[R-sig-ME] Plotting lmer estimates with individual points from residuals
Andy Fugard
andy.fugard at sbg.ac.at
Sat Jul 4 19:30:51 CEST 2009
Dear all,
Are there any good reasons not to graph data points from
fixed effects estimates + observation-level residuals
in models with random effects at levels above residuals?
Some code below to demonstrate what I mean.
I can see arguments against doing this when there are varying slopes in
the model, but perhaps a separate graph can be used nearby to show how
the slopes vary between (e.g.) subjects.
Interesting for the sleepstudy dataset that plotting the varying
intercept (only) model shows a bow-tie effect, pointing to a need for
random slopes.
Words of wisdom and pointers to literature very welcome.
Best wishes,
Andy
######################################################################
require(lme4)
# Varying intercept model
M1 = lmer(Reaction ~ Days + (1|Subject), sleepstudy)
# Varying slope model
M2 = lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
# Grab the fixed effect estimates
cs1 = fixef(M1)
cs2 = fixef(M1)
days = sleepstudy$Days
# Save residuals and predictions from fixed effects
sleepstudy$resid1 = resid(M1)
sleepstudy$fixedPred1 = with(sleepstudy, cs1[1] + cs1[2]*Days)
sleepstudy$resid2 = resid(M2)
sleepstudy$fixedPred2 = with(sleepstudy, cs2[1] + cs2[2]*Days)
# Plot
par(mfrow = c(1,3))
plot(Reaction ~ Days, sleepstudy, main = "Original data")
plot(I(fixedPred1+resid1) ~ Days, sleepstudy,
main = "Varying intercept", ylab = "Reaction")
curve(cs1[1] + cs1[2]*x, min(days), max(days), add=T)
plot(I(fixedPred2+resid2) ~ Days, sleepstudy,
main = "Varying slope + intercept", ylab = "Reaction")
curve(cs2[1] + cs2[2]*x, min(days), max(days), add=T)
par(mfrow = c(1,1))
######################################################################
--
Andy Fugard, Post-doc, ESF LogICCC (LcpR) project
Fachbereich Psychologie, Universitaet Salzburg
Hellbrunnerstr. 34, 5020 Salzburg, Austria
+43 (0)680 2199 346 http://figuraleffect.googlepages.com
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