tag:blogger.com,1999:blog-73443196978791417.post3415184268538978848..comments2024-01-26T05:13:08.664-05:00Comments on Deciphering life: One bit at a time: Reproducible publications as R packages... and markdown vignettes!Anonymoushttp://www.blogger.com/profile/11732353840939638830noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-73443196978791417.post-17745642483159057272013-04-06T15:29:48.601-04:002013-04-06T15:29:48.601-04:00You were not stealing from me -- we were both stea...You were not stealing from me -- we were both stealing from Duncan Temple Lang and Robert Gentleman :) I made some comments on their paper in a book chapter in http://www.crcpress.com/product/isbn/9781466561595 Basically they were hoping something like XML would rule the world, but I do not think that is going to happen... There are tons of extremely powerful authoring languages in the world like LaTeX and XML, but I believe the "weak" languages like Markdown will win the mass.Yihui Xiehttps://www.blogger.com/profile/12537405521727345502noreply@blogger.comtag:blogger.com,1999:blog-73443196978791417.post-63520460268041652482013-04-06T00:01:29.682-04:002013-04-06T00:01:29.682-04:00I like the idea. I took a similar approach with my...I like the idea. I took a similar approach with my latest paper that we're working on formatting for submission, but modified it slightly. In our case, we were working on a new software methodology, so I wanted to ensure that we had the code developed as a stand-alone package which could be reused without having to download all sorts of extra data and defunct functions.<br /><br />So I released the methods/useful code in one package/repo: https://github.com/QBRC/ENA<br />And the research/knit-able document in another: https://github.com/QBRC/ena-research<br /><br />I kind of like this approach as it allows me to set aside the functions which I may want to re-use later on down the road, but I can certainly see the benefit of having an entire project wrapped up in one package (data size permitting).Anonymoushttps://www.blogger.com/profile/13334840737813537383noreply@blogger.comtag:blogger.com,1999:blog-73443196978791417.post-19549151507492356222013-04-05T23:59:30.099-04:002013-04-05T23:59:30.099-04:00This comment has been removed by the author.Sage.https://www.blogger.com/profile/14187425829929296916noreply@blogger.comtag:blogger.com,1999:blog-73443196978791417.post-33711600184094834582013-04-05T22:05:14.648-04:002013-04-05T22:05:14.648-04:00Sorry to steal your thunder Yihui. It's funny,...Sorry to steal your thunder Yihui. It's funny, I realized that Sweave and knitr were great for producing reproducible documents, but I hadn't thought about the data and custom function aspects. IE I thought more about creating a different package with functions, a separate data file, and then the document itself. But the package would make it much easier, and take care of dependencies, etc.<br /><br />I really hope this approach catches on for general rep. documents using R, and other engines that knitr will support.Anonymoushttps://www.blogger.com/profile/11732353840939638830noreply@blogger.comtag:blogger.com,1999:blog-73443196978791417.post-30944906832578506512013-04-05T14:38:17.504-04:002013-04-05T14:38:17.504-04:00You have written what I intended to write for my n...You have written what I intended to write for my next blog post :) I said something similar here a while ago: http://permalink.gmane.org/gmane.comp.lang.r.devel/32952<br /><br />I need to push kntir 1.2 to CRAN before I can shout out loud why everybody needs to upgrade to R 3.0.0 for a wonderful world of reproducible research.Yihui Xiehttps://www.blogger.com/profile/12537405521727345502noreply@blogger.comtag:blogger.com,1999:blog-73443196978791417.post-23094457309684813472013-04-05T11:16:18.411-04:002013-04-05T11:16:18.411-04:00Couldn't agree more. My last two papers were ...Couldn't agree more. My last two papers were done this way (ROxygen, knitr, markdown, etc) https://github.com/cboettig/treeBASE, appearing in MEE (10.1111/j.2041-210X.2012.00247.x)<br /><br />and https://github.com/cboettig/rfishbase, appearing in J. Fish Biology (10.1111/j.1095-8649.2012.03464.x)<br /><br />Admittedly these were about R packages, but I have resolved to do this for my research papers as well. (drafts online, e.g. multiple_uncertainty & pdg_control)<br /><br />I'd add a note that Gentleman and Lang (2007, 10.1198/106186007X178663) propose this idea with Sweave, but it is much easier now with Rmd. I'd also mention pandoc -- J Fish Biology didn't take the pdf, so pandoc let me generate a .docx from the markdown. <br /><br />Carlhttps://www.blogger.com/profile/17998217796660657289noreply@blogger.com