
kf <- dim(int\$fixed)
plot(int\$fixed[,2], kf:1,
xlab="x", ylab="", xlim=range(int\$fixed),
axes=FALSE)
axis(1)
axis(2, kf:1, dimnames(int\$fixed)[])
segments(int\$fixed[,1], kf:1,
int\$fixed[,3], kf:1)
abline(v=0)

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
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