[GenABEL-dev] RepeatABEL
L.C. Karssen
lennart at karssen.org
Wed Nov 11 10:40:48 CET 2015
Dear Lars,
On 09-11-15 08:26, Lars Rönnegård wrote:
> Dear Lennart,
>
> I would very much appreciate if RepeatABEL is added to the list at
> http://www.genabel.org/packages
Done, see www.genabel.org/packages/RepeatABEL.
If you'd like to change the contents of that page, please let me know
and I will send you instructions on how to create an account.
> 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.
Excellent, for me to be able to add you to the R-forge project you need
to create an R-forge account, see the New Account link in the top right
corner of [1]. Next, go to [2] and in the Project Members column select
the Join option. Then I can add you to the team and give you commit
privileges on the SVN server.
>
>
>
> If possible, I would like to get it all done this week.
That should be no problem.
Best,
Lennart.
[1] https://r-forge.r-project.org/
[2] https://r-forge.r-project.org/projects/genabel/
>
>
>
> Best regards,
>
> Lars
>
>
>
>
>
>
> *From:*Xia Shen [mailto:xia.shen at ki.se]
> *Sent:* den 6 november 2015 17:31
> *To:* L.C. Karssen <l.c.karssen at polyomica.com>
> *Cc:* Lars Rönnegård <lrn at du.se>; Yurii Aulchenko
> (yurii.aulchenko at gmail.com) <yurii.aulchenko at gmail.com>;
> genabel-devel at lists.r-forge.r-project.org
> *Subject:* Re: RepeatABEL
>
>
>
> Thanks Lennart,
>
>
>
> I suggest including Lars as one developer in our R-Forge project so that
> he can commit the package via SVN.
>
>
>
> Editing genabel.org <http://genabel.org> 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.
>
>
>
> Xia
>
> On 06 Nov 2015, at 16:25, L.C. Karssen <l.c.karssen at polyomica.com
> <mailto:l.c.karssen at polyomica.com>> wrote:
>
>
>
> Dear Lars, Xia,
>
> On 06-11-15 15:06, Lars Rönnegård wrote:
>
> *Dear Lennart and Yurii,*
>
> *I attach the revised version of the RepeatABEL package
> following Xia’s
> review comments, which were very useful.*
>
>
> Xia, thank you for doing the review!
>
>
>
>
> * *
>
> *If you find my revision acceptable, I would be happy to have the
> package within the GenABEL suite of packages.*
>
>
>
> This looks great! Thank you for the updates according to Xia's comments.
> We would be happy to accept RepeatABEL into the GenABEL suite.
>
> Some questions related to the GenABEL "membership":
>
> 1) A technical question: would you like to save the RepeatABEL code in a
> public version control repository? The advantage would be that other
> people could more easily contribute to the development of the package,
> e.g. by fixing bugs.
> For the GenABEL Project we currently use the Subversion repository on
> R-forge [1] or Github [2].
>
> 2) To increase the visibility of your package we can list it on
> http://www.genabel.org/packages. Is that OK with you?
>
> 3) In addition to the above we can give you access to the content
> management system running www.genabel.org <http://www.genabel.org>
> so you can customise the
> RepeatABEL package page (see e.g. [3]), would you be interested in that?
>
>
> Finally, please take note of the responsibilities we expect from package
> maintainers [4].
>
>
> Best regards,
>
>
> Lennart.
>
>
> [1] https://r-forge.r-project.org/scm/?group_id=505
> [2] https://github.com/GenABEL-Project
> [3] http://www.genabel.org/packages/PredictABEL
> [4] http://www.genabel.org/developers#maintainer_responsibilities
>
>
>
>
>
>
> * *
>
> *Best regards,*
>
> *Lars Rönnegård*
>
> * *
>
> * *
>
> * *
>
> ------------------------------------------------------------------------
>
> *From:* Xia Shen <xia.shen at ki.se <mailto:xia.shen at ki.se>
> <mailto:xia.shen at ki.se>>
> *Sent:* Tuesday, October 27, 2015 06:19
> *To:* Lars Rönnegård
> *Cc:* L.C. Karssen
> *Subject:* Re: RepeatABEL
>
>
>
> Review of Package RepeatABEL v. 0.1
>
> Xia Shen
>
> Oct 26, 2015
>
>
>
> 1. Introduction
>
>
>
> This is a novel contribution for the GenABEL project. Although the
> underlying model is more or less the same as polygenic_hglm +
> mmscore,
> the main motivation is that the GenABEL package does not deal with
> repeated measurements. The package is easy to use and provides
> an useful
> analytical framework for GWAS with repeated measurements, identical
> twins, clones, etc.
>
>
>
> 2. Legal issues
>
> 2.1. Is the copyright holder clearly mentioned?
>
>
>
> The author and maintainer are listed in DESCRIPTION and package
> help. It
> could also be displayed while loading the package.
>
>
>
> 2.2. Is there a clear (standard) license?
>
>
>
> Yes. GPL.
>
>
>
> 3. Technical quality
>
> 3.1. Is the installation procedure clearly documented? Is the
> code easy
> to compile and run?
>
>
>
> Not documented in the tutorial, but easy to install as a standard R
> package. The compilation and basic running were successful.
>
>
>
> 3.2. [For R packages] Does the package pass CRAN checks ()? At
> minimum,
> run "R CMD check …" and "R CMD check –as-cran …"
>
>
>
> The beginning of DESCRIPTION is redundant in CRAN check
> standard: 'The
> RepeatABEL package is used to'.
>
>
>
> R CMD check --as-cran produces:
>
>
>
> The Title field should be in title case, current version then in
> title case:
>
> ‘GWAS for multiple observations on related individuals’
>
> ‘GWAS for Multiple Observations on Related Individuals’
>
>
>
> The Date field is over a month old.
>
>
>
> Rd file 'preFitmodel.Rd':
>
> \usage lines wider than 90 characters:
>
> preFitModel(fixed=y~1, random=~1|id, id.name="id", genabel.data,
> phenotype.data, corStruc=NULL, GRM=NULL, Neighbor.Matrix=NULL)
>
> \examples lines wider than 100 characters:
>
> Mod1 <- preFitModel(fixed, random=~1|id, genabel.data =
> gen.data,
> phenotype.data = Phen.Data, corStruc=list( id=list("GRM","Ind") ))
>
> Mod2 <- preFitModel(fixed, random=~1|id + 1|nest, genabel.data =
> gen.data, phenotype.data = Phen.Data, corStruc=list(
> id=list("GRM","In
> ... [TRUNCATED]
>
> Mod3 <- preFitModel(fixed, random=~1|id + 1|nest, genabel.data =
> gen.data, phenotype.data = Phen.Data, corStruc=list(
> id=list("GRM","In
> ... [TRUNCATED]
>
>
>
> Rd file 'rGLS.rd':
>
> \usage lines wider than 90 characters:
>
> rGLS(formula.FixedEffects = y ~ 1, genabel.data, phenotype.data,
> id.name = "id", GRM = NULL, V = NULL, memory=1e8)
>
>
>
> Rd file 'simulate_PhenData.Rd':
>
> \usage lines wider than 90 characters:
>
> simulate_PhenData(formula.FixedEffects = y ~ 1, genabel.data,
> n.obs, SNP.eff = NULL, SNP.nr = NULL, beta = NULL, VC = c(1, 1,
> 1), GRM
> = ... [TRUNCATED]
>
> \examples lines wider than 100 characters:
>
> Phen.Sim <- simulate_PhenData(y ~ age,
> genabel.data=gen.data, n.obs=rep(4, nids(gen.data)), SNP.eff=1,
> SNP.nr=1000, VC=c(1,1,1) ... [TRUNCATED]
>
>
>
> These lines will be truncated in the PDF manual.
