R help - Jul 2005 - Plotting confidence intervals for lme

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.

-- 
Ghislain Vieilledent
30, rue Bernard Ortet 31 500 TOULOUSE
06 24 62 65 07

	[[alternative HTML version deleted]]

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)[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.
333 West San Carlos Street Suite 700
San Jose, CA 95110, USA

spencer.graves at pdf.com
www.pdf.com <http://www.pdf.com>
Tel:  408-938-4420
Fax: 408-280-7915

---------- Forwarded message ----------
From: Ghislain Vieilledent <ghislainv@gmail.com>
Date: 7 juil. 2005 11:38
Subject: Re: [R] Plotting confidence intervals for lme
To: Spencer Graves <spencer.graves@pdf.com>

That's what I was looking for. Thanks a lot!

That's true units are mixing and that values of coef depend on the contrasts
but I want to use this graph in order to compare levels' coefficient of each
of the factor taken independantly, not to compare factors' coefficients to 
eachothers. Does it mean something?

Thanks again. 

Ghislain Vieilledent.



2005/7/6, Spencer Graves <spencer.graves@pdf.com>:
> 
> 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)[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.
> 333 West San Carlos Street Suite 700
> San Jose, CA 95110, USA
> 
> spencer.graves@pdf.com
> www.pdf.com <http://www.pdf.com> <http://www.pdf.com>
> Tel: 408-938-4420
> Fax: 408-280-7915 
> 


-- 
Ghislain Vieilledent
30, rue Bernard Ortet 31 500 TOULOUSE
06 24 62 65 07 


-- 
Ghislain Vieilledent
30, rue Bernard Ortet 31 500 TOULOUSE
06 24 62 65 07

	[[alternative HTML version deleted]]