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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Dear Lennart,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">I would very much appreciate if RepeatABEL is added to the list at
</span><a href="http://www.genabel.org/packages"><span lang="EN-US">http://www.genabel.org/packages</span></a>
<span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">
and would appreciate if I get access to the content management system. After including me as developer in the R-Forge project I will commit the package via SVN.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">If possible, I would like to get it all done this week.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Lars<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><br>
<br>
<br>
</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Xia Shen [mailto:xia.shen@ki.se]
<br>
<b>Sent:</b> den 6 november 2015 17:31<br>
<b>To:</b> L.C. Karssen <l.c.karssen@polyomica.com><br>
<b>Cc:</b> Lars Rönnegård <lrn@du.se>; Yurii Aulchenko (yurii.aulchenko@gmail.com) <yurii.aulchenko@gmail.com>; genabel-devel@lists.r-forge.r-project.org<br>
<b>Subject:</b> Re: RepeatABEL<o:p></o:p></span></p>
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<p class="MsoNormal">Thanks Lennart, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I suggest including Lars as one developer in our R-Forge project so that he can commit the package via SVN.<o:p></o:p></p>
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<p class="MsoNormal">Editing <a href="http://genabel.org">genabel.org</a> sounds great. I wonder whether I should do the same for the MultiABEL package, but I think I can wait until the main papers get reviewed.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Xia<o:p></o:p></p>
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<p class="MsoNormal">On 06 Nov 2015, at 16:25, L.C. Karssen <<a href="mailto:l.c.karssen@polyomica.com">l.c.karssen@polyomica.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Dear Lars, Xia,<br>
<br>
On 06-11-15 15:06, Lars Rönnegård wrote:<br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">*Dear Lennart and Yurii,*<br>
<br>
*I attach the revised version of the RepeatABEL package following Xia’s<br>
review comments, which were very useful.*<o:p></o:p></p>
</blockquote>
<p class="MsoNormal"><br>
Xia, thank you for doing the review!<br>
<br>
<br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><br>
* *<br>
<br>
*If you find my revision acceptable, I would be happy to have the<br>
package within the GenABEL suite of packages.*<o:p></o:p></p>
</blockquote>
<p class="MsoNormal"><br>
<br>
This looks great! Thank you for the updates according to Xia's comments.<br>
We would be happy to accept RepeatABEL into the GenABEL suite.<br>
<br>
Some questions related to the GenABEL "membership":<br>
<br>
1) A technical question: would you like to save the RepeatABEL code in a<br>
public version control repository? The advantage would be that other<br>
people could more easily contribute to the development of the package,<br>
e.g. by fixing bugs.<br>
For the GenABEL Project we currently use the Subversion repository on<br>
R-forge [1] or Github [2].<br>
<br>
2) To increase the visibility of your package we can list it on<br>
<a href="http://www.genabel.org/packages">http://www.genabel.org/packages</a>. Is that OK with you?<br>
<br>
3) In addition to the above we can give you access to the content<br>
management system running <a href="http://www.genabel.org">www.genabel.org</a> so you can customise the<br>
RepeatABEL package page (see e.g. [3]), would you be interested in that?<br>
<br>
<br>
Finally, please take note of the responsibilities we expect from package<br>
maintainers [4].<br>
<br>
<br>
Best regards,<br>
<br>
<br>
Lennart.<br>
<br>
<br>
[1] <a href="https://r-forge.r-project.org/scm/?group_id=505">https://r-forge.r-project.org/scm/?group_id=505</a><br>
[2] <a href="https://github.com/GenABEL-Project">https://github.com/GenABEL-Project</a><br>
[3] <a href="http://www.genabel.org/packages/PredictABEL">http://www.genabel.org/packages/PredictABEL</a><br>
