Blog Archives

My knitr LaTeX template: manuscript and supplement interleaved in one source file

June 14, 2016
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Most of the time between starting manuscript and having it accepted after peer-review is spent writing, re-writing and re-arranging content. In Word, keeping track of figure numbers is a big pain, even more so when figures are moved between the main manuscript and the supplement. Moving my Word manuscript to knitr, I first had to decide between RMarkdown and LaTeX....

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My knitr LaTeX template: manuscript and supplement interleaved in one source file

June 14, 2016
By

Most of the time between starting manuscript and having it accepted after peer-review is spent writing, re-writing and re-arranging content. In Word, keeping track of figure numbers is a big pain, even more so when figures are moved between the main ma...

Read more »

Display element ids for debugging Shiny apps

April 19, 2016
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Display element ids for debugging Shiny apps

My current Shiny project contains at least five tables and I constantly forget how they are called. So I whipped up a little bookmarklet that uses jQuery to show the id of each div and input. Some of those can be ignored as they are internal names set by Shiny, but most are the actual names you define in...

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Display element ids for debugging Shiny apps

April 19, 2016
By
Display element ids for debugging Shiny apps

My current Shiny project contains at least five tables and I constantly forget how they are called. So I whipped up a little bookmarklet that uses jQuery to show the id of each div and input. Some of those can be ignored as they are internal names set ...

Read more »

New R package: a dictionary with arbitrary keys and values

March 11, 2016
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Coming from Python, the absence of a real dictionary in R has annoyed me for quite some time. Now, I actually needed to use vectors as keys in R:library(dict)d

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New R package: a dictionary with arbitrary keys and values

March 11, 2016
By

Coming from Python, the absence of a real dictionary in R has annoyed me for quite some time. Now, I actually needed to use vectors as keys in R:__ library(dict)__ d -____ d] __ d] __ d] __ d] 42__ d] "Hello!"Under the hood, separate C++ dictionaries (unordered_map) are created for the different types of keys. Using...

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Avoiding unnecessary memory allocations in R

March 8, 2016
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As a rule, everything I discover in R has already been discussed by Hadley Wickham. In this case, he writes:The reason why the C++ function is faster is subtle, and relates to memory management. The R version needs to create an intermediate vector the ...

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Avoiding unnecessary memory allocations in R

March 8, 2016
By

As a rule, everything I discover in R has already been discussed by Hadley Wickham. In this case, he writes:The reason why the C++ function is faster is subtle, and relates to memory management. The R version needs to create an intermediate vector the ...

Read more »

Creating composite figures with ggplot2 for reproducible research

March 10, 2015
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Creating composite figures with ggplot2 for reproducible research

So far, I have been preparing composite figures by plotting the data using ggplot2, and then putting the panels together in OmniGraffle or Adobe Illustrator. Of course, every time the data is updated, I would need to go back to the vector editing progr...

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Introducing parallelRandomForest: faster, leaner, parallelized

September 23, 2013
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Together with other members of Andreas Beyer's research group, I participated in the DREAM 8 toxicogenetics challenge. While the jury is still out on the results, I want to introduce my improvement of the R randomForest package, namely parall...

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