README.md

In jarad/ISDSWorkshop: International Society for Disease Surveillance R Workshop

ISDSWorkshop

An R package for the Introduction to R for Biosurveillance pre-conference training for the International Society for Disease Surveillance.

Prior to the conference, please install R, Rstudio (not required, but highly recommended), and the ISDSWorkshop R package. You will need to have internet access and administrator privileges to install everything.

Install R (may require administrator privileges)

Please go to http://www.r-project.org/ and click on download R. You will be asked to select a CRAN mirror. I select https://rweb.crmda.ku.edu/cran/ as it is geographically close and uses the secure http protocol (HTTPS). In the download and install R section, Click on the correct link depending on your operating system: Linux, (Mac) OS X, or Windows.

Windows

Click on base and then the link to Download R X.X.X for Windows (where the X will be numbers representing the current version of R). Install this program like any other program on Windows using all the defaults.

(Mac) OS X

Click on the appropriate .pkg file depending on which version of Mac OS X you are using. Install this program like any other program on OS X using all the defaults.

Linux

If you are using Linux, then I trust you know what you are doing. You can install R from source or you can use a package manager.

Install RStudio (may require administrator privileges)

The installation of RStudio is optional, but highly recommended. It provides an improved interface to R, but has projects which help to quickly switch between (oddly enough) projects. Go to http://www.rstudio.com/products/rstudio/download/ and choose the correct platform under Installers for ALL Platforms. Install like any other program.

Install the ISDSWorkshop R package (should not require administrator privileges)

Start RStudio (or R GUI if you did not install RStudio). At the command prompt (>) in the Console window of R, copy-paste the following code. This will download and install a number of packages that we will need and create vignettes (this could take a while). You will need internet access during this process.

install.packages(c("devtools","dplyr","ggplot2","tidyr"))
devtools::install_github("jarad/ISDSWorkshop")

If it asks you to choose a repository, choose a repository that is geographically close to you. If asked to create a personal library, say yes.

(Optional) Install additional packages

There are a few other packages that will be used lightly or referenced during the workshop. These packages are listed under "Suggests:" in the DESCRIPTION file. To install these packages, in R run

ISDSWorkshop::install_additional_packages()

A warning will be issued for any packages that could not be installed.

(Optional) Test your installation

If you want to test that everything is working, in R run

ISDSWorkshop::workshop(FALSE, FALSE)

which should open a web-browser with an outline for the workshop.

Exit R

Regardless of which method above you used, exit R by running

q("no")

in R.

jarad/ISDSWorkshop documentation built on May 18, 2019, 2:39 p.m.