[R-sig-ME] LMER - Plotting of a quadratic effect interacting with time

[Matthew Boden]

Thank you, John.  Worked like a charm.
Also, good catch on exclusion of quadratic FTE as a random effect. Made no
sense.

Matt

On Thu, Jan 31, 2019 at 11:56 AM Fox, John <jfox using mcmaster.ca> wrote:

> Dear Mathew,
>
> > -----Original Message-----
> > From: R-sig-mixed-models [mailto:r-sig-mixed-models-bounces using r-
> > project.org] On Behalf Of Boden, Matthew T. via R-sig-mixed-models
> > Sent: Wednesday, January 30, 2019 4:27 PM
> > To: r-sig-mixed-models using r-project.org
> > Subject: [R-sig-ME] LMER - Plotting of a quadratic effect interacting
> with time
> >
> > Hello,
> >
> > I have a question related to fitting and plotting a longitudinal linear
> mixed
> > model that includes an interaction between a quadratic effect and time.
> Data
> > attached.
> >
> > I fit the following:
> >
> > Q1 <- lmer(Patients ~ Time*FTE + Time*I(FTE^2) +  (FTE  | ID), data =
> SHARE)
> >
> > #Yes, the variables are on very different scales - will take care of
> that later
> >
> > I find a sizeable quadratic effect.
> >
> > Fixed effects:
> >                 Estimate Std. Error t value
> > (Intercept)    6.760e+03  5.347e+02  12.642
> > Time           2.033e+01  1.011e+01   2.011
> > FTE            9.728e+01  8.583e+00  11.335
> > I(FTE^2)      -5.155e-01  4.000e-02 -12.890
> > Time:FTE      -5.560e-01  2.254e-01  -2.467
> > Time:I(FTE^2)  7.371e-03  1.052e-03   7.006
> >
> > To plot the quadratic interaction, I attempt to use the effects package.
> > However, effects are displayed for Time x FTE, not time by FTE^2. Time x
> FTE
> > is clearly not the plot that I want (I think...).
> >
> > e1 <- effect(term="Time:I(FTE^2)", mod=Q1)
> > ed1<-as.data.frame(e1)
> > ed1
> >    Time FTE       fit        se     lower     upper
> > 1     1  17  8277.635  464.3995  7366.770  9188.500
> > 2     4  17  8316.650  463.3763  7407.792  9225.508
> > ......
> >
> > I tried a workaround, by fitting a model that included FTE^2 as a second,
> > calculated variable in the data set. Using the effects package, I do
> indeed
> > obtain Time * FTE_sq.
> >
> > Q2 <- lmer(Patients ~ Time*FTE + Time*FTE_sq +  (FTE  | ID), data =
> SHARE)
> >
> > e2 <- effect(term="Time*FTE_sq", mod=Q2)
> > ed2<-as.data.frame(e2)
> > ed2
> >
> >    Time FTE_sq        fit        se      lower      upper
> > 1     1    300 14678.1413  564.5423 13570.8582 15785.4243
> > 2     4    300 14606.9253  563.3827 13501.9166 15711.9340
> > ......
> >
> > But the plot does not at all look like what I would expect. All lines
> > representing FTE_sq over time are straight.
>
> Try, plot(Effect(c("Time", "FTE"), Q1)) .
>
> More generally, why not fit the model as  Q1 <- lmer(Patients ~
> Time*poly(FTE, 2) +  (FTE  | ID), data = SHARE)  or Q1 <- lmer(Patients ~
> Time*poly(FTE, 2, raw=TRUE) +  (FTE  | ID), data = SHARE) ? Also, do you
> really want the linear term in FTE to be random and the quadratic term only
> fixed?
>
> I hope this helps,
>  John
>
> >
> > ggplot(ed2, aes(x=Time, y=fit, color=FTE_sq,group=FTE_sq)) +
> >    geom_point() +
> >    geom_line(size=1.2) +
> >    labs(title = "Time x FTE^2", x= "Time",
> >         y="Patients", color="FTE^2", fill="FTE^2") + theme_classic() +
> >         theme(text=element_text(size=10))
> >
> > Does my problem (obtaining effects for FTE^2*Time and accurately plotting
> > them) relate to my use of the effects package, ggplot, both?
> >
> > Thank you for the feedback.
> >
> > Matthew Boden, Ph.D.
> > Senior Evaluator
> > Program Evaluation & Resource Center
> > Office of Mental Health & Suicide Prevention Veterans Health
> Administration
> >
> > _______________________________________________
> > R-sig-mixed-models using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
> _______________________________________________
> R-sig-mixed-models using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>

	[[alternative HTML version deleted]]