[R-sig-ME] Model average error message

Wed Jul 25 19:15:03 CEST 2018

Hi Phil

I have run the lapply code and this was the output

lapply(get.models(models,subset=delta<5),formula)

$`720`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:t + p:s + s:t

$`976`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:t + p:s + p:t + s:t

$`9168`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:t + p:s + p:t + s:t + p:s:t

$`9120`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + p:s + p:t + s:t + p:s:t

$`640`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + s:t

$`768`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + s:t

$`896`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:t + s:t

$`1024`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t

$`1792`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + s:t + d:p:s

$`2048`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + d:p:s

$`2944`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:t + s:t + d:p:t

$`3072`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + d:p:t

$`4096`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + d:p:s + d:p:t

$`4736`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + s:t + d:s:t

$`4864`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + s:t + d:s:t

$`4992`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:t + s:t + d:s:t

$`5120`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + d:s:t

$`5888`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + s:t + d:p:s + d:s:t

$`6144`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + d:p:s + d:s:t

$`7040`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:t + s:t + d:p:t + d:s:t

$`7168`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + d:p:t + d:s:t

$`8192`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + d:p:s + d:p:t + d:s:t

$`9216`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + p:s:t

$`10240`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + d:p:s + p:s:t

$`11264`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + d:p:t + p:s:t

$`12288`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + d:p:s + d:p:t + p:s:t

$`13312`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + d:s:t + p:s:t

$`14336`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + d:p:s + d:s:t + p:s:t

$`15360`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + d:p:t + d:s:t + p:s:t

$`16384`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + d:p:s + d:p:t + d:s:t + p:s:t

$`32768`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + s:t + d:p:s + d:p:t + d:s:t + p:s:t + d:p:s:t

$`960`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + p:s + p:t + s:t

$`1984`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + p:s + p:t + s:t + d:p:s

$`9152`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + p:s + p:t + s:t + p:s:t

$`10176`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + p:s + p:t + s:t + d:p:s + p:s:t

$`736`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:t + p:s + s:t

$`992`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:t + p:s + p:t + s:t

$`3040`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:t + p:s + p:t + s:t + d:p:t

$`9184`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:t + p:s + p:t + s:t + p:s:t

$`11232`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:t + p:s + p:t + s:t + d:p:t + p:s:t

$`624`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:s + d:t + s:t

$`752`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:s + d:t + p:s + s:t

$`880`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:s + d:t + p:t + s:t

$`1008`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:s + d:t + p:s + p:t + s:t

$`4720`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:s + d:t + s:t + d:s:t

$`4848`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:s + d:t + p:s + s:t + d:s:t

$`4976`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:s + d:t + p:t + s:t + d:s:t

$`5104`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:s + d:t + p:s + p:t + s:t + d:s:t

$`9200`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:s + d:t + p:s + p:t + s:t + p:s:t

$`13296`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:s + d:t + p:s + p:t + s:t + d:s:t + p:s:t

$`622`

cbind(numerator, total - numerator) ~ d + s + t + (1 | random) + d:s + d:t + s:t

$`4718`

cbind(numerator, total - numerator) ~ d + s + t + (1 | random) + d:s + d:t + s:t + d:s:t

$`590`

cbind(numerator, total - numerator) ~ d + s + t + (1 | random) + d:t + s:t

$`608`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:t + s:t

$`864`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:t + p:t + s:t

$`2912`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:t + p:t + s:t + d:p:t

$`592`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:t + s:t

$`848`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:t + p:t + s:t

$`704`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + p:s + s:t

$`1728`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + p:s + s:t + d:p:s

$`7`

cbind(numerator, total - numerator) ~ p + s + (1 | random)

$`76`

cbind(numerator, total - numerator) ~ d + p + t + (1 | random) + d:t

$`332`

cbind(numerator, total - numerator) ~ d + p + t + (1 | random) + d:t + p:t

$`92`

cbind(numerator, total - numerator) ~ d + p + t + (1 | random) + d:p + d:t

$`348`

cbind(numerator, total - numerator) ~ d + p + t + (1 | random) + d:p + d:t + p:t

$`2396`

cbind(numerator, total - numerator) ~ d + p + t + (1 | random) + d:p + d:t + p:t + d:p:t

$`5`

cbind(numerator, total - numerator) ~ s + (1 | random)

$`184`

cbind(numerator, total - numerator) ~ d + p + s + (1 | random) + d:p + d:s + p:s

$`1208`

cbind(numerator, total - numerator) ~ d + p + s + (1 | random) + d:p + d:s + p:s + d:p:s

$`928`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + p:s + p:t + s:t

$`135`

cbind(numerator, total - numerator) ~ p + s + (1 | random) + p:s

$`152`

cbind(numerator, total - numerator) ~ d + p + s + (1 | random) + d:p + p:s

$`112`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:s + d:t

$`240`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:s + d:t + p:s

$`368`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:s + d:t + p:t

$`496`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:s + d:t + p:s + p:t

$`448`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + p:s + p:t

$`1472`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + p:s + p:t + d:p:s

$`128`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t

$`256`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s

$`384`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:t

$`512`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t

$`1280`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + d:p:s

$`1536`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + d:p:s

$`2432`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:t + d:p:t

$`2560`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + d:p:t

$`3584`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:s + d:t + p:s + p:t + d:p:s + d:p:t

$`78`

cbind(numerator, total - numerator) ~ d + s + t + (1 | random) + d:t

$`80`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:t

$`336`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:t + p:t

$`96`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:t

$`352`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:t + p:t

$`2400`

cbind(numerator, total - numerator) ~ d + p + s + t + (1 | random) + d:p + d:t + p:t + d:p:t

Does this help?

