reproducible documents/analytics in R: the knitr package

June 26, 2012 | ricckli

When I am working in new institutions and I am asking: “Do you have a document management system?” I often get the answer:”Yap, we are using folders” … OKAY. Making analysis, developing applications and keeping an eye on code, data and applications make this even harder as it has to ... [Read more...]

R Workshop: Reproducible Research using Sweave for Beginers

April 27, 2012 | Corey Chivers

Monday, April 30, 2012  14h-16h. Stewart Biology Rm w6/12 (Montreal) guRu: Denis Haine (Université de Montréal) Topics Reproducible research was first coined by Pr. Jon Claerbout, professor of geophysics at Stanford University, to describe that the results from researches can be replicated by other scientists by making available data, procedures, ... [Read more...]

useR! 2012 Simple Abstract Helper

January 3, 2012 | BioStatMatt

useR! 2012 has issued a call for abstracts! I've extended the WebSweave concept to offer a tool to create simple abstracts online, including those with markup, which may then be submitted at the conference website. Use the following link for the Simple Abstract Helper. [Read more...]

The Joy of R: A Feline Guide

November 5, 2011 | Mario Pineda-Krch

Just because it’s caturday Images by Mario Pineda-Krch (CC BY-NC-SA 3.0) This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta. Filed under: cats, computing, humour, R, Sweave [Read more...]

Using Sweave with XeLaTeX

October 23, 2011 | mages

Using R with LaTeX via Sweave is a great way to create reproducible output. However, using specific fonts, e.g. your corporate fonts, can be painful with pdflatex. Over the last few weeks I have fallen in love with the TeX formatXeLaTeX and its XeTeX e...
[Read more...]

David Banks on Reproducible Research

June 8, 2011 | BioStatMatt

Just got an email linking to Reproducible Research: A Range of Response, in the new journal Statistics, Politics, and Policy 2(1) by David Banks, who is also the journal's editor. Interestingly, the commentary doesn't mention the journal's policy (if one exists) on the reproducibility of research submitted there. Banks' writing is ... [Read more...]

Sweave diagram, following Knuth’s original

June 2, 2011 | BioStatMatt

In preparation for a talk, I updated Knuth's original diagram in Donald E. Knuth. Literate programming. The Computer Journal, 27(2):97–111, May 1984. The new diagram is Sweave specific. Click the Sweave diagram for a PDF version, or right-click and select 'save image as' for the PNG version. Permission is granted for any ... [Read more...]

Sweave and pgfSweave in LyX 2.0.x (experimental)

May 25, 2011 | Yihui Xie

bout half a year ago, I wrote a post on the configuration of (pgf)Sweave and LyX, which was intended to save us some efforts in going through all the details during the configuration. Now many things have changed: LyX 2.0 has internal support for Sweave, and fortunately I have been ... [Read more...]

Makefiles and Sweave

May 12, 2011 | csgillespie

A Makefile is a simple text file that controls compilation of a target file. The key benefit of using Makefile is that it uses file time stamps to determine if a particular action is needed. In this post we discuss how to use a simple Makefile that compiles a tex ... [Read more...]


April 6, 2011 | BioStatMatt

A recent R-help post asks for examples of Sweave use for web appliations. I think there is very little out there; maybe nothing. Below is a proof of concept for web-based Sweave-ing with rApache. But, it will soon be possible to do this with R's built-in web server. The idea ... [Read more...]

R versus Matlab in Mathematical Psychology

February 20, 2011 | Jeromy Anglim

I recently attended the 2011 Australasian Mathematical Psychology Conference.This post summarises a few thoughts I had on the use of R, Matlab and othertools in mathematical psychology flowing from discussions with researchers atthe conference.I wanted...
[Read more...]

Teach Yourself How to Create Functions in R

February 1, 2011 | --

As you can tell from my previous posts, I am diving in head first into learning how to program (and simplify) my analytical life using R.  I have always learned by example and have never really prospered from the “learn from scratch” school of thought.  As I follow along with ... [Read more...]

A Special Graphics Device in R: the Null Device

December 22, 2010 | Yihui Xie

It is well-known that R has several graphics devices — either the screen devices (X11(), windows(), …) or the off-screen devices (pdf(), png(), …). We can query the default graphics device in options(): getOption('device') In a non-interactive session, the default device is pdf(). This is why Sweave has to create a file ... [Read more...]

R Workflow

December 7, 2010 | Daniel Hocking

When working with R you end up using a large number of datasets, packages, functions, objects, output files, workspaces, etc.  It can get a bit overwhelming trying to keep everything organized.  That is why a consistent, well-organized workf...
[Read more...]
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