Matt.

On Friday, April 5, 2013, Mark Seeto wrote:

Thanks for your reply Matt (and thank you to you and your colleagues
for providing this great software!).

If I ignore my two nominal variables, the highest correlation is 0.92
(and I'm confident that there's no correlation problem with the
nominal variables). I tried using findLinearCombos, but it appears not
to work with data having missing values.

I'm happy to just use version 1.6.1, but I'm looking to use the
"priors" argument for the first time. I note that the package news
page says that in version 1.7 a bug with priors was fixed - how
serious was that bug, and does it mean that using priors with version
1.6.1 would be a bad idea?

Thanks,
Mark

On Fri, Apr 5, 2013 at 11:26 PM, Matt Blackwell
<m.blackwell@rochester.edu> wrote:
> Hi Mark,
>
> We changed the infrastructure of Amelia in 1.7 to improve the speed
> considerably, but there may be consequences in terms of tolerance for highly
> correlated data. You might want to check to see if there are variables in
> the data with correlation above .95 or use the "findLinearCombos" function
> from the "caret" package to see if there are linear combinations hidden
> somewhere in the data. Unfortunately, a lot has changed from 1.6.1 to 1.7.1,
> so it's hard to exactly pin down your issues, but it seems very likely due
> to the structure of the data.
>
> Hope that helps!
>
> Cheers,
> matt.
>
> ~~~~~~~~~~~
> Matthew Blackwell
> Assistant Professor of Political Science
> University of Rochester
> url: http://www.mattblackwell.org
>
>
> On Fri, Apr 5, 2013 at 12:27 AM, Mark Seeto <markseeto@gmail.com> wrote:
>>
>> Dear Amelia mailing list,
>>
>> I have some code that runs in Amelia 1.6.1 (with R 2.15.0) without any
>> problems. When I run that same code in Amelia 1.7.1 (with R 3.0.0), a
>> few imputations might finish without any error messages, but many
>> finish with the message "The resulting variance matrix was not
>> invertible. Please check your data for highly collinear variables".
>> I understand that this suggests that there may be a problem with the
>> data, but I don't understand why there would be a problem in version
>> 1.7.1 but not in 1.6.1.
>>
>> Also, when I'm using Amelia 1.7.1 in R 3.0.0, R will sometimes crash
>> during the imputation process. I'm running R in emacs in Windows, and
>> I'll sometimes get a pop-up window saying "R for Windows terminal
>> front-end has stopped working", with the following message appearing
>> in emacs:
>>
>> "error: chol(): failed to converge
>>
>> This application has requested the Runtime to terminate it in an unusual
>> way.
>> Please contact the application's support team for more information.
>> terminate called after throwing an instance of 'std::runtime_error'
>> what():
>>
>> Process R exited abnormally with code 3 at Fri Apr 05 15:04:58 2013"
>>
>> Amelia 1.7.1 worked without any problems when I tried it on some small
>> made-up data, but not on my real data. I understand that it's almost
>> impossible to diagnose problems without a reproducible example, but I
>> was wondering whether others have had similar problems.
>>
>> Thanks for any comments you can give.
>>
>> Mark Seeto
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>