Tools for Epidemiologists

Last updated: January 18, 2021

Last updated: February 2019

This is a curated list of online resources and software for epidemiologists. Am I missing something? Please make a suggestion.

Reproducibility

Consider keeping your data analysis code on GitHub. You can sign up for a free account with unlimited private repositories.
Open Science Framework has some interesting tools for reproducibility, and integrates with GitHub.
Code Ocean is a platform for hosing code for reproducible research. It essentially combines version control with the ability to run uploaded code with a single click. It supports Jupyter notebooks and Stata code, among other things.

Draw.io Free, web-based diagramming application.
Google Drive Drawing
Another free, web-based diagramming application, integrated into Google Drive (née Google Docs).
LibreOffice Draw
Free, cross-platform diagramming application. It’s part of the LibreOffice suite, an open-source replacement for Microsoft Office. I believe it’s compatible with Visixo files (see below).
OmniGraffle
Premier Mac-only diagramming application. (Education discount available.)
Visio
Premier Windows-only diagramming application.
You can also use PowerPoint, but you may have better luck with one of the other applications mentioned here. For example, diagramming applications have better support for guides to assist with alignment. Personally, I would much rather use LibreOffice Draw or one the free web-based applications in favor of PowerPoint.

STROBE Statement

STROBE stands for an international, collaborative initiative of epidemiologists, methodologists, statisticians, researchers and journal editors involved in the conduct and dissemination of observational studies, with the common aim of STrengthening the Reporting of OBservational studies in Epidemiology.

(Hat tip: Chris.)
Teach Epi
Good resource for both basic epi lectures and general information on succeeding in grad school. (Hat tip: Chris.)
Isaac Newton Institute presentations
Presentations on some advanced epi topis. Worth reading through the list to see if anything in it is of interest.
UCSF Virtual Library
List of links to resources for wide variety of epidemiology-related topics. (Hat tip: Kristen.)
CDC Epidemiology Resources
A list of epidemiology related resources, mostly resources available from the CDC. (Hat tip: Kristen.)
Partners in Information Access for the Public Health Workforce

Partners in Information Access for the Public Health Workforce is a collaboration of U.S. government agencies, public health organizations, and health sciences libraries which provides timely, convenient access to selected public health resources on the Internet.

A wide variety of sources for public health professionals, both on specific research topics and more genearl information about policy, career development, funding, and networking. (Hat tip: Kristen.)
What is epidemiology?
(Hat tip: Brianna.)

UCLA statistics website
You’ve probably run across this site if you’ve ever done a Google search on a stats question. It’s a great resource, with sections devoted to R, SAS, SPSS, and Stata. (Hat tip: Chris.)

Specifically, this page is helpful in figuring out what statistical tet to use. (Hat tip: Brianna.)
Handbook of Biological Statistics
Well-written explanations of lots of common statistical tests, including SAS code.
Statistics Done Wrong
A catalog of common statistical errors. (Hat tip: Brianna.)
Points of Significance – Nature Methods
A very accessible monthy column on common statistical topics and methods of visualization. (Hat tip: Brianna.)
simplystatistics.org
A general stats blog that’s worth reading.
Conditional probability visualization
A good visualization of conditional probability (e.g. $$P(A \mid B)$$).

If you’re wondering about what the most common stats packages are, or which ones I think you should learn, see this post.
In addition to the “Big 3” commercial packages (SAS, SPSS, Stata) and R (the main open source option), there are some other open source packages that may be of interest (I haven’t used these so I can’t vouch for them):
- PSPP, an open source replacement for SPSS.
- JASP, a friendly GUI-based stats package powered by R.
- jamovi, another friendly GUI-based, R-powered stats package.
- Radiant, yet another front-end for R. This one is more focused on “business intelligence” (read: visualization and exploration) than stats, but it does have a fair amount of stats functionality.

sasfix
A free tool for properly formatting SAS output for pasting into a presentation, email, etc. Replaces funny ƒ characters with the appropriate lines and removes excess white space.
StatTransfer
Software for converting data from one format into another. This is the best way to get CSV or Excel data into SAS, get SAS data into Excel, or convert SAS to Stata format and vice versa.
SAS code matched to Stata code
Helpful if you are going from one statistics package to the other.
Plot.ly
A tool for building complex graphs in a web browser, and sharing interactive versions of these graphs.

Hemingway App
Analyzes complexity of writing. Might be especially useful for making sure consent forms are not confusing.

Speaking.io
General advice on presentations/public speaking.
Deckset A Mac app that uses Markdown to make slides. It is substantially faster for creating good-looking slides than PowerPoint or Keynote.
presentationskills.me
A lot of advice on all aspects of presenting/public speaking.
Presentations Field Guide by David Sparks