[R-sig-ME] LMER: Visualizing three-way interaction

[Thierry Onkelinx]

Dear Klemens,

Here is my €0.02

library(ggplot2)
dataset <- expand.grid(
  x = seq(0, 1, length = 41),
  y = seq(0, 1, length = 41),
  z =factor( c("A", "B"))
)
dataset$fit <- with(dataset,
  ifelse(
    z == "A",
     x - 2 * x^2 + 0.5 * x * y + 3 * y - y ^ 2,
    -x - 1 * x^2 - 2 * x * y - 3 * y + y ^ 2
  )
)
ggplot(dataset, aes(x = x, y = y, fill = fit)) +
  geom_raster() +
  facet_wrap(~ z) +
  scale_fill_gradient2()
ggplot(dataset, aes(x = x, y = y, z = fit)) +
  geom_contour(aes(colour = ..level..), binwidth = 0.25) +
  facet_wrap(~ z) +
  scale_colour_gradient2()
ggplot(dataset, aes(x = x, y = y)) +
  geom_raster(aes(fill = fit)) +
  geom_contour(aes(z = fit), binwidth = 0.25) +
  facet_wrap(~ z) +
  scale_fill_gradient(low = "black", high = "white")

Best regards,

Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

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more than asking him to perform a post-mortem examination: he may be
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given body
of data. ~ John Tukey


2017-04-12 19:06 GMT+02:00 Evan Palmer-Young <ecp52 op cornell.edu>:
> Dear Klemens,
> I also have been asked to remove plot3d plots that I thought were
> stupendous, but I guess not everybody likes them!
> How about two two-way interaction plots for the regressions of continuous
> variable 1 vs 2, with separate panels for the levels of the categorical
> variable?
> You can get fitted model values and CI's with the lsmeans function, using
> the "at" argument to specify covariate values.
> If the plot is too bland, you can sprinkle the raw data on top as an extra
> layer of points.
> Best wishes, Evan
>
>
> On Wed, Apr 12, 2017 at 5:41 AM, Klemens Knöferle <knoeferle op gmail.com>
> wrote:
>
>> Hi all,
>>
>> I'm trying to visualize a three-way interaction from a rather complex
>> linear mixed model in R (lmer function from the lme4 package; the model has
>> a complex random-effects structure). The interaction consists of two
>> continuous variables and one categorical variable (two experimental
>> conditions).
>>
>> So far, I have graphed the interaction via two 3D-surface plots using
>> visreg2d from the visreg package. But my reviewers found these plots
>> confusing and asked for a different illustration, such as conditional
>> coefficient plots (i.e., plots of the strength of coefficient 1 as
>> coefficient 2 increases).
>>
>> I've tried to find a package that allows me to create these kind of plots,
>> but failed. The existing packages only allow coefficient plots for two-way
>> interactions (for instance the interplot package;
>> https://cran.r-project.org/web/packages/interplot/
>> vignettes/interplot-vignette.html).
>> That means I only get a conditional coefficient plot of the two-way
>> interaction, collapsed across both levels of the categorical variable.
>>
>> Is there a package for my case? If not, I probably have to manually extract
>> fitted values from my model (e.g., using broom) and somehow plot them in
>> ggplot2. But I don't really know how to do this, whether or not to take
>> into account random effects (and how), etc. Any ideas would be much
>> appreciated...
>>
>> Klemens Knöferle, Ph.D.
>> Associate Professor - Department of Marketing
>> BI Norwegian Business School
>> Visiting address: Nydalsveien 37, 0484 Oslo
>>
>>         [[alternative HTML version deleted]]
>>
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>
>
>
>
> --
> Evan Palmer-Young
> PhD candidate
> Department of Biology
> 221 Morrill Science Center
> 611 North Pleasant St
> Amherst MA 01003
> https://sites.google.com/a/cornell.edu/evan-palmer-young/
> epalmery op cns.umass.edu
> ecp52 op cornell.edu
>
>         [[alternative HTML version deleted]]
>
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