Hello everyone, <http://aka.ms/weboutlook> I am learning how to use glmmTMB and I encountered the following issue: I cannot get coefplot2 to work with my glmmTMB model. None of the options work (e.g coeftab). When I apply coefplot2 to the simple glmer model coeftab returns the following error: Error in UseMethod("coeftab", object) : no applicable method for 'coeftab' applied to an object of class "c('glmerMod', 'merMod')" I am not sure what to do as I would like to be able to get a plot of the regression estimates for the these two models. So far, even though coeftab is not working, I can only plot the estimates for the glmer model. I suspect it is because both glmerMod and glmmTMb are S4 objects. Thank you all very much! Best, Dani N-M
coefplot2 in conjunction with glmmTMB and glmer
3 messages · Ben Bolker, dani
coefplot2 is pretty well deprecated now, in favor of the "broom"
package. In order to get nice coefficient plots/tables for glmmTMB
objects, I would suggest
1. install my fork of broom, which knows how to deal with those objects:
devtools::install_github("bbolker/broom")
2a. use tidy() to extract the coefficient table and ggplot to plot the
coefficient plots (geom_pointrange is useful), or
2b. install the dotwhisker package, which should (in conjunction with
broom) do this automatically
e.g.
library(glmmTMB)
example(glmmTMB)
library(dotwhisker)
dwplot(m3) ## hmm, RE standard dev disappears
dwplot(m3,effects="fixed") ## maybe we didn't want it anyway
On 17-10-21 05:28 PM, dani wrote:
Hello everyone, <http://aka.ms/weboutlook> I am learning how to use glmmTMB and I encountered the following issue: I cannot get coefplot2 to work with my glmmTMB model. None of the options work (e.g coeftab). When I apply coefplot2 to the simple glmer model coeftab returns the following error: Error in UseMethod("coeftab", object) : no applicable method for 'coeftab' applied to an object of class "c('glmerMod', 'merMod')" I am not sure what to do as I would like to be able to get a plot of the regression estimates for the these two models. So far, even though coeftab is not working, I can only plot the estimates for the glmer model. I suspect it is because both glmerMod and glmmTMb are S4 objects. Thank you all very much! Best, Dani N-M [[alternative HTML version deleted]]
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
Hello Ben, Thank you so much for your prompt response! Much appreciated! Best regards! Dani
From: R-sig-mixed-models <r-sig-mixed-models-bounces at r-project.org> on behalf of Ben Bolker <bbolker at gmail.com>
Sent: Saturday, October 21, 2017 2:36 PM
To: r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] coefplot2 in conjunction with glmmTMB and glmer
Sent: Saturday, October 21, 2017 2:36 PM
To: r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] coefplot2 in conjunction with glmmTMB and glmer
coefplot2 is pretty well deprecated now, in favor of the "broom"
package. In order to get nice coefficient plots/tables for glmmTMB
objects, I would suggest
1. install my fork of broom, which knows how to deal with those objects:
devtools::install_github("bbolker/broom")
2a. use tidy() to extract the coefficient table and ggplot to plot the
coefficient plots (geom_pointrange is useful), or
2b. install the dotwhisker package, which should (in conjunction with
broom) do this automatically
e.g.
library(glmmTMB)
example(glmmTMB)
library(dotwhisker)
dwplot(m3) ## hmm, RE standard dev disappears
dwplot(m3,effects="fixed") ## maybe we didn't want it anyway
On 17-10-21 05:28 PM, dani wrote:
> Hello everyone,
>
> <http://aka.ms/weboutlook>
>
> I am learning how to use glmmTMB and I encountered the following issue:
>
> I cannot get coefplot2 to work with my glmmTMB model. None of the options work (e.g coeftab). When I apply coefplot2 to the simple glmer model coeftab returns the following error:
> Error in UseMethod("coeftab", object) :
> no applicable method for 'coeftab' applied to an object of class "c('glmerMod', 'merMod')"
>
> I am not sure what to do as I would like to be able to get a plot of the regression estimates for the these two models. So far, even though coeftab is not working, I can only plot the estimates for the glmer model.
>
> I suspect it is because both glmerMod and glmmTMb are S4 objects.
>
> Thank you all very much!
> Best,
> Dani N-M
>
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
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