Articles by strictlystat

A Faster Scale Function

February 23, 2016 | 0 Comments

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 ...
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How I build up a ggplot2 figure

February 19, 2016 | 0 Comments

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): ...
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Dealing with Imposter Syndrome in Graduate School

October 14, 2015 | 0 Comments

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 ...
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Recommendations for First Year Graduate Students

October 12, 2015 | 0 Comments

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 ... [Read more...]

A better interactive neuroimage plotter in R

August 21, 2015 | 0 Comments

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 ...
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Rendering LaTeX Math Equations in GitHub Markdown

July 31, 2015 | 0 Comments

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 ... [Read more...]

#rstats Make arrays into vectors before running table

July 29, 2015 | 0 Comments

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 ... [Read more...]

A small neuroimage interactive plotter

April 9, 2015 | 0 Comments

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 ...
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matlabr: a Package to Calling MATLAB from R with system

April 8, 2015 | 0 Comments

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 ... [Read more...]

White Matter Segmentation in R

April 7, 2015 | 0 Comments

Goals and Overall Approach We will use multiple packages and pieces of software for white matter (and gray matter/cerebro spinal fluid (CSF)) segmentation. The overall approach will be, with the required packages in parentheses: N4 Inhomogeneity Bias-Field Correction (extrantsr and ANTsR) Brain extraction using BET and additional tools (extrantsr ...
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The Unofficial ENAR 2015 Itinerary Maker

March 10, 2015 | 0 Comments

It’s almost ENAR 2015! The final program is out with all the sessions. The last conference I went to, the International Stroke Conference, had a program planner hosted by abstracts online. Although there are parts of this system I would like to change, I believe it is helpful for looking ...
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Using Tables for Statistics on Large Vectors

March 1, 2015 | 0 Comments

This is the first post I’ve written in a while. I have been somewhat radio silent on social media, but I’m jumping back in. Now, I work with brain images, which can have millions of elements (referred to as voxels). Many of these elements are zero (for background). ...
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The average Stripe employee! Congrats to Alyssa!

January 2, 2015 | 0 Comments

Recently, my colleague and fellow blogger Alyssa Frazee accepted a job at Stripe. All of us at JHU Biostat are happy for her, yet sad to see her go. While perusing Stripe’s website, I found the About page, where each employee has a photo of themselves. I’ve been ...
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Adding Cost Functions to ROCR performance objects

December 22, 2014 | 0 Comments

In my last post, I gave an introduction of the ROCR package and how to use it for ROC analysis. In the ROCR reference manual, it states “new performance measures can be added using a standard interface”, but I have not found that to be so. I may have missed ...
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A small introduction to the ROCR package

December 19, 2014 | 0 Comments

I've been doing some classification with logistic regression in brain imaging recently. I have been using the ROCR package, which is helpful at estimating performance measures and plotting these measures over a range of cutoffs. The prediction and performance functions are the workhorses of most of the analyses in ROCR ...
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My Commonly Done ggplot2 graphs: Part 2

December 18, 2014 | 0 Comments

In my last post I described some of my commonly done ggplot2 graphs. It seems as though some people are interested in these, so I was going to follow this up with other plots I make frequently. Scatterplot colored by continuous variable The setup of the data for the scatterplots ...
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My Commonly Done ggplot2 graphs

October 30, 2014 | 0 Comments

In my last post, I discussed how ggplot2 is not always the answer to the question “How should I plot this” and that base graphics were still very useful. Why Do I use ggplot2 then? The overall question still remains: why (do I) use ggplot2? ggplot2 vs lattice For one, ... [Read more...]

Working with NIfTI images in R

October 1, 2014 | 0 Comments

The oro.nifti package is awesome for NeuRoimaging (couldn't help myself). It has functions to read/write images, introduces the S4 nifti class, and has useful plotting functions. There are some limitations and some gotchas that are important to discuss if you are working with these objects in R. Dataset ... [Read more...]

Sorted HTML Tables and Javascript Libraries

August 4, 2014 | 0 Comments

A few days ago StatsInTheWild asked the following question In the R function “sortable.html.table”, it's sorting 9.2 higher than 30.5 because of the leading digit. How do I fix this? — SITW (@StatsInTheWild) July 23, 2014 So we had a few exchanges where I thought you could use sprintf and be done but ... [Read more...]
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