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]]