[R] package installtion

[Uwe Ligges]

On 16.11.2011 16:08, Scott Raynaud wrote:
> All right.  I upped my level 2 sample size to 60.  My log displays the following:
>
>                   Simulation for sample sizes of  60  macro and unbalanced micro units
>   Iteration remain= 990
>   Iteration remain= 980
> There were 27 warnings (use warnings() to see them)
> Error in diag(vcov(fitmodel)) :
>    error in evaluating the argument 'x' in selecting a method for function 'diag': Error in asMethod(object) : matrix is not symmetric [1,2]
>
> Looking at the warnings I see:
>
> 26: glm.fit: algorithm did not converge
> 27: In mer_finalize(ans) : gr cannot be computed at initial par (65)
>
> The first 25 are like 26.  So, it seems I'm having the same problem as before.  Again, if this is due to a column of zeroes in my x matrix, the best solution would be to assign zeroes to the fixed effects, but I'm not sure if there's a way to do this.

Why don't you simply delete that variable and hence don't estimate 
coefficients for it....

Uwe Ligges




>
> ----- Forwarded Message -----
> From: Scott Raynaud<scott.raynaud at yahoo.com>
> To: "r-help at r-project.org"<r-help at r-project.org>
> Cc:
> Sent: Wednesday, November 16, 2011 7:28 AM
> Subject: Re: [R] package installtion
>
> Well, I could increase the sample size for my second level in hopes that my simulation would run correctly.  However, a better solution would be to assign values of 0 to the fixed effects for this pass through the simulation.  I'm such a novice with R that I don't know if that can be done.  I've looked at the documentation but it's still not clear.
>
>
> ----- Original Message -----
> From: Uwe Ligges<ligges at statistik.tu-dortmund.de>
> To: Scott Raynaud<scott.raynaud at yahoo.com>
> Cc: "r-help at r-project.org"<r-help at r-project.org>
> Sent: Wednesday, November 16, 2011 2:44 AM
> Subject: Re: [R] package installtion
>
>
>
> On 15.11.2011 21:34, Scott Raynaud wrote:
>> OK, I think I see the problem.  Rather than setting method="nAGQ" I need nAGQ=1.  Doing so throws the following error:
>
> Congratulations, now you understood what R meant with its message
> "Argument ‘method’ is deprecated."
>
>> "Warning messages:
>> 1: glm.fit: algorithm did not converge
>> 2: In mer_finalize(ans) : gr cannot be computed at initial par (65)
>> Error in diag(vcov(fitmodel)) :
>>      error in evaluating the argument 'x' in selecting a method for function 'diag': Error in asMethod(object) : matrix is not symmetric [1,2]"
>>
>> I need some help interpreting and debugging this.  One thing that I suspect is that there is a column of zeroes in the design matrix,
>
> So have you not even tried to get rid of that? Oh, come on.
>
> Uwe Ligges
>
>
>
>> but I'm not sure.  Any other possibilities here and how can I diagnose?
>>
>> ----- Original Message -----
>> From: Scott Raynaud<scott.raynaud at yahoo.com>
>> To: "r-help at r-project.org"<r-help at r-project.org>
>> Cc:
>> Sent: Tuesday, November 15, 2011 2:11 PM
>> Subject: Re: package installtion
>>
>> Never mind-I fixed it.
>>
>> My script is throwing the following error:
>>
>> "Error in glmer(formula = modelformula, data = data, family = binomial(link = logit),  :
>>      Argument ‘method’ is deprecated.
>> Use ‘nAGQ’ to choose AGQ.  PQL is not available."
>>
>> I remember hearing somewhere that PQL is no longer available on lme4 but I have AGQ specified.
>>
>> Here's the line that fits my model:
>>
>> (fitmodel<- lmer(modelformula,data,family=binomial(link=logit),method="AGQ"))
>>
>> If I change it to nAGQ I still get an error.
>>
>> Any ideas as to what's going on?
>>
>> ----- Original Message -----
>> From: Scott Raynaud<scott.raynaud at yahoo.com>
>> To: "r-help at r-project.org"<r-help at r-project.org>
>> Cc:
>> Sent: Tuesday, November 15, 2011 1:50 PM
>> Subject: package installtion
>>
>> I'm getting the following error in a script: "Error: could not find function "lmer."    I'm wondering of my lme4 package is installed incorrectly.  Can someone tell me the installation procedure?  I looked at the support docs but couldn't translate that into anything that would work.
>>
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>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.