Many thanks

Helen

From: Helen McCallin<mailto:helenmccallin using hotmail.com>
Sent: 25 July 2018 16:17
To: Phillip Alday<mailto:phillip.alday using mpi.nl>
Cc: r-sig-mixed-models using r-project.org<mailto:r-sig-mixed-models using r-project.org>
Subject: Re: [R-sig-ME] Model average error message

Apologies, very new to this! I am currently away from my computer but as soon as I am home (within the hour) I will get those for you.

Many thanks again

Helen

> On 25 Jul 2018, at 16:09, Phillip Alday <phillip.alday using mpi.nl> wrote:
>
> (Please keep the list in CC.)
>
> The output of
>
> get.models(models,subset=delta<5)
>
> would be more interesting. Or even better:
>
> lapply(get.models(models,subset=delta<5), formula)
>
> So that we see which formulas are being labelled as identical.
>
> Phillip
>
>> On 07/25/2018 04:56 PM, Helen McCallin wrote:
>> Hi Phil
>>
>> Thank you so much for your reply. Please find the codes I am using
>> below. Is this what you mean?
>>
>> ae <- read.csv(file=file.choose())
>>
>> options(na.action="na.fail")
>>
>> global.model<-glmer(
>>
>>
>> cbind(numerator,total-numerator)~d+s+t+p+d:s:t:p+d:s:t+d:s:p+d:t:p+s:t:p+d:t+d:s+d:p+s:t+s:p+t:p+(1|random),
>>
>>     data=ae, family=binomial)
>>
>> options(max.print=1000000)
>>
>> dredge(global.model,beta=c("none"),evaluate=TRUE,rank="AICc")
>>
>> ae.model <- glmer(
>>
>>
>> cbind(numerator,total-numerator)~d+s+t+p+d:s:t:p+d:s:t+d:s:p+d:t:p+s:t:p+d:t+d:s+d:p+s:t+s:p+t:p+(1|random),
>>
>>    data=ae,family=binomial)
>>
>> models <- dredge(ae.model)
>>
>> summary(model.avg(get.models(models,subset=delta<5)))
>>
>>
>> Many thanks for any help.
>>
>> Best wishes
>>
>> Helen
>>
>> On 25 Jul 2018, at 13:50, Phillip Alday <phillip.alday using mpi.nl
>> <mailto:phillip.alday using mpi.nl>> wrote:
>>
>>> Hi Helen,
>>>
>>> model.avg() tells you which models are duplicates. What do the formulas
>>> look like for those models? Seeing the formulae may help identify what
>>> model.avg() gets stuck on.
>>>
>>> Best,
>>> Phillip
>>>
>>>> On 07/23/2018 11:33 AM, Helen McCallin wrote:
>>>> Hi
>>>>
>>>>
>>>> I am running a glmer model on a response variable with binomial
>>>> distribution and random term. My data has 3 explanatory categorical
>>>> variables and I have successfully run dredge() on them and their
>>>> interactions to get AICc values.
>>>>
>>>>
>>>> I want model averaging to provide output with coefficients and an
>>>> index of relative importance of fixed effects from those models;
>>>> within a delta constraint that I specify.I can get this using the
>>>> code below for alternative datasets but not for this dataset.
>>>>
>>>>
>>>> model.avg() produces this error message:
>>>>
>>>> Error in model.avg.default(get.models(models, subset = delta < 5)) :
>>>> models are not unique. Duplicates: '2 = 3 = 4' and '10 = 11'
>>>>
>>>>
>>>> This doesn't make sense, DREDGE does not (cannot) produce duplicate
>>>> models � each model is a unique iteration within the full model, yet
>>>> the error message indicates that MODEL AVERAGE identified �duplicate�
>>>> models from within DREDGE output. R fails to run MODEL AVERAGE under
>>>> these circumstances - producing no further output.
>>>>
>>>>
>>>> Has anyone else experienced similar problem (with 'not unique',
>>>> duplicate models) via MODEL AVERAGE?
>>>>
>>>>
>>>> Is there a workaround for the error that prevents me running MODEL
>>>> AVERAGE due to perceived �duplicate� models in DREDGE?
>>>>
>>>>
>>>> Many thanks for any help anyone can provide.
>>>>
>>>>
>>>>
>>>>   [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
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>>>> <mailto:R-sig-mixed-models using r-project.org> mailing list
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