Hi all, I?m trying to plot confidence intervals for the fitted values I get with my lme model in R. Is there any way I can plot this in the form of a shaded band, like the output of geom_smooth() in ggplot2 package. ggplot2 seems to use only lm, glm, gam, loess and rlm as smoothing methods. Any advice on the functions I should use to accomplish this will be very helpful. Thank you very much. Ben -- View this message in context: http://r.789695.n4.nabble.com/confidence-interval-as-shaded-band-lme-tp3727645p3727645.html Sent from the R help mailing list archive at Nabble.com.
I don't know lme models very well, but if you have standard errors for your values, this shouldn't be too hard (as a last resort) using polygon() For example x = 1:10 y = x^2 y.Err = 2*x y.Up = y + y.Err; y.Dn =y-y.Err # This graph is actually quite ugly so don't copy the formatting.... plot(x,y,type="n") polygon(c(x,rev(x)),c(y.Up,rev(y.Dn)),col="grey",border="red") # Use the rev commands so the border moves logically around the shaded area lines(x,y,type="b",lwd=3) # put the means back on top of the polygon Still, this is a little brute force and I'd imagine that someone else will shortly let you know how R can already do automatically. Michael Weylandt On Mon, Aug 8, 2011 at 1:07 PM, bjmjarrett <bjmjarrett@gmail.com> wrote:> Hi all, > > I’m trying to plot confidence intervals for the fitted values I get with my > lme model in R. > > Is there any way I can plot this in the form of a shaded band, like the > output of geom_smooth() in ggplot2 package. ggplot2 seems to use only lm, > glm, gam, loess and rlm as smoothing methods. > > Any advice on the functions I should use to accomplish this will be very > helpful. > > Thank you very much. > > Ben > > -- > View this message in context: > http://r.789695.n4.nabble.com/confidence-interval-as-shaded-band-lme-tp3727645p3727645.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
Hi: On Mon, Aug 8, 2011 at 10:07 AM, bjmjarrett <bjmjarrett at gmail.com> wrote:> Hi all, > > I?m trying to plot confidence intervals for the fitted values I get with my > lme model in R.Which fitted values? The ones conditional on the random effects or the ones averaged over the random effects? The standard errors of the two sets of predictions are not the same.> > Is there any way I can plot this in the form of a shaded band, like the > output of geom_smooth() in ggplot2 package. ggplot2 seems to use only lm, > glm, gam, loess and rlm as smoothing methods.You can fake it with geom_ribbon(), but it would be convenient to have the endpoints of the CIs in a data frame you could input into ggplot2. HTH, Dennis> > Any advice on the functions I should use to accomplish this will be very > helpful. > > Thank you very much. > > Ben > > -- > View this message in context: http://r.789695.n4.nabble.com/confidence-interval-as-shaded-band-lme-tp3727645p3727645.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >