HTML vignettes crashing your RStudio? This may be the reason

Short version: if RStudio on Windows 7 crashes when viewing vignettes in HTML format, it may be because those packages specify knitr::rmarkdown as the vignette engine, instead of knitr::knitr¬†and you’re using rmarkdown v1.

Longer version with details – read on.

update: looks like this issue relates to the installed version of rmarkdown (1.3 in my case) – see here for details.

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Quilt plots. Like heat maps, only…heat maps

Stephen tweets:

A "quilt plot"

A “quilt plot”

Quilt plots. Sounds interesting. The link points to a short article in PLoS ONE, containing a table and a figure. Here is Figure 1.

If you looked at that and thought “Hey, that’s a heat map!”, you are correct. That is a heat map. Let’s be quite clear about that. It’s a heat map.

So, how do the authors justify publishing a method for drawing heat maps and then calling them “quilt plots”?
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No-one cares about your bioinformatics software

Here’s a tip. When you write an article about your software, the title of which indicates that open-source is important:

A universal open-source Electronic Laboratory Notebook

but you then:

  • provide almost no details in the abstract
  • do not provide a link to a website or repository from which your “free” software can be obtained
  • choose not to make the article open access
  • and put the installation instructions in a supplementary data file which is also not open access

Don’t be surprised when no-one uses your software.

Or is the publication more important to you than the product?

The RStudio IDE: first impressions are positive

Integrated development environments (IDEs) are software development tools, providing an interface that enables you to write, debug, run and view the output of your code.

Whether you need an IDE or find them useful depends very much on your own preferences and style of working. In my own case for example, I’ve tried both Eclipse and NetBeans, but I find them bloated and rather “overkill”. On the other hand, my LaTeX productivity shot up when I started to use Kile.

Most of my coding involves either Ruby or R, written using Emacs. For Ruby (including Rails), I use a bundled set of plugins named my_emacs_for_rails, which includes the Emacs Code Browser (ECB). For R, I occasionally use Emacs Speaks Statistics (ESS), but I’m just as likely to run code from a terminal or use the R console.

RStudio, released yesterday, is a new open-source IDE for R. It’s getting a lot of attention at R-bloggers and it’s easy to see why: this is open-source software development done right.
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