[4] <a href="http://www.genabel.org/developers#maintainer_responsibilities">http://www.genabel.org/developers#maintainer_responsibilities</a><br>
<br>
<br>
<br>
<br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
* *<br>
<br>
*Best regards,*<br>
<br>
*Lars Rönnegård*<br>
<br>
* *<br>
<br>
* *<br>
<br>
* *<br>
<br>
------------------------------------------------------------------------<br>
<br>
*From:* Xia Shen <<a href="mailto:xia.shen@ki.se">xia.shen@ki.se</a> <<a href="mailto:xia.shen@ki.se">mailto:xia.shen@ki.se</a>>><br>
*Sent:* Tuesday, October 27, 2015 06:19<br>
*To:* Lars Rönnegård<br>
*Cc:* L.C. Karssen<br>
*Subject:* Re: RepeatABEL<br>
<br>
<br>
<br>
Review of Package RepeatABEL v. 0.1<br>
<br>
Xia Shen<br>
<br>
Oct 26, 2015<br>
<br>
<br>
<br>
1. Introduction<br>
<br>
<br>
<br>
This is a novel contribution for the GenABEL project. Although the<br>
underlying model is more or less the same as polygenic_hglm + mmscore,<br>
the main motivation is that the GenABEL package does not deal with<br>
repeated measurements. The package is easy to use and provides an useful<br>
analytical framework for GWAS with repeated measurements, identical<br>
twins, clones, etc.<br>
<br>
<br>
<br>
2. Legal issues<br>
<br>
2.1. Is the copyright holder clearly mentioned?<br>
<br>
<br>
<br>
The author and maintainer are listed in DESCRIPTION and package help. It<br>
could also be displayed while loading the package.<br>
<br>
<br>
<br>
2.2. Is there a clear (standard) license?<br>
<br>
<br>
<br>
Yes. GPL.<br>
<br>
<br>
<br>
3. Technical quality<br>
<br>
3.1. Is the installation procedure clearly documented? Is the code easy<br>
to compile and run?<br>
<br>
<br>
<br>
Not documented in the tutorial, but easy to install as a standard R<br>
package. The compilation and basic running were successful.<br>
<br>
<br>
<br>
3.2. [For R packages] Does the package pass CRAN checks ()? At minimum,<br>
run "R CMD check …" and "R CMD check –as-cran …"<br>
<br>
<br>
<br>
The beginning of DESCRIPTION is redundant in CRAN check standard: 'The<br>
RepeatABEL package is used to'. <br>
<br>
<br>
<br>
R CMD check --as-cran produces:<br>
<br>
<br>
<br>
The Title field should be in title case, current version then in title case:<br>
<br>
‘GWAS for multiple observations on related individuals’<br>
<br>
‘GWAS for Multiple Observations on Related Individuals’<br>
<br>
<br>
<br>
The Date field is over a month old.<br>
<br>
<br>
<br>
Rd file 'preFitmodel.Rd':<br>
<br>
\usage lines wider than 90 characters:<br>
<br>
preFitModel(fixed=y~1, random=~1|id, id.name="id", genabel.data,<br>
phenotype.data, corStruc=NULL, GRM=NULL, Neighbor.Matrix=NULL)<br>
<br>
\examples lines wider than 100 characters:<br>
<br>
Mod1 <- preFitModel(fixed, random=~1|id, genabel.data = gen.data,<br>
phenotype.data = Phen.Data, corStruc=list( id=list("GRM","Ind") ))<br>
<br>
Mod2 <- preFitModel(fixed, random=~1|id + 1|nest, genabel.data =<br>
gen.data, phenotype.data = Phen.Data, corStruc=list( id=list("GRM","In<br>
... [TRUNCATED]<br>
<br>
Mod3 <- preFitModel(fixed, random=~1|id + 1|nest, genabel.data =<br>
gen.data, phenotype.data = Phen.Data, corStruc=list( id=list("GRM","In<br>
... [TRUNCATED]<br>
<br>
<br>
<br>
Rd file 'rGLS.rd':<br>
<br>
\usage lines wider than 90 characters:<br>
<br>
rGLS(formula.FixedEffects = y ~ 1, genabel.data, phenotype.data,<br>
id.name = "id", GRM = NULL, V = NULL, memory=1e8)<br>
<br>
<br>
<br>
Rd file 'simulate_PhenData.Rd':<br>
<br>
\usage lines wider than 90 characters:<br>
<br>
simulate_PhenData(formula.FixedEffects = y ~ 1, genabel.data,<br>
n.obs, SNP.eff = NULL, SNP.nr = NULL, beta = NULL, VC = c(1, 1, 1), GRM<br>
= ... [TRUNCATED]<br>
<br>
\examples lines wider than 100 characters:<br>
<br>
Phen.Sim <- simulate_PhenData(y ~ age,<br>
genabel.data=gen.data, n.obs=rep(4, nids(gen.data)), SNP.eff=1,<br>
SNP.nr=1000, VC=c(1,1,1) ... [TRUNCATED]<br>
<br>
<br>
<br>
These lines will be truncated in the PDF manual.<br>
<br>
<br>
<br>
Please fix.<br>
<br>
<br>
<br>
3.3. Is the package documented? What is the quality of the documentation?<br>
<br>
<br>
<br>
