[R-sig-ME] Error in initializePtr() : updateMu: Size mismatch

[Pamela Ochungo]

Hi Cesko,

Thanks! I see my mistake now! I have called the summary and it works
perfectly well!

How would you visualize the results? Graphing residuals?

Cheers and thanks once again!

Pamela

On Sat, May 2, 2020 at 12:48 PM Voeten, C.C. <c.c.voeten using hum.leidenuniv.nl>
wrote:

> Hi Pamela,
>
> Re gam(): it looks like you merely didn't call summary() on your fitted
> model object?
>
> Re separate models: whether or not this is appropriate depends entirely on
> your data and what you want to do with them. If you want to compare the
> different dependent variables to one another, or if you want to assume that
> there is correlation between them, then you need a multivariate model. But
> if the different dependent variables represent wholly separate measures and
> they are uncorrelated (or your substantive question permits you to leave
> such correlation out of the analysis), then I see no problem with running
> separate models instead.
>
> Best,
> Cesko
>
> From: Pamela Ochungo <pamochungo using gmail.com>
> Sent: Friday, May 1, 2020 10:15 PM
> To: Voeten, C.C. <c.c.voeten using hum.leidenuniv.nl>
> Cc: r-sig-mixed-models using r-project.org
> Subject: Re: [R-sig-ME] Error in initializePtr() : updateMu: Size mismatch
>
> Hi Cesko,
>
> Thanks for your reply! I have tried the second option, function gam() from
> mgcv. However I get an unexpected result as below:
>
> Family: Multivariate normal
> Link function:
>
> Formula:
> transpopbees ~ Varroa + s(Site, bs = "re") + s(Colony,
>     bs = "re")
> transbrood ~ Varroa + s(Site, bs = "re") + s(Colony, bs = "re")
> transhoney ~ Varroa + s(Site, bs = "re") + s(Colony, bs = "re")
> transpollen ~ Varroa + s(Site, bs = "re") + s(Colony, bs = "re")
> transeggs ~ Varroa + s(Site, bs = "re") + s(Colony, bs = "re")
>
> Estimated degrees of freedom:
> 0.0001 0.7631 0.0000 0.0003 1.7061 0.0003 1.7192
> 0.0002 0.0000 0.0003  total = 29.19
>
> REML score: 547.659
>
> How do I interpret this? I was rather hoping to get a result showing model
> coefficients and p-values for each dependent variable.
>
>
> Question: Is it acceptable to carry out LMM (lmer) for each of the 5
> dependent variables separately against Varroa?
>
> Cheers
>
> Pamela
>
> On Fri, May 1, 2020 at 10:25 PM Voeten, C.C. <mailto:
> c.c.voeten using hum.leidenuniv.nl> wrote:
> Hi Pamela,
>
> lmer/glmer do not support models with multiple dependent variables via the
> cbind() syntax. An alternative approach is to convert your data to long
> format and run the model in the following way:
>
> value ~ 0+variable/Varroa + (0+variable|Site) + (0+variable|Colony)
>
> with 'variable' the column containing "transpopbees", "transbrood", ...,
> and 'value' the column containing their values.
> Alternatively, function gam() from package mgcv can fit your model. You
> would then use something like:
>
> gam(list(transpopbees ~ Varroa + s(Site,bs='re') + s(Colony,bs='re'),
> transbrood ~ Varroa + s(Site,bs='re') + s(Colony,bs='re'),
> .....),family=mvn(5),data=pollencolony)
>
> Hope this helps,
> Cesko
>
> -----Original Message-----
> From: R-sig-mixed-models <mailto:r-sig-mixed-models-bounces using r-project.org>
> On Behalf Of Pamela Ochungo
> Sent: Friday, May 1, 2020 9:00 PM
> To: mailto:r-sig-mixed-models using r-project.org
> Subject: [R-sig-ME] Error in initializePtr() : updateMu: Size mismatch
>
> Hallo,
>
> I want to run a linear mixed model featuring 5 response variables and only
> one predictor variable. I also have two random effects in the model. I am
> using this code:
>
> lm1 <- lmer(cbind(transpopbees, transbrood, transhoney, transpollen,
> transeggs) ~ Varroa+(1|Site)+(1|Colony),data=pollencolony)
>
> However I get this error message:
>
> Error in initializePtr() : updateMu: Size mismatch
>
> What does this mean and what am I doing wrong?
>
> Thanks
>
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