[R] [effects] Wrong xlevels in effects plot for mixed effects model when multiline = TRUE
John Fox
j|ox @end|ng |rom mcm@@ter@c@
Thu Nov 12 01:52:07 CET 2020
Dear Gerrit,
The bug you reported should now be fixed in the development version
4.2-1 of the effects package, which you can currently install from
R-Forge via install.packages("effects",
repos="http://R-Forge.R-project.org") . Eventually, the updated version
of the effects package will be submitted to CRAN.
Thank you again for the bug report,
John
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/
On 2020-11-09 4:51 p.m., Gerrit Eichner wrote:
> Dear John,
>
> thank you for prompt reply and your hints. The problem is that our
> lmer model is much more complicated and has several interaction
> terms:
>
> Mass ~ Sex + I(YoE - 1996) + I(PAI/0.1 - 16) + I(gProt/10 - 6.2) +
> I(Age/10 - 7.2) + I((Age/10 - 7.2)^2) + Diuretics +
> Sex:I(PAI/0.1 - 16) + Sex:I(gProt/10 - 6.2) +
> Sex:I(Age/10 - 7.2) + Sex:I((Age/10 - 7.2)^2) +
> I(YoE - 1996):I(Age/10 - 7.2) + I(PAI/0.1 - 16):I(Age/10 - 7.2) +
> I(gProt/10 - 6.2):I(Age/10 - 7.2) +
> (I(Age/10 - 7.2) + I((Age/10 - 7.2)^2) | ID)
>
> so that allEffects is quite efficient, and since I want to place
> several interaction terms with Age in one figure with Age on the
> horizontal axis the argument x.var = "Age" in plot would be very
> helpful. :-)
>
> Further hints using the above complex model: The following works well:
> eff <- Effect(c("gProt", "Age"), m,
> xlevels = list(gProt = 1:6 * 30, Age = 60:100))
> plot(eff, lines=list(multiline=TRUE), x.var = "Age")
>
> But this fails (note that Age is missing in xlevels):
> eff <- Effect(c("gProt", "Age"), m, xlevels = list(gProt = 1:6 * 30))
> plot(eff, lines=list(multiline=TRUE), x.var = "Age")
>
>
> And that just led me to a solutution also for allEffects: Specifying
> Age in xlevels for allEffects (although it seems unnecessary when
> x.var = "Age" is used in plot) produces the correct graphical
> output! :-)
>
> Thank you very much for your support and the brilliant effects
> package in general! :-)
>
> Best regards -- Gerrit
>
> ---------------------------------------------------------------------
> 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
> Fax: +49-(0)641-99-32109 http://www.uni-giessen.de/eichner
> ---------------------------------------------------------------------
>
> Am 09.11.2020 um 19:51 schrieb 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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