Blog Archives

A Faster Scale Function

February 23, 2016
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A Faster Scale Function

Problem Setup In recent question on LinkedIn’s R user group, a user asked “How to normalize by the row sums of the variable?”. Now first, we must define what we mean by “normalize” a matrix/data.frame. One way to standardize/normalize a row is to subtract by the mean and divide by the max to put the

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How I build up a ggplot2 figure

February 19, 2016
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How I build up a ggplot2 figure

Recently, Jeff Leek at Simply Statistics discussed why he does not use ggplot2. He notes “The bottom line is for production graphics, any system requires work.” and describes a default plot that needs some work: To break down what is going on, here is what R interprets (more or less): Make a container for data

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Dealing with Imposter Syndrome in Graduate School

October 14, 2015
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Dealing with Imposter Syndrome in Graduate School

In my post of recommendations for first-year students, I discussed some tips and viewpoints to help the practical, pragmatic aspects about being a first year student. In this post, I'd like to discuss the common misconceptions/viewpoints that are destructive to new students. The Dunning-Kruger effect I know something, so everyone else is dumb You just

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Recommendations for First Year Graduate Students

October 12, 2015
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Recommendations for First Year Graduate Students

This blog post is a little late; I wanted to get it out sooner. As new students have flooded the halls for the new terms at JHU Biostat, I figured I would give some recommendations to our new students, and biostatistics students in general. Some of these things may be specific to our department, but

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A better interactive neuroimage plotter in R

August 21, 2015
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A better interactive neuroimage plotter in R

In a previous post, I described how you can interactively explore a 3D nifti object in R. I used the manipulate package, but the overall results were sluggish and not really usable. I was introduced to a a good neuroimaging viewer called Mango, by a friend or two and use it somewhat inconsistently. One major

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Rendering LaTeX Math Equations in GitHub Markdown

July 31, 2015
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Rendering LaTeX Math Equations in GitHub Markdown

The Problem: GitHub README.md won't render LaTeX I have many times wondered about getting LaTeX math to render in a README file on GitHub. Apparently, many others ( 1, 2, 3 ), have asked the same question. The common answers are: It cannot (and in some cases, shouldn't) be done. GitHub parsing is done by

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#rstats Make arrays into vectors before running table

July 29, 2015
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#rstats Make arrays into vectors before running table

Setup of Problem While working with nifti objects from the oro.nifti, I tried to table the values of the image. The table took a long time to compute. I thought this was due to the added information about a medical image, but I found that the same sluggishness happened when coercing the nifti object to

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Line plots of longitudinal summary data in R using ggplot2

July 9, 2015
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Line plots of longitudinal summary data in R using ggplot2

I recently had an email for a colleague asking me to make a figure like this in ggplot2 or trellis in R: As I know more about how to do things in ggplot2, I chose to use that package (if it wasn't obvious from the plot or other posts). Starting Point Cookbook R/) has a

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A small neuroimage interactive plotter

April 9, 2015
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A small neuroimage interactive plotter

Manipulate Package The manipulate from RStudio allows you to create simple Tcl/Tk operators for interactive visualization. I will use it for a simple slider to view different slices of an image. fslr package I'm calling the fslr package because I know that if you have it installed, you will likely have FSL and have a

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matlabr: a Package to Calling MATLAB from R with system

April 8, 2015
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matlabr: a Package to Calling MATLAB from R with system

In my research, I primarily use R, but I try to use existing code if available. In neuroimaging and other areas, that means calling MATLAB code. There are some existing solutions for the problem of R to MATLAB: namely the R.matlab package and the RMatlab package (which can call R from MATLAB as well). I

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