From lennart at karssen.org  Wed Jun 24 09:55:32 2015
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 24 Jun 2015 09:55:32 +0200
Subject: [GenABEL-dev] DOI for the GenABEL tutorial
Message-ID: <558A6274.70204@karssen.org>

Dear list,

I have the following idea in mind and would like to hear your opinion.

With its 26 pages, the GenABEL tutorial [1,2] is an excellent source of
information for GenABEL users. To make it easier to cite it, I propose
to upload it to e.g. www.zenodo.org so that it gets a DOI. Uploading to
zenodo will also function as an archive (even though it is a young
service, it is backed by EU-funded projects and CERN).

Please let me know what you think. If I don't hear from you within the
next few days, I will proceed with the upload and inform you when I've
got the DOI.


Best regards,

Lennart.


[1]
https://r-forge.r-project.org/scm/viewvc.php/tutorials/GenABEL_general/?root=genabel
[2] http://www.genabel.org/tutorials
-- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From nicola.pirastu at burlo.trieste.it  Wed Jun 24 10:00:11 2015
From: nicola.pirastu at burlo.trieste.it (Pirastu Nicola)
Date: Wed, 24 Jun 2015 08:00:11 +0000
Subject: [GenABEL-dev] DOI for the GenABEL tutorial
In-Reply-To: <558A6274.70204@karssen.org>
References: <558A6274.70204@karssen.org>
Message-ID: <4226F370-66EB-4F67-BAD9-913B7EDCAF10@burlo.trieste.it>

Dear Lennart,

good idea.

Nicola

Il giorno 24/giu/2015, alle ore 09:55, L.C. Karssen <lennart at karssen.org> ha scritto:

> Dear list,
>
> I have the following idea in mind and would like to hear your opinion.
>
> With its 26 pages, the GenABEL tutorial [1,2] is an excellent source of
> information for GenABEL users. To make it easier to cite it, I propose
> to upload it to e.g. www.zenodo.org so that it gets a DOI. Uploading to
> zenodo will also function as an archive (even though it is a young
> service, it is backed by EU-funded projects and CERN).
>
> Please let me know what you think. If I don't hear from you within the
> next few days, I will proceed with the upload and inform you when I've
> got the DOI.
>
>
> Best regards,
>
> Lennart.
>
>
> [1]
> https://r-forge.r-project.org/scm/viewvc.php/tutorials/GenABEL_general/?root=genabel
> [2] http://www.genabel.org/tutorials
> --
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
> GPG key ID: A88F554A
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel messaggio, o responsabili per la sua consegna alla persona, o se avete ricevuto il messaggio per errore, siete pregati di non trascriverlo, copiarlo o inviarlo a nessuno. In tal caso vi invitiamo a cancellare il messaggio ed i suoi allegati. Grazie. CONFIDENTIALITY NOTICE Confidential information may be contained in this message or in its attachments. If you are not the addressee indicated in this message, or responsible for message delivering to that person, or if you have received this message in error, you may not transcribe, copy or deliver this message to anyone. In that case, you should delete this message and its attachments. Thank you.

From yurii.aulchenko at gmail.com  Wed Jun 24 12:25:48 2015
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 24 Jun 2015 12:25:48 +0200
Subject: [GenABEL-dev] DOI for the GenABEL tutorial
In-Reply-To: <4226F370-66EB-4F67-BAD9-913B7EDCAF10@burlo.trieste.it>
References: <558A6274.70204@karssen.org>
 <4226F370-66EB-4F67-BAD9-913B7EDCAF10@burlo.trieste.it>
Message-ID: <D413CEF4-F3F5-4731-8DBE-45F69114A6FF@gmail.com>

I also like the idea a lot 

Correction: 260 pages, not 26 :)



----------------------
Yurii Aulchenko 
(sent from mobile device)

