[R] [effects] Wrong xlevels in effects plot for mixed effects model when multiline = TRUE

[John Fox]

Dear Gerrit,

This looks like a bug in plot.eff(), which I haven't yet tracked down, 
but the following should give you what you want:

eff <- Effect(c("gProt", "Age"), m, xlevels = list(gProt = 1:6 * 30, 
Age=60:100))
plot(eff, lines=list(multiline=TRUE))

or

eff <- predictorEffect("Age", m, xlevels = list(gProt = 1:6 * 30))
plot(eff, lines=list(multiline=TRUE))

A couple of comments on your code, unrelated to the bug in plot.eff():

You don't need allEffects() because there's only one high-order fixed 
effect in the model, I(gProt/10 - 6.2):I(Age/10 - 7.2) (i.e., the 
interaction of gProt with Age).

x.var isn't intended as an argument for plot() with allEffects() because 
there generally isn't a common horizontal axis for all of the high-order 
effect plots.

Finally, thank you for the bug report. Barring unforeseen difficulties, 
we'll fix the bug in due course.

I hope this helps,
  John

John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/

On 2020-11-09 8:06 a.m., Gerrit Eichner wrote:
> Dear list members,
> 
> I observe a strange/wrong graphical output when I set the xlevels
> in (e. g.) allEffects for an lmer model and plot the effects with
> multiline = TRUE. I have compiled a reprex for which you need the
> lmer model and the environment in which the model was fitted. They
> are contained in the zip file at
> https://jlubox.uni-giessen.de/dl/fiSzTCc3bW8z2npZvPpqG1xr/m-and-G1.zip
> After unpacking the following should work:
> 
> m <- readRDS("m.rds")   # The lmer-model.
> G1 <- readRDS("G1.rds") # Environment in which the model
>                           # was fitted; needed by alaEffects.
> summary(m) # Just to see the model.
> 
> library(effects)
> aE <- allEffects(m, xlevels = list(gProt = 1:6 * 30))
>                       # Non-default values for xlevels.
> 
> plot(aE)                      # Fine.
> plot(aE, x.var = "Age")       # Fine.
> plot(aE, lines = list(multiline = TRUE))  # Fine.
> 
> plot(aE, lines = list(multiline = TRUE),
>        x.var = "Age")        # Nonsense.
> 
> 
> Anybody any idea about the reason, my mistake, or a
> workaround? Thx for any hint!
> 
>    Regards  --  Gerrit
> 
> 
> PS:
>   > sessionInfo()
> R version 4.0.2 (2020-06-22)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 18363)
> 
> Matrix products: default
> 
> locale:
> [1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
> [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
> [5] LC_TIME=German_Germany.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] effects_4.2-0 carData_3.0-4
> 
> loaded via a namespace (and not attached):
>    [1] Rcpp_1.0.5       lattice_0.20-41  MASS_7.3-53      grid_4.0.2 
> DBI_1.1.0
>    [6] nlme_3.1-149     survey_4.0       estimability_1.3 minqa_1.2.4 
> nloptr_1.2.2.2
> [11] Matrix_1.2-18    boot_1.3-25      splines_4.0.2    statmod_1.4.34 
> lme4_1.1-23
> [16] tools_4.0.2      survival_3.2-3   yaml_2.2.1       compiler_4.0.2 
> colorspace_1.4-1
> [21] mitools_2.4      insight_0.9.5    nnet_7.3-14
> 
> ---------------------------------------------------------------------
> Dr. Gerrit Eichner                   Mathematical Institute, Room 212
> gerrit.eichner using math.uni-giessen.de   Justus-Liebig-University Giessen
> Tel: +49-(0)641-99-32104          Arndtstr. 2, 35392 Giessen, Germany
> http://www.uni-giessen.de/eichner
> 
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