"effects" package with "lme4"
Dear Axel,
On May 15, 2020, at 7:39 PM, Axel Urbiz <axel.urbiz at gmail.com> wrote: Dear John, Thank you for your response. My apologies as I?m only recently getting exposed to mixed-model. My understanding, is that the model specified below also has random intercepts and slope, as they vary by Subject. `coef(fm1)` shows this. I was looking to plot the fitted splines by Subject. Sorry if my interpretation is incorrect.
There's no need to apologize.
The functions in the effects package compute and graph fixed effects for mixed models. You could compute and graph the BLUP for the fitted spline for each subject (see below) but it's not what the effects package does.
I think that the following does what you want:
-------- snip ----------
subjects <- levels(sleepstudy$Subject)
fits <- matrix(0, length(subjects), 10)
rownames(fits) <- subjects
for (subject in subjects){
fits[subject, ] <- predict(fm1, newdata=data.frame(Subject=subject, Days=0:9))
}
plot(c(0, 10), range(fits), type="n", xlab="Days", ylab="Reaction")
for (subject in subjects) lines(0:9, fits[subject, ])
-------- snip ----------
Best,
John
Best, Axel.
On May 15, 2020, at 5:51 PM, Fox, John <jfox at mcmaster.ca> wrote: Dear Axel, There only one fixed effect in the model, ns(Days, 3), so I don't know what you expected. Best, John -------------------------------------- John Fox, Professor Emeritus McMaster University Hamilton, Ontario, Canada Web: socialsciences.mcmaster.ca/jfox/
-----Original Message-----
From: Axel Urbiz <axel.urbiz at gmail.com>
Sent: Friday, May 15, 2020 5:33 PM
To: Fox, John <jfox at mcmaster.ca>; R-help at r-project.org
Subject: "effects" package with "lme4"
Hello John and others,
I?d appreciate your help as I?m trying to plot the effect of predictor
?Days? on Reaction by Subject. I?m only getting one plot in the example
below.
### Start example
library(lme4)
library(splines)
data("sleepstudy")
fm1 <- lmer(Reaction ~ ns(Days, 3) + (ns(Days, 3) | Subject), sleepstudy)
coef(fm1)
plot(allEffects(fm1))
### End example
Thanks,
Axel.