Comments for Mario's Entangled Bank

Comment on Special section in Science on reproducible research by Steph

Steph — Wed, 22 Feb 2012 20:01:55 +0000

And another “big fish” broaches the subject: http://www.nature.com/nature/journal/v482/n7386/full/nature10836.html?WT.ec_id=NATURE-20120223

Comment on Starting an Open Notebook Science project by shabbychef

shabbychef — Tue, 21 Feb 2012 23:26:55 +0000

I maintain a trac wiki at my job, and have found that the MathJax plugin ( http://trac-hacks.org/wiki/TracMathJaxPlugin ) is much better than the image-based LatexFormulaMacro plugin. It looks better, scales better, and doesn’t leave all these image files laying around. YMMV.

Comment on The Joy of R: A Feline Guide by iray

iray — Tue, 07 Feb 2012 10:20:01 +0000

Hi there, are you using word for your sweaving parties here ???
More seriously, do you have a post here on your toolset on a Mac ?

Comment on To Sweave, or not to Sweave, that is the question by Yihui

Yihui — Sun, 18 Dec 2011 20:17:37 +0000

I wrote almost everything in Sweave, which motivated my re-invention of the wheel — the knitr package (http://yihui.github.com/knitr/). Now my answer to your question is definitely yes, since it takes me 10 seconds to set up a document with LyX and knitr from scratch (see this short video http://vimeo.com/32948939), so why not?

I think a broader question is how our journals in this age should change towards a reproducible manner. Traditional papers are published in a “fixed” manner — once submitted, they are “dead”. I believe at least electronic journals like JSS may try to provide an environment like CRAN to rebuild papers periodically from source; original authors should be notified in case of errors. Why software packages must be re-built and re-checked periodically but scientific papers should not?

Comment on To Sweave, or not to Sweave, that is the question by Reinhold Kliegl

Reinhold Kliegl — Sat, 17 Dec 2011 13:27:46 +0000

The complications discussed in this blog are some of the reasons why we decided to develop the Potsdam Mind Research Repository (http://read.psych.uni-potsdam.de/pmr2/ ; see also “About”). All the journals in our field (experimental psychology) have some form of open access policy (usually green way). This gives us the option to publish preprint, postprint, or pdf and associate data and analyses scripts with each peer-reviewed publication (“paper package”). We also are ready to include “paper packages” from other labs working on related topics. We think that such small communities are more likely to engage exchange and re-analyses of published data than large all-purpose archives.

Comment on To Sweave, or not to Sweave, that is the question by Ben Bolker

Ben Bolker — Sat, 17 Dec 2011 01:35:20 +0000

Oops. How about http://www.math.mcmaster.ca/bolker/misc/bolker_jrsi.tgz ? (I know that defeats the purpose; if I get to it I’ll try to nag the JRSI editorial office.)

Comment on To Sweave, or not to Sweave, that is the question by Jaime Ashander (@jaimedash)

Jaime Ashander (@jaimedash) — Sat, 17 Dec 2011 00:14:17 +0000

I think Ben Bolker’s being too modest. If the files posted on his website don’t mislead, he’s published a swoven _book_ as well.

One addition, the paper Ben links too looks like a good read by itself, but I wanted to have a look at the sweave file. There is a “data supplement”, but strangely enough it appears as just the text “R code and data files” (http://rsif.royalsocietypublishing.org/content/early/2009/10/27/rsif.2009.0384/suppl/DC1)

Comment on To Sweave, or not to Sweave, that is the question by Achim Zeileis

Achim Zeileis — Fri, 16 Dec 2011 23:34:50 +0000

For the Journal of Statistical Software (http://www.jstatsoft.org/) we do encourage usage of Sweave but do not actually use it directly in the production. For the accepted papers we require submission of .tex and graphics (plus .bib) and a .R file with replication code – and all of that can be conveniently produced from the .Rnw. If authors want to share the original .Rnw as well, we encourage to include it as a vignette in their package. Thus, on a more conceptual level: We publish a static snapshot (that was reviewed) of the dynamic Sweave document.

