[GenABEL-dev] FW: RepeatABEL

Lars Rönnegård lrn at du.se
Fri Nov 6 15:06:32 CET 2015 

Dear Lennart and Yurii,
I attach the revised version of the RepeatABEL package following Xia's review comments, which were very useful.

If you find my revision acceptable, I would be happy to have the package within the GenABEL suite of packages.

Best regards,
Lars Rönnegård



________________________________
From: Xia Shen <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>> 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



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