FAQ
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

Thank you very much.

Ben

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•  at Aug 8, 2011 at 5:35 pm ⇧
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 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

Thank you very much.

Ben

--
View this message in context:
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
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
•  at Aug 8, 2011 at 8:07 pm ⇧
Hi:
On Mon, Aug 8, 2011 at 10:07 AM, bjmjarrett 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

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
and provide commented, minimal, self-contained, reproducible code.
•  at Aug 8, 2011 at 8:40 pm ⇧
Would someone tell me how they propose to go from "standard errors" to
confidence intervals*. I suspect Doug Bates would probably like to
know, also, as he has expended a lot of effort on this over the years,
I believe. :-)

-- Bert

* Note +/- 2 std errors is almost certainly not the right answer --
how far wrong it is ... that's the question.

Cheers,
Bert
On Mon, Aug 8, 2011 at 1:07 PM, Dennis Murphy wrote:
Hi:
On Mon, Aug 8, 2011 at 10:07 AM, bjmjarrett 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

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
and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
and provide commented, minimal, self-contained, reproducible code.

--
"Men by nature long to get on to the ultimate truths, and will often
be impatient with elementary studies or fight shy of them. If it were
possible to reach the ultimate truths without the elementary studies
usually prefixed to them, these would not be preparatory studies but
superfluous diversions."

-- Maimonides (1135-1204)

Bert Gunter
Genentech Nonclinical Biostatistics

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