Re: [R] Plotting confidence intervals for lme

From: Spencer Graves <spencer.graves_at_pdf.com>
Date: Thu 07 Jul 2005 - 02:44:29 EST

fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1) int <- intervals(fm2)
class(int\$fixed)
kf <- dim(int\$fixed)[1]
plot(int\$fixed[,2], kf:1,

```      xlab="x", ylab="", xlim=range(int\$fixed),
axes=FALSE)
```

axis(1)
axis(2, kf:1, dimnames(int\$fixed)[[1]])
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
Senior Development Engineer
PDF Solutions, Inc.
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spencer.graves@pdf.com
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