The reason is that compiling and maintaining the dynamic documents would currently still take more resources than we have. We retain a lot of the reproducibility but lose some “literate” aspects.

Personally, I use the same strategy of submitting static snapshots of Sweave documents for almost all of my papers. If the targeted journal has facilities for sharing replication material already in the reviewing stage, I include code in my submissions. Otherwise I often try to include it in one of my CRAN packages if appropriate. Probably also not the ideal solution but still better than what is available for many “standard” papers.

Comment on To Sweave, or not to Sweave, that is the question by jrminter

jrminter — Fri, 16 Dec 2011 23:32:29 +0000

I’d like to hear what you decide. I have been using LaTeX, R, and Sweave for my work in microscopy, image processing and analysis for about a year now. I have used Sweave for a few documents. However, for my work, the data processing can take a while and I don’t want to re-do the data analysis each time I edit the report. Haven’t yet tried CacheSweave. I tend to use either shell scripts or batch files (I use Linux, MacOSX, and Windows.) I may go to makefiles. But basically, I have a series of scripts to do the analysis and can run as many as I need if things change. I like the idea of a “one script that rules them all” approach that I can use to generate the final document from the get-go as the last step. I also use git and maintain all this with version control.

Comment on To Sweave, or not to Sweave, that is the question by Ben Bolker

Ben Bolker — Fri, 16 Dec 2011 21:36:12 +0000

(oops, sorry, bib details got swallowed: Bolker et al 2010, http://rsif.royalsocietypublishing.org/content/7/46/811.short )

Comment on To Sweave, or not to Sweave, that is the question by Ben Bolker

Ben Bolker — Fri, 16 Dec 2011 21:35:15 +0000

I have published one Swoven paper: Bolker, B. M., doi:10.1098/rsif.2009.0384. . I don’t remember any details (after trying at PNAS, this was published in J Roy Soc Interface). All my other recent papers have been done in collaboration with non-Sweavers (a bigger obstacle than the editorial offices of journals, I would say). This is likely to be particularly simple because you are probably not going to leave exposed (echo=TRUE) code chunks in your manuscript, and everything else gets converted to “vanilla” LaTeX in the Sweaving process …

Comment on To Sweave, or not to Sweave, that is the question by Tal Galili

Tal Galili — Fri, 16 Dec 2011 20:20:59 +0000

Good piece –
I hope to read a followup on the ramifications of your Sweaving your next paper

Comment on Cycles in finite populations: A reproducible seminar in three acts by To Sweave, or not to Sweave, that is the question | Mario's Entangled Bank

To Sweave, or not to Sweave, that is the question | Mario's Entangled Bank — Fri, 16 Dec 2011 18:18:28 +0000

[...] am about to start writing up the manuscript of my recent biomath seminar (Act 3). While the slides for the talk were put together using Sweave to illustrate how the [...]

Comment on Happy Birthday Origin of Species with a homage to Morse Peckham by Leo Dauagherty

Leo Dauagherty — Mon, 12 Dec 2011 10:52:12 +0000

p.s.: Typo alert: My name is Leo Daugherty

Comment on Happy Birthday Origin of Species with a homage to Morse Peckham by Leo Dauagherty

Leo Dauagherty — Mon, 12 Dec 2011 10:51:26 +0000

Hi, Mario! Many thanks for this. Morse Peckham was my friend and mentor, and I am as much in the dark as you are about why his VARIORUM ORIGIN isn’t better known. I’m also puzzled that HE isn’t better known as the writer, social theorist, and all-around brilliant man who produced twenty or more amazing, witty books.