> On 24 Jun 2015, at 10:00, Pirastu Nicola <nicola.pirastu at burlo.trieste.it> wrote:
> 
> Dear Lennart,
> 
> good idea.
> 
> Nicola
> 
>> Il giorno 24/giu/2015, alle ore 09:55, L.C. Karssen <lennart at karssen.org> ha scritto:
>> 
>> Dear list,
>> 
>> I have the following idea in mind and would like to hear your opinion.
>> 
>> With its 26 pages, the GenABEL tutorial [1,2] is an excellent source of
>> information for GenABEL users. To make it easier to cite it, I propose
>> to upload it to e.g. www.zenodo.org so that it gets a DOI. Uploading to
>> zenodo will also function as an archive (even though it is a young
>> service, it is backed by EU-funded projects and CERN).
>> 
>> Please let me know what you think. If I don't hear from you within the
>> next few days, I will proceed with the upload and inform you when I've
>> got the DOI.
>> 
>> 
>> Best regards,
>> 
>> Lennart.
>> 
>> 
>> [1]
>> https://r-forge.r-project.org/scm/viewvc.php/tutorials/GenABEL_general/?root=genabel
>> [2] http://www.genabel.org/tutorials
>> --
>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>> L.C. Karssen
>> Utrecht
>> The Netherlands
>> 
>> lennart at karssen.org
>> http://blog.karssen.org
>> GPG key ID: A88F554A
>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>> 
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 
> AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel messaggio, o responsabili per la sua consegna alla persona, o se avete ricevuto il messaggio per errore, siete pregati di non trascriverlo, copiarlo o inviarlo a nessuno. In tal caso vi invitiamo a cancellare il messaggio ed i suoi allegati. Grazie. CONFIDENTIALITY NOTICE Confidential information may be contained in this message or in its attachments. If you are not the addressee indicated in this message, or responsible for message delivering to that person, or if you have received this message in error, you may not transcribe, copy or deliver this message to anyone. In that case, you should delete this message and its attachments. Thank you.
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

From lennart at karssen.org  Wed Jun 24 12:27:19 2015
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 24 Jun 2015 12:27:19 +0200
Subject: [GenABEL-dev] DOI for the GenABEL tutorial
In-Reply-To: <D413CEF4-F3F5-4731-8DBE-45F69114A6FF@gmail.com>
References: <558A6274.70204@karssen.org>
 <4226F370-66EB-4F67-BAD9-913B7EDCAF10@burlo.trieste.it>
 <D413CEF4-F3F5-4731-8DBE-45F69114A6FF@gmail.com>
Message-ID: <558A8607.9030506@karssen.org>

On 24-06-15 12:25, Yurii Aulchenko wrote:
> I also like the idea a lot 

Happy to hear that.

> 
> Correction: 260 pages, not 26 :)

Oops! Factor of 10 missing indeed...




Lennart.

> 
> 
> 
> ----------------------
> Yurii Aulchenko 
> (sent from mobile device)
> 
>> On 24 Jun 2015, at 10:00, Pirastu Nicola <nicola.pirastu at burlo.trieste.it> wrote:
>>
>> Dear Lennart,
>>
>> good idea.
>>
>> Nicola
>>
>>> Il giorno 24/giu/2015, alle ore 09:55, L.C. Karssen <lennart at karssen.org> ha scritto:
>>>
>>> Dear list,
>>>
>>> I have the following idea in mind and would like to hear your opinion.
>>>
>>> With its 26 pages, the GenABEL tutorial [1,2] is an excellent source of
>>> information for GenABEL users. To make it easier to cite it, I propose
>>> to upload it to e.g. www.zenodo.org so that it gets a DOI. Uploading to
>>> zenodo will also function as an archive (even though it is a young
>>> service, it is backed by EU-funded projects and CERN).
>>>
>>> Please let me know what you think. If I don't hear from you within the
>>> next few days, I will proceed with the upload and inform you when I've
>>> got the DOI.
>>>
>>>
>>> Best regards,
>>>
>>> Lennart.
>>>
>>>
>>> [1]
>>> https://r-forge.r-project.org/scm/viewvc.php/tutorials/GenABEL_general/?root=genabel
>>> [2] http://www.genabel.org/tutorials
>>> --
>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>>> L.C. Karssen
>>> Utrecht
>>> The Netherlands
>>>
>>> lennart at karssen.org
>>> http://blog.karssen.org
>>> GPG key ID: A88F554A
>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>>
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
>> AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel messaggio, o responsabili per la sua consegna alla persona, o se avete ricevuto il messaggio per errore, siete pregati di non trascriverlo, copiarlo o inviarlo a nessuno. In tal caso vi invitiamo a cancellare il messaggio ed i suoi allegati. Grazie. CONFIDENTIALITY NOTICE Confidential information may be contained in this message or in its attachments. If you are not the addressee indicated in this message, or responsible for message delivering to that person, or if you have received this message in error, you may not transcribe, copy or deliver this message to anyone. In that case, you should delete this message and its attachments. Thank you.
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

-- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From yurii.aulchenko at gmail.com  Fri Jun 26 19:46:29 2015
From: yurii.aulchenko at gmail.com (Yury Aulchenko)
Date: Fri, 26 Jun 2015 19:46:29 +0200
Subject: [GenABEL-dev] Tolerance level in GenABEL RUnit test
In-Reply-To: <554CBFAD.4030008@karssen.org>
References: <554CB99F.10502@karssen.org> <554CBFAD.4030008@karssen.org>
Message-ID: <52454531-C43C-4D1F-918A-81DF824BB26B@gmail.com>

Interesting. I suspect what may be the reason (the way inverse is computer, or rather, not computed, by the new procedure, which makes difference in case of bad/poor GRMs), let me have a look in this when I get a little time. 

----------------
Sent from mobile device, please excuse possible typos

> On 08 May 2015, at 15:52, L.C. Karssen <lennart at karssen.org> wrote:
> 
> I spoke too early: in fact almost all checks in runit.polylik.R fail:
> 
>> checkEquals(h2htNew$h2an$est,h2htOld$h2an$est, tolerance = tol)
> Error in checkEquals(h2htNew$h2an$est, h2htOld$h2an$est, tolerance = tol) :
>  Mean relative difference: 3.36492e-05
> 
>>    checkEquals(h2htNew$h2an$min,h2htOld$h2an$min, tolerance = tol)
> Error in checkEquals(h2htNew$h2an$min, h2htOld$h2an$min, tolerance = tol) :
>  Mean relative difference: 5.961843e-06
> 
>> checkEquals(h2htNew$residualY,h2htOld$residualY, tolerance = tol)
> Error in checkEquals(h2htNew$residualY, h2htOld$residualY, tolerance =
> tol) :
>  Mean relative difference: 4.462787e-05
> 
>>    checkEquals(h2htNew$pgresidualY,h2htOld$pgresidualY, tolerance = tol)
> Error in checkEquals(h2htNew$pgresidualY, h2htOld$pgresidualY, tolerance
> = tol) :
>  Mean relative difference: 0.001496624
> 
>> checkEquals(h2htNew$InvSigma,h2htOld$InvSigma, tolerance = tol)
> Error in checkEquals(h2htNew$InvSigma, h2htOld$InvSigma, tolerance = tol) :
>  Mean relative difference: 0.004265527
> 
>>    checkEquals(h2htNew$measuredIDs,h2htOld$measuredIDs, tolerance = tol)
> [1] TRUE
> 
> 
> So the question remains: is this to be expected and should the tolerance
> be set less strict or is this a true bug that needs fixing?
> 
> 
> Thanks,
> 
> Lennart.
> 
>> On 08-05-15 15:26, L.C. Karssen wrote:
>> Dear list,
>> 
>> I just ran the unit tests in GenABEL's /insts/unitTests/ directory and
>> get the following error:
>> 
>>  1 Test Suite :
>>  GenABEL unit testing - 21 test functions, 0 errors, 1 failure
>>  FAILURE in test.polylik: Error in checkEquals(h2htNew$h2an$est,
>> h2htOld$h2an$est, tolerance = tol) :
>>    Mean relative difference: 8.295007e-05
>>  Error:
>> 
>>  unit testing failed (#test failures: 1, #R errors: 0)
>> 
>> 
>> This is a test in the runit.polylik.R file. The variable "tol" is set to
>> 2*.Machine$double.eps^0.5, which is equal to 2.980232e-08 on my
>> machine. As you can see the difference in the unit test is more than
>> three orders of magnitude higher.
>> 
>> The two variables that are compared are calculated like this:
>>  h2htOld <- polygenic(formula,kin=gkin,df,llfun="polylik")
>>  h2htNew <- polygenic(formula,kin=gkin,df,llfun="polylik_eigen")
>> 
>> Since I'm not an expert on the finer details of the various functions
>> used in polygenic() I was hoping one of you could enlighten me and tell
>> me if we should expect the comparison to give a difference of order 1e-8
>> or that 1e-4 is good enough.
>> 
>> 
>> Thanks for your help,
>> 
>> Lennart.
>> 
>> 
>> 
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 
> -- 
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
> L.C. Karssen
> Utrecht
> The Netherlands
> 
> lennart at karssen.org
> http://blog.karssen.org
> GPG key ID: A88F554A
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel