Note: Unfortunately, the latest version of the DSAIDE package didn’t make it to CRAN in time (they are on vacation). Thus you need to install it from GitHub and also need a recent version of R for things to work. Here’s a quick overview of what you need.
remotes R package. Use the remotes package command install_github('ahgroup/DSAIDE') to install the latest version of DSAIDE (see more details in the DSAIDE Get Started tutorial). Make sure you have version 0.8.6 or newer (I’ll be releasing new versions as the course goes on).If you are new to R, please go through all the documents of this module, as well as those linked from there in the indicated order. Otherwise you will likely miss things.
This document provides a brief introduction to the DSAIDE package, which we will use a lot in this course.
DSAIDE package.DSAIDE, which stands for Dynamical Systems Approach to Infectious Disease Epidemiology is an R package I wrote. The goal is for users to explore infectious disease models and topics without having to implement their own models and write code.
Go to the DSAIDE website and read through the main page and the Get started section. Follow any instructions for steps that you haven’t done yet, namely installing R and RStudio and the DSAIDE package.
You can skip or skim over the “Level 2” and “Level 3” sections. We won’t use this approach to interact with DSAIDE in the course - though you are of course allowed to do so.
If you haven’t done already, load DSAIDE. You should see a short message on the screen. Some packages show messages when you load them, and others don’t. In this case, the package tells you that you can start using it by typing dsaidemenu() into the R console. Do that to start it
dsaidemenu()A menu should open in your browser, from which you can explore different models/apps. Make sure the version and date shown at the top is recent and corresponds to the version you are asked to have. Right now this is version 0.8.6. I’ll be releasing new versions as the course goes on.
You can explore DSAIDE now as much as you want, but you can also close it for now, as we’ll be coming back to it and working through most of the apps as part of the course.
This source covers more or less the same material that you just read, so checking it out is optional.
I published a paper describing the package. The paper is by now somewhat outdated with regards to the details of the package, but it describes the overall idea and context well.