Yes. Good tutorial with standard Rd documentation.<br>
<br>
<br>
<br>
3.4. [For R packages] Does help(PackageName) provide an adequate summary<br>
of the package and a review of the major functions?<br>
<br>
<br>
<br>
Yes. But the displayed version number is different from what's in<br>
DESCRIPTION. Please check.<br>
<br>
<br>
<br>
3.5. [For R packages] Does the package use Roxygen2 for documentation?<br>
<br>
<br>
<br>
No. Roxygen2 is recommended, which keeps doc and code in the same R file<br>
and auto-generates Rd files.<br>
<br>
<br>
<br>
3.6. Are examples of usage provided?<br>
<br>
<br>
<br>
Yes.<br>
<br>
<br>
<br>
3.7. Does the package provide a tutorial/vignette? Can you comment on<br>
the tutorial?<br>
<br>
<br>
<br>
Yes. The tutorial is good and easy to follow. <br>
<br>
<br>
<br>
3.8. Is the source code of the tutorial/vignette provided?<br>
<br>
<br>
<br>
No. I recommend including the tutorial as a vignette.<br>
<br>
<br>
<br>
3.9. Does the package make use of unit/integration/etc. tests?<br>
<br>
<br>
<br>
No.<br>
<br>
<br>
<br>
3.10. [For R packages] Does the package make use of unit tests (e.g.<br>
RUnit or testthat)?<br>
<br>
<br>
<br>
No.<br>
<br>
<br>
<br>
3.11. Does the code comply with the GenABEL coding standards?<br>
<br>
<br>
<br>
Not entirely. Please refer<br>
to <a href="http://genabel.r-forge.r-project.org/codingstyle.html">http://genabel.r-forge.r-project.org/codingstyle.html</a><br>
<br>
<br>
<br>
3.12. Is the code readable/understandable?<br>
<br>
<br>
<br>
More or less.<br>
<br>
<br>
<br>
3.13. Does the code contain explanatory comments?<br>
<br>
<br>
<br>
Yes.<br>
<br>
<br>
<br>
3.14. Were the design and methods implemented in package discussed<br>
during the development process (e.g. on the genabel-devel mailing list)?<br>
<br>
<br>
<br>
Yes. A little.<br>
<br>
<br>
<br>
4. Content<br>
<br>
4.1. Does the package address a problem in the domain of statistical<br>
genomics?<br>
<br>
<br>
<br>
Yes.<br>
<br>
<br>
<br>
4.2. Is it streamlining analyses not covered elsewhere in the GenABEL<br>
suite? If not, does it improve the analysis already covered?<br>
<br>
<br>
<br>
No and yes. <br>
<br>
<br>
<br>
4.3. Should it become a separate package or rather be incorporated into<br>
an existing package?<br>
<br>
<br>
<br>
A separate package is the current form and in this case would be easy to<br>
maintain in practice, although I also feel that it could actually be<br>
easy to integrate the main rGLS function into the GenABEL package.<br>
<br>
<br>
<br>
4.4. Does the package use any of the data types defined in other GenABEL<br>
packages?<br>
<br>
<br>
<br>
Yes. The gwaa.data class of GenABEL is used.<br>
<br>
<br>
<br>
4.5. Does the package use code/functions/data defined in other GenABEL<br>
packages?<br>
<br>
<br>
<br>
Yes.<br>
<br>
<br>
<br>
5. Recommendations<br>
<br>
5.1. What are the major issues that should be addressed?<br>
<br>
<br>
<br>
Nothing specifically more than above. After fixing the above issues, the<br>
package can be committed to GenABEL project R-Forge SVN.<br>
<br>
<br>
<br>
5.2. What other (optional) suggestions do you have for the author?<br>
<br>
<br>
<br>
Nothing specifically.<br>
<br>
<br>
<br>
On 26 Oct 2015, at 08:30, Lars Rönnegård <<a href="mailto:lrn@du.se">lrn@du.se</a><br>
<<a href="mailto:lrn@du.se">mailto:lrn@du.se</a>>> wrote:<br>
<br>
<br>
<br>
Xia,<br>
<br>
Have you had time to look at the package yet? I received the review<br>
on the paper today with minor revision and I am expected to submit<br>
the revision within 3 weeks so it would be great if I could have<br>
revised the package according to your comments by then.<br>
<br>
<br>
<br>
Best regards,<br>
<br>
Lars<br>
<br>
<br>
<br>
<br>
<br>
<br>
<o:p></o:p></p>
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-- <br>
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*<br>
Lennart C. Karssen<br>
PolyOmica<br>
Groningen<br>
The Netherlands<br>
<br>
<a href="mailto:l.c.karssen@polyomica.com">l.c.karssen@polyomica.com</a><br>
GPG key ID: 1A15AF2A<br>
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-<o:p></o:p></p>
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