[R-sig-ME] [EXT] Re: partial effects plots

[John Fox]

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 Lüdecke 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.
>>
>> -----Ursprüngliche Nachricht-----
>> Von: R-sig-mixed-models <r-sig-mixed-models-bounces using r-project.org> Im 
>> Auftrag von Ben Bolker
>> Gesendet: Dienstag, 30. Juli 2024 22:18
>> An: r-sig-mixed-models using 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 using fws.gov<mailto:Laura_Lee using fws.gov>
>>> #############################
>>>
>>>
>>>
>>>      [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
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>>
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>>
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