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<p class="MsoNormal" style="background:white"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Dear Lennart and Yurii,<o:p></o:p></span></b></p>
<p class="MsoNormal" style="background:white"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I attach the revised version of the RepeatABEL package following Xia’s review comments, which were very useful.<o:p></o:p></span></b></p>
<p class="MsoNormal" style="background:white"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></b></p>
<p class="MsoNormal" style="background:white"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">If you find my revision acceptable, I would be happy to have the package within the GenABEL suite of packages.<o:p></o:p></span></b></p>
<p class="MsoNormal" style="background:white"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></b></p>
<p class="MsoNormal" style="background:white"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Best regards,<o:p></o:p></span></b></p>
<p class="MsoNormal" style="background:white"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Lars Rönnegård<o:p></o:p></span></b></p>
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<p class="MsoNormal" align="center" style="text-align:center;background:white"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></b></p>
<p class="MsoNormal" style="background:white"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></b></p>
<p class="MsoNormal" style="background:white"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></b></p>
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<p class="MsoNormal" style="background:white"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span></span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Xia
Shen <</span><a href="mailto:xia.shen@ki.se"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">xia.shen@ki.se</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">><br>
<b>Sent:</b><span class="apple-converted-space"> </span>Tuesday, October 27, 2015 06:19<br>
<b>To:</b><span class="apple-converted-space"> </span>Lars Rönnegård<br>
<b>Cc:</b><span class="apple-converted-space"> </span>L.C. Karssen<br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: RepeatABEL</span><span lang="EN-US" style="font-family:"Calibri",sans-serif">
<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Review of Package RepeatABEL v. 0.1<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Xia Shen<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Oct 26, 2015<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">1. Introduction<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">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.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">2. Legal issues<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">2.1. Is the copyright holder clearly mentioned?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">The author and maintainer are listed in DESCRIPTION and package help. It could also be displayed while loading the package.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">2.2. Is there a clear (standard) license?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Yes. GPL.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">3. Technical quality<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">3.1. Is the installation procedure clearly documented? Is the code easy to compile and run?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Not documented in the tutorial, but easy to install as a standard R package. The compilation and basic running were successful.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">3.2. [For R packages] Does the package pass CRAN checks ()? At minimum, run "R CMD check …" and "R CMD check –as-cran …"<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">The beginning of DESCRIPTION is redundant in CRAN check standard: 'The RepeatABEL package is used to'. <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">R CMD check --as-cran produces:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">The Title field should be in title case, current version then in title case:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">‘GWAS for multiple observations on related individuals’<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">‘GWAS for Multiple Observations on Related Individuals’<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">The Date field is over a month old.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Rd file 'preFitmodel.Rd':<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"> \usage lines wider than 90 characters:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"> preFitModel(fixed=y~1, random=~1|id, id.name="id", genabel.data, phenotype.data, corStruc=NULL, GRM=NULL, Neighbor.Matrix=NULL)<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"> \examples lines wider than 100 characters:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"> Mod1 <- preFitModel(fixed, random=~1|id, genabel.data = gen.data, phenotype.data = Phen.Data, corStruc=list( id=list("GRM","Ind") ))<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"> Mod2 <- preFitModel(fixed, random=~1|id + 1|nest, genabel.data = gen.data, phenotype.data = Phen.Data, corStruc=list( id=list("GRM","In ... [TRUNCATED]<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"> Mod3 <- preFitModel(fixed, random=~1|id + 1|nest, genabel.data = gen.data, phenotype.data = Phen.Data, corStruc=list( id=list("GRM","In ... [TRUNCATED]<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Rd file 'rGLS.rd':<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"> \usage lines wider than 90 characters:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"> rGLS(formula.FixedEffects = y ~ 1, genabel.data, phenotype.data, id.name = "id", GRM = NULL, V = NULL, memory=1e8)<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Rd file 'simulate_PhenData.Rd':<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"> \usage lines wider than 90 characters:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"> 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]<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"> \examples lines wider than 100 characters:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"> 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]<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">These lines will be truncated in the PDF manual.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Please fix.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">3.3. Is the package documented? What is the quality of the documentation?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Yes. Good tutorial with standard Rd documentation.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">3.4. [For R packages] Does help(PackageName) provide an adequate summary of the package and a review of the major functions?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Yes. But the displayed version number is different from what's in DESCRIPTION. Please check.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">3.5. [For R packages] Does the package use Roxygen2 for documentation?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">No. Roxygen2 is recommended, which keeps doc and code in the same R file and auto-generates Rd files.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">3.6. Are examples of usage provided?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Yes.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">3.7. Does the package provide a tutorial/vignette? Can you comment on the tutorial?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Yes. The tutorial is good and easy to follow. <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">3.8. Is the source code of the tutorial/vignette provided?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">No. I recommend including the tutorial as a vignette.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">3.9. Does the package make use of unit/integration/etc. tests?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">No.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">3.10. [For R packages] Does the package make use of unit tests (e.g. RUnit or testthat)?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">No.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">3.11. Does the code comply with the GenABEL coding standards?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Not entirely. Please refer to<span class="apple-converted-space"> </span></span><a href="http://genabel.r-forge.r-project.org/codingstyle.html"><span lang="EN-US" style="font-family:"Calibri",sans-serif">http://genabel.r-forge.r-project.org/codingstyle.html</span></a><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">3.12. Is the code readable/understandable?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">More or less.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">3.13. Does the code contain explanatory comments?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Yes.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">3.14. Were the design and methods implemented in package discussed during the development process (e.g. on the genabel-devel mailing list)?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Yes. A little.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">4. Content<o:p></o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">4.1. Does the package address a problem in the domain of statistical genomics?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Yes.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">4.2. Is it streamlining analyses not covered elsewhere in the GenABEL suite? If not, does it improve the analysis already covered?<o:p></o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">No and yes. <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">4.3. Should it become a separate package or rather be incorporated into an existing package?<o:p></o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">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.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">4.4. Does the package use any of the data types defined in other GenABEL packages?<o:p></o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Yes. The gwaa.data class of GenABEL is used.<o:p></o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">4.5. Does the package use code/functions/data defined in other GenABEL packages?<o:p></o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Yes.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">5. Recommendations<o:p></o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">5.1. What are the major issues that should be addressed?<o:p></o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Nothing specifically more than above. After fixing the above issues, the package can be committed to GenABEL project R-Forge SVN.<o:p></o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">5.2. What other (optional) suggestions do you have for the author?<o:p></o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Nothing specifically.<o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">On 26 Oct 2015, at 08:30, Lars Rönnegård <</span><a href="mailto:lrn@du.se"><span lang="EN-US" style="font-family:"Calibri",sans-serif">lrn@du.se</span></a><span lang="EN-US" style="font-family:"Calibri",sans-serif">>
wrote:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">Xia,<o:p></o:p></span></p>
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<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif">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.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif">Best regards,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif">Lars<o:p></o:p></span></p>
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</div>
</blockquote>
</div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
</div>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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