Comment on Top 10 things that suck about Sweave by Yihui

Yihui — Mon, 05 Dec 2011 04:14:35 +0000

It is time to take a look at the knitr package now: http://yihui.github.com/knitr/ (AFAICS, it can solve the all the issues you mentioned except the first two)

Comment on Happy Birthday Origin of Species with a homage to Morse Peckham by Anniece Ross

Anniece Ross — Sun, 04 Dec 2011 09:04:30 +0000

Mario: delighted by your recognition of the Peckham Variorium. It shows how Darwin, interacting with colleagues, evolved his ideas: looking at possibilities for change and selecting what to include in the next edition. Mivart could be especially interesting for you. Darwin changed his text RE Mivart in response to the explanation by Chauncey Wright, mathematician, astronomer, computer, and philosopher of science that what Mivart meant by species was not at all what Darwin meant by species. Mivart meant by species fixed; Darwin’s intent was exactly to show species are not fixed. As a mathematician, Chauncey Wright looked at natural selection as a statistical phenomenon and made this analysis clear enough to young scientists at Harvard that Charles Sanders Peirce could say Darwin applied to populations of organisms the method of Brownian motion. Part of my celebration of 150th was to give each member of my family the Peckham Variorum. Fascinating work you are doing. Thanks for sharing. atr BTW Chauncey Wright also analyzed the competition of ideas and gave in his essay on Arrangement of Leaves an illustration and defense of hypothesis as one step in the method of science.

Comment on F1000 review: Open science is a research accelerator by Jayant

Jayant — Sat, 03 Dec 2011 16:08:50 +0000

Rightly commented in this blog that enough eyeballs would make all scientific problems shallow. After all the validity of a scientific argument/interpretation is a certain type of consensus which get developed among the fore thinkers at particular and the general mind in general.

Comment on Happy Birthday Origin of Species with a homage to Morse Peckham by Pablo Almaraz

Pablo Almaraz — Mon, 28 Nov 2011 20:59:41 +0000

Thanks Mario for this!!
I did not even know about the OOS Variorum edition from Peckham, so I’ve just bought one!! Great post!
Viva Darwin (and Peckham)!!

Comment on Turbo charged Open Science: this sort of thing is my bag, baby by F1000 review: Open science is a research accelerator | Mario's Entangled Bank

Mon, 14 Nov 2011 21:20:23 +0000

[...] promised previously, today the following post-publication evaluation of Open Science is a research [...]

Comment on The Joy of R: A Feline Guide by Tal Galili

Tal Galili — Sun, 06 Nov 2011 15:12:33 +0000

Well you know, cats like to gRRRR
(ok, ok – I’m stopping!)

Comment on The Joy of R: A Feline Guide by Mario Pineda-Krch

Mario Pineda-Krch — Sun, 06 Nov 2011 15:05:31 +0000

I seem to be rubbing R-bloggers the wrong way this week. Thanks for letting it stay. The cat approves your decision.

Cheers,
Mario

Comment on The Joy of R: A Feline Guide by Tal Galili

Tal Galili — Sun, 06 Nov 2011 08:43:56 +0000

I would have erased this post from R-bloggers. But I just…. ca_’t

Cheers,
Tal

Comment on Causal basis of the ice cream-shark correlation fallacy by Cause à effet cigogne | Desillusions

Cause à effet cigogne | Desillusions — Sat, 05 Nov 2011 17:56:36 +0000

[...] Voici l’un des exemples de justification hasardeuse les plus cités (mais dont Dr Igor n’a pas retrouvé l’origine) : bien que l’on observe une corrélation positive (c’est-à-dire de même sens) entre augmentation des ventes de crème glacée et hausse du nombre d’attaques de requins, il est évidemment faux d’en conclure que vendre plus de glaces provoque plus d’attaques de requin ! C’est juste que les deux phénomènes ont la fâcheuse tendance de se produire à une même époque de l’année (si l’explication ne vous convainc pas, tant pis, allez donc choisir parmi les explications suivantes). [...]

Comment on Cycles in finite populations: A reproducible seminar in three acts by Tal Galili

Tal Galili — Sat, 05 Nov 2011 15:32:39 +0000

Great, thanks