[R-sig-ME] broom package and MCMCglmm estimates

[dani]

Hello again,


That is fantastic, thank you so much, Dr Bolker!

I had tried earlier today and I got the same error message several times. I tried again after I received your message and I got several other error messages - one of them saying that the broom.rdb was corrupt, so I guess I might have messed up somehow because I was trying different things and I installing many packages. I removed them all and re- installed "broom" as you suggested and it worked nicely for a glmmTMB model as well as for a MCMC model. Now I hope everything goes nicely to visualize them.


I appreciate all your help and all your work in the field and in making everything easier to understand!

This is truly wonderful and I cannot emphasize more how great this mailing list is for me!

Best regards everyone!

________________________________
From: R-sig-mixed-models <r-sig-mixed-models-bounces at r-project.org> on behalf of Ben Bolker <bbolker at gmail.com>
Sent: Tuesday, October 24, 2017 3:04 PM
To: r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] broom package and MCMCglmm estimates


  There is an MCMCglmm method in my fork of broom :

devtools::install_github("bbolker/broom")
library(broom)
library(MCMCglmm)
data(PlodiaPO)
model1 <- MCMCglmm(PO~1, random=~FSfamily, data=PlodiaPO,
  verbose=FALSE,  nitt=1300, burnin=300, thin=1)
tidy(model1)
##   effect        term estimate  std.error
## 1  fixed (Intercept) 1.162818 0.01656339

  I make no claims as to its completeness, but am happy to accept issues
or pull requests.  Eventually the stuff in my fork will get migrated to
a separate "broom.mixed" (or some such) package.



On 17-10-24 05:56 PM, dani wrote:
> Hello Pierre,
>
>
> Thank you so much for your prompt response, I will follow your advice and report back.
>
>
> best,
>
> daniNm
>
> ________________________________
> From: Pierre de Villemereuil <pierre.de.villemereuil at mailoo.org>
> Sent: Tuesday, October 24, 2017 1:47 PM
> To: r-sig-mixed-models at r-project.org
> Cc: dani
> Subject: Re: [R-sig-ME] broom package and MCMCglmm estimates
>
> Hi,
>
> As far as I can see, there is no method to tidy up MCMCglmm output in broom. You can see that by looking at the "tidiers" functions in broom using:
> library(help = broom) #No MCMCglmm
>
> However, MCMCglmm output contains "mcmc" class objects that can be tidied up using tidyMCMC():
> - fixed effects: tidyMCMC(model$Sol)
> - random effects: tidyMCMC(model$VCV)
>
> Look up ?tidyMCMC for more options. I'm afraid it's difficult to get the pMCMC back though. You can get 95% credible intervals are a replacement for those (set conf.int = TRUE).
>
> I have also seen that Ben Bolker is working on a fork/split of broom for mixed models especially, maybe he plans on having a specific tidier for MCMCglmm?
>
> Best,
> Pierre.
>
>
> On Tuesday, 24 October 2017 20:13:53 NZDT dani wrote:
>> Hi everyone,
>>
>>
>> I would like to visualize the estimates from a MCMC glmm model and I tried using broom but I received the following message:
>>
>> Error in as.data.frame.default(mj) :
>>   cannot coerce class ""MCMCglmm"" to a data.frame
>> I was wondering what should I do about this?
>> Thank you in advance for all your help!
>> Best,
>> DaniNM
>>
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