R

Package Building: How `DESCRIPTION`, `NAMESPACE`, `roxygen`, and `devtools::document` work together

As part of my new year’s resolution to learn new things about R, I’m trying to plug some holes in my R knowledge by writing more vignettes to explain them to myself this year. This week I finally think I understand more about namespaces in R and why you should use them in your R package. Namespaces: Why Bother? In short, we need namespaces because of the ambiguity of function names.

Things we learned teaching clinical data wrangling

Well, we just finished our clinical data wrangling workshop. This was a 12 hour workshop (spread over 4 days) where students got to work with a real research dataset (the Sleep Heart Health Study data). This is a workshop that we developed as part of an National Library of Medicine T15 training supplement in Data Science. The following is a short report describing the workshop and its outcomes. Intended Audience We designed the workshop for our incoming informatics students (both clinical and biological majors) in order to introduce them to the difficulties of working with clinical data.

A gRadual Introduction to Shiny

I just gave a workshop teaching the basics of Shiny (the interactive web visualization framework) for a group of PDX R users. We had 10 people attend, and most of the attendees managed to get through the material and had lots of good questions. I really enjoyed talking with everyone and I hope everyone learned something. We’re planning to give the workshop again to the larger PDX R user community, and some of the attendees last night have volunteered to be TAs.

Clinical Data Wrangling Workshop

10 hour/multi-day workshop on understanding clinical data quality issues through both didactic lecturing and active data exploration. With Eilis Boudreau and Nicole Weiskopf. DOI

Data Analytics

Practical coursework in R/SQL for our hybrid Data Analytics Course taught with Kaiser Permanente. This course has been taught from 2013 to the present during summer quarter for students in the Biomedical Informatics program at OHSU..

Introduction to igraph

Introductory workshop to the igraph package in R

R Bootcamp

In this course, we cover the basics of visualization, data munging, and basic statistics using the tidyverse in R. It is freely available to everyone, but registration is required. Written with Jessica Minnier and Chester Ismay.