>
>
>
> Please fix.
>
>
>
> 3.3. Is the package documented? What is the quality of the
> documentation?
>
>
>
> Yes. Good tutorial with standard Rd documentation.
>
>
>
> 3.4. [For R packages] Does help(PackageName) provide an adequate
> summary
> of the package and a review of the major functions?
>
>
>
> Yes. But the displayed version number is different from what's in
> DESCRIPTION. Please check.
>
>
>
> 3.5. [For R packages] Does the package use Roxygen2 for
> documentation?
>
>
>
> No. Roxygen2 is recommended, which keeps doc and code in the
> same R file
> and auto-generates Rd files.
>
>
>
> 3.6. Are examples of usage provided?
>
>
>
> Yes.
>
>
>
> 3.7. Does the package provide a tutorial/vignette? Can you
> comment on
> the tutorial?
>
>
>
> Yes. The tutorial is good and easy to follow.
>
>
>
> 3.8. Is the source code of the tutorial/vignette provided?
>
>
>
> No. I recommend including the tutorial as a vignette.
>
>
>
> 3.9. Does the package make use of unit/integration/etc. tests?
>
>
>
> No.
>
>
>
> 3.10. [For R packages] Does the package make use of unit tests (e.g.
> RUnit or testthat)?
>
>
>
> No.
>
>
>
> 3.11. Does the code comply with the GenABEL coding standards?
>
>
>
> Not entirely. Please refer
> to http://genabel.r-forge.r-project.org/codingstyle.html
>
>
>
> 3.12. Is the code readable/understandable?
>
>
>
> More or less.
>
>
>
> 3.13. Does the code contain explanatory comments?
>
>
>
> Yes.
>
>
>
> 3.14. Were the design and methods implemented in package discussed
> during the development process (e.g. on the genabel-devel
> mailing list)?
>
>
>
> Yes. A little.
>
>
>
> 4. Content
>
> 4.1. Does the package address a problem in the domain of statistical
> genomics?
>
>
>
> Yes.
>
>
>
> 4.2. Is it streamlining analyses not covered elsewhere in the
> GenABEL
> suite? If not, does it improve the analysis already covered?
>
>
>
> No and yes.
>
>
>
> 4.3. Should it become a separate package or rather be
> incorporated into
> an existing package?
>
>
>
> A separate package is the current form and in this case would be
> easy to
> maintain in practice, although I also feel that it could actually be
> easy to integrate the main rGLS function into the GenABEL package.
>
>
>
> 4.4. Does the package use any of the data types defined in other
> GenABEL
> packages?
>
>
>
> Yes. The gwaa.data class of GenABEL is used.
>
>
>
> 4.5. Does the package use code/functions/data defined in other
> GenABEL
> packages?
>
>
>
> Yes.
>
>
>
> 5. Recommendations
>
> 5.1. What are the major issues that should be addressed?
>
>
>
> Nothing specifically more than above. After fixing the above
> issues, the
> package can be committed to GenABEL project R-Forge SVN.
>
>
>
> 5.2. What other (optional) suggestions do you have for the author?
>
>
>
> Nothing specifically.
>
>
>
> On 26 Oct 2015, at 08:30, Lars Rönnegård <lrn at du.se
> <mailto:lrn at du.se>
> <mailto:lrn at du.se>> wrote:
>
>
>
> Xia,
>
> Have you had time to look at the package yet? I received the
> review
> on the paper today with minor revision and I am expected to
> submit
> the revision within 3 weeks so it would be great if I could have
> revised the package according to your comments by then.
>
>
>
> Best regards,
>
> Lars
>
>
>
>
>
>
>
> --
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
> Lennart C. Karssen
> PolyOmica
> Groningen
> The Netherlands
>
> l.c.karssen at polyomica.com <mailto:l.c.karssen at polyomica.com>
> GPG key ID: 1A15AF2A
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>
>
>
>
>
> _______________________________________________
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>
--
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands
lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
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