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:***@hotmail.com>
Sent: 25 July 2018 16:17
To: Phillip Alday<mailto:***@mpi.nl>
Cc: r-sig-mixed-***@r-project.org<mailto:r-sig-mixed-***@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 <***@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 <***@mpi.nl
>> <mailto:***@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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>>>>
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