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> #############################
partial effects plots
9 messages · Daniel Lüdecke, Ben Bolker, John Fox +2 more
? 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> ############################# [[alternative HTML version deleted]]
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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> ############################# [[alternative HTML version deleted]]
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_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models -- _____________________________________________________________________ Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Christian Gerloff (Vorsitzender), Joachim Pr?l?, Prof. Dr. Blanche Schwappach-Pignataro, Corinna Wriedt _____________________________________________________________________
? 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> ############################# [[alternative HTML version deleted]]
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_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models -- _____________________________________________________________________ Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Christian Gerloff (Vorsitzender), Joachim Pr?l?, Prof. Dr. Blanche Schwappach-Pignataro, Corinna Wriedt _____________________________________________________________________
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> >>> ############################# >>> >>> >>> >>> ???? [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> R-sig-mixed-models at r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models >> _______________________________________________ >> R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/ >> mailman/listinfo/r-sig-mixed-models >> >> -- >> >> _____________________________________________________________________ >> >> Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen >> Rechts; Gerichtsstand: Hamburg | www.uke.de >> Vorstandsmitglieder: Prof. Dr. Christian Gerloff (Vorsitzender), >> Joachim Pr?l?, Prof. Dr. Blanche Schwappach-Pignataro, Corinna Wriedt >> _____________________________________________________________________ > > _______________________________________________ > R-sig-mixed-models at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
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 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>
#############################
[[alternative HTML version deleted]]
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/ mailman/listinfo/r-sig-mixed-models -- _____________________________________________________________________ Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Christian Gerloff (Vorsitzender), Joachim Pr?l?, Prof. Dr. Blanche Schwappach-Pignataro, Corinna Wriedt _____________________________________________________________________
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
-- _____________________________________________________________________ Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Christian Gerloff (Vorsitzender), Joachim Pr?l?, Prof. Dr. Blanche Schwappach-Pignataro, Corinna Wriedt _____________________________________________________________________
Dear Daniel,
On 2024-07-31 2:37 a.m., Daniel L?decke wrote:
[You don't often get email from d.luedecke at uke.de. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] 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>
#############################
[[alternative HTML version deleted]]
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/ mailman/listinfo/r-sig-mixed-models -- _____________________________________________________________________ Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Christian Gerloff (Vorsitzender), Joachim Pr?l?, Prof. Dr. Blanche Schwappach-Pignataro, Corinna Wriedt _____________________________________________________________________
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
--
_____________________________________________________________________ Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Christian Gerloff (Vorsitzender), Joachim Pr?l?, Prof. Dr. Blanche Schwappach-Pignataro, Corinna Wriedt _____________________________________________________________________
Thanks, everyone, for your quick response. I am interested in the relationship between the outcome and each explanatory variable. I am interested in creating plots similar to Figures 4a and 4b in the paper at https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2023.1154689/full#h10. I tried running peplot() using the code from the link Daniel (https://rpubs.com/milesdwilliams15/328471), but could not get it to work. I was able to extract effects using the 'remef' package (https://github.com/hohenstein/remef), but I am not sure where to go from there. Best, Laura -----Original Message----- From: Daniel L?decke <d.luedecke at uke.de> Sent: Wednesday, July 31, 2024 2:38 AM To: 'John Fox' <jfox at mcmaster.ca>; 'Ben Bolker' <bbolker at gmail.com>; Lee, Laura M <laura_lee at fws.gov> Cc: r-sig-mixed-models at r-project.org Subject: [EXTERNAL] AW: [EXT] Re: [R-sig-ME] Re: partial effects plots This email has been received from outside of DOI - Use caution before clicking on links, opening attachments, or responding. 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 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://gith/ ub.com%2Fhohenstein%2Fremef&data=05%7C02%7CLaura_Lee%40fws.gov%7C9c1f9 42cac544a28211c08dcb12bdd0a%7C0693b5ba4b184d7b9341f32f400a5494%7C0%7C0 %7C638580049186171278%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQ IjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=cZEOirnq pSl%2BOiEfZJNbguKdfw2Szm7jznMZTDXi7X0%3D&reserved=0 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>
#############################
[[alternative HTML version deleted]]
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://st/ at.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-mixed-models&data=05%7C02%7C Laura_Lee%40fws.gov%7C9c1f942cac544a28211c08dcb12bdd0a%7C0693b5ba4b1 84d7b9341f32f400a5494%7C0%7C0%7C638580049186175290%7CUnknown%7CTWFpb GZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6M n0%3D%7C0%7C%7C%7C&sdata=Iu%2F%2Fa6Lh6WVYhRuJztyjq5%2ByY2ogprNblZSpl taIFzA%3D&reserved=0
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Hi Laura, These plots can be produced with the gratia package: https://gavinsimpson.github.io/gratia/ Please note that these plots are based on GAMMs and not GLMMs. The easiest way to see this is that the effect of each variable on the x-axis does not follow a simple parametric form (e.g., linear or curvilinear) but is non-linear and recovered from the data (using a spline). If you want to produce such a plot, you need to fit a GAM, which you can do using package mgcv. Best, Henrik Am Mi., 31. Juli 2024 um 14:09 Uhr schrieb Lee, Laura M via R-sig-mixed-models <r-sig-mixed-models at r-project.org>:
Thanks, everyone, for your quick response. I am interested in the relationship between the outcome and each explanatory variable. I am interested in creating plots similar to Figures 4a and 4b in the paper at https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2023.1154689/full#h10 . I tried running peplot() using the code from the link Daniel ( https://rpubs.com/milesdwilliams15/328471), but could not get it to work. I was able to extract effects using the 'remef' package ( https://github.com/hohenstein/remef), but I am not sure where to go from there. Best, Laura -----Original Message----- From: Daniel L?decke <d.luedecke at uke.de> Sent: Wednesday, July 31, 2024 2:38 AM To: 'John Fox' <jfox at mcmaster.ca>; 'Ben Bolker' <bbolker at gmail.com>; Lee, Laura M <laura_lee at fws.gov> Cc: r-sig-mixed-models at r-project.org Subject: [EXTERNAL] AW: [EXT] Re: [R-sig-ME] Re: partial effects plots This email has been received from outside of DOI - Use caution before clicking on links, opening attachments, or responding. 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 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://gith/ ub.com%2Fhohenstein%2Fremef&data=05%7C02%7CLaura_Lee%40fws.gov%7C9c1f9 42cac544a28211c08dcb12bdd0a%7C0693b5ba4b184d7b9341f32f400a5494%7C0%7C0 %7C638580049186171278%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQ IjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=cZEOirnq pSl%2BOiEfZJNbguKdfw2Szm7jznMZTDXi7X0%3D&reserved=0 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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