Publications by strictlystat
ENAR 2014 Searcher #ENAR2014
To those going to ENAR this year: Are you trying to find who’s presenting at ENAR from your department but all that pdf searching got you down? Are you trying to make an itinerary but dislike copying and pasting from a pdf? Well I have a Shiny App for you! At https://muschellij2.shinyapps.io/ENAR_2014, you can see all the sessions for ENAR...
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brainR: Put your brain on the Cloud!
In my work, we have come across problems where we wanted to visualize data in 4 dimensions (4D). The data came as brains, which are represented as 3D volumes and we wanted to visualize them at different time points (hence 4D). We were using images that are acquired one image per visit (CT structural scans, particularly), where each patient had a ...
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SMART Hackathon 2014
Today is our SMART group's 2014 Hackathon! We will be at an undisclosed location, just plugging away at code/packages/apps. The mission statement: There's no structure except that you have to work on a software project and you have to present what you accomplished or didn't at a subsequent SMART meeting. We will be tweeting at #JHUSMARThack fo...
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SMART Hackathon: Day 1
So day 1 of the #JHUSMARTHack 2014 is over and day 2 is underway. It's been awesome. One student estimated he did “one week's worth of work”. Some interesting (I think) things I thought about: Flooding rain is good weather for coding. (As long as no sinkholes arise) The Admiral Fell Inn is a pretty sweet place to host this event (and su...
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SMART Hackathon: Day 2: Writing Packages in RStudio
So day 2 of the #JHUSMARTHack was last week, but I figured this would be a good time to discuss what was accomplished. I created some packages that are somewhat specialized and aren't fully finished yet, so I'll hold off. What I really want to discuss though is why I like using RStudio for making packages. What was accomplished? I had spoken b...
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Making Back-to-Back Histograms
A colleage of mine asked me how to do back to back histograms (instead of on top of each other). I feel as though there should be a function like voilin plot from the vioplot package. Voilin plots are good for displaying data, but the violin must have the left and right (or top and bottom) of the violin to be from the same distribution, and the...
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fslr: An R Package Interfacing with FSL for Neuroimaging Analysis
I use a set of neuroimaging tools, but my language of choice is R. FSL, which is from the University of Oxford's Functional MRI of the Brain (FMRIB), and stands for FMRIB Software Library, is one tool I commonly use. I wrote some wrapper functions into an R package called fslr and wanted to discuss some of the functions. FSL – what is it? F...
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Be Careful with Using Model Design in R
In R, useful functions for making design matrices are model.frame and model.matrix. I will to discuss some of the differences of behavior across and within the two functions. I also have an example where I have run into this problme and it caused me to lose time. Using model.frame for a design matrix Whenever I use the word “design” I mean...
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R is a Language: Treat it Like One
I'm helping out with teaching a class on an introduction to R for students this week. I figured it'd be a good time to discuss my thoughts on programming in R and how a newcomer should feel about learning the language. Those Who Teach R, Should Use R Many of the students in the class at the beginning are overwhelmed. They see a bunch of differen...
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Sometimes Table is not the Answer – a Faster 2×2 Table
The table command is great in its simplicity for cross tabulations. I have run into some settings where it is slow and I wanted to demonstrate one simple example here of why you may want to use other functions or write your own tabler. This example is a specific case where, for some examples and functions, you don't need all the good error-chec...
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