[EXT] Re: Re: partial effects plots

Dear Daniel,
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Caution: External email.

Dear all,
yes, partial *residuals* are possible with the effects package (see https://cran.r-project.org/web/packages/effects/vignettes/partial-residuals.pdf) or ggeffects (https://strengejacke.github.io/ggeffects/articles/introduction_partial_residuals.html).

I don't think partial *regression* plots are possible for any of those packages (maybe for the effects package, I'm not sure).

Laura, maybe you can clarify what kind of plots you would like to have? Terminology may be unclear here. I'm not sure if I confused partial *effects* with partial *regression* plots. Beside the mentioned functions in the car-package, this website describes partial-effects plots: https://rpubs.com/milesdwilliams15/328471
This document says that, "Partial effect plots go by serval [sic] names 
(partial residual plots, added variable plots, adjusted variable plots, 
etc.)."  "Partial residual plots" and "added variable plots" have 
conventional definitions, and they are not the same.

The document goes on to define a function that computes added-variable 
(partial-regression) plots for linear models fit by unweighted least 
squares. One can more generally compute AV plots for linear models fit 
by weighted least squares and for generalized linear models (see, e.g., 
the avPlots() function in the far package). I'm unaware of a 
generalization beyond that.

Best,
  John
Best
Daniel

-----Urspr?ngliche Nachricht-----
Von: John Fox <jfox at mcmaster.ca>
Gesendet: Dienstag, 30. Juli 2024 23:08
An: Ben Bolker <bbolker at gmail.com>; Daniel L?decke <d.luedecke at uke.de>; Laura_Lee at fws.gov
Cc: r-sig-mixed-models at r-project.org
Betreff: [EXT] Re: [R-sig-ME] Re: partial effects plots

Dear Ben, Daniel, and Laura,

First, added-variable (partial-regression) plots are often confused with component + residuals (partial-residual) plots, but they are not the same.

Second, "effect" plots are essentially component + residuals plots (possibly without the residuals).

Finally, it's possible to show partial residuals in effect plots for mixed models constructed by the effects package.

I hope this helps,
   John

--
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://www.john-fox.ca/
--

On 2024-07-30 4:52 p.m., Ben Bolker wrote:
Caution: External email.

    OK, in this case you'll need to be able to generate partial
residuals, which may be doable via the package at
https://github.com/hohenstein/remef

On 7/30/24 16:30, Daniel L?decke wrote:
I'm not sure if the partial effects plots differ from what emmeans,
ggeffects, effects etc. plot by default.
Isn't another name for "partial effects plots" the "added variables
plot", implemented in car::avPlot() / car::avPlots()?

Not sure if mixed models are supported, though.

-----Urspr?ngliche Nachricht-----
Von: R-sig-mixed-models <r-sig-mixed-models-bounces at r-project.org> Im
Auftrag von Ben Bolker
Gesendet: Dienstag, 30. Juli 2024 22:18
An: r-sig-mixed-models at r-project.org
Betreff: [EXT] Re: [R-sig-ME] partial effects plots

     Start with emmeans or effects packages? In particular

library(effects)

plot(allEffects(fitted_model))

On 7/30/24 15:44, Lee, Laura M via R-sig-mixed-models wrote:
Hello all,

I have fit a GLMM to presence/absence data (family = binomial) from
an acoustic telemetry study. I have five fixed effects-Year (a
factor), Day of Year, Hour of Day, Sex (a factor), and water
temperature-and one random effect-Fish ID (a factor). I am looking
to create partial effects plots for the covariates. Can anyone
direct me to some sample code or suggest a package to help me get
started. My Google searches haven't been very fruitful.

I would appreciate any assistance on this matter. Thank you for your
time!

Best,

Laura

#############################
Laura M. Lee
USFWS - Northeast Fishery Center
P.O. Box 75
308 Washington Ave.
Lamar, PA  16848
Phone: 570-726-4247 x 50122
Laura_Lee at fws.gov<mailto:Laura_Lee at fws.gov>
#############################

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[EXT] Re: Re: partial effects plots

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