Characterization Installation Guide

Jenna Reps

2024-04-19

Introduction

This vignette describes how you need to install the Observational Health Data Sciences and Informatics (OHDSI) Characterization package under Windows, Mac, and Linux.

Software Prerequisites

Windows Users

Under Windows the OHDSI Characterization package requires installing:

• R (https://cran.cnr.berkeley.edu/ ) - (R >= 3.3.0, but latest is recommended)
• Rstudio (https://www.rstudio.com/ )
• Java (http://www.java.com )
• RTools (https://cran.r-project.org/bin/windows/Rtools/)

Mac/Linux Users

Under Mac and Linux the OHDSI Characterization package requires installing:

• R (https://cran.cnr.berkeley.edu/ ) - (R >= 3.3.0, but latest is recommended)
• Rstudio (https://www.rstudio.com/ )
• Java (http://www.java.com )
• Xcode command line tools(run in terminal: xcode-select –install) [MAC USERS ONLY]

Installing the Package

The preferred way to install the package is by using remotes, which will automatically install the latest release and all the latest dependencies.

If you do not want the official release you could install the bleeding edge version of the package (latest develop branch).

Note that the latest develop branch could contain bugs, please report them to us if you experience problems.

Installing Characterization using remotes

To install using remotes run:

install.packages("remotes")
remotes::install_github("OHDSI/Characterization")

When installing make sure to close any other Rstudio sessions that are using Characterization or any dependency. Keeping Rstudio sessions open can cause locks that prevent the package installing.

Installation issues

Installation issues need to be posted in our issue tracker: http://github.com/OHDSI/Characterization/issues

The list below provides solutions for some common issues:

1. If you have an error when trying to install a package in R saying ‘Dependency X not available …’ then this can sometimes be fixed by running install.packages('X') and then once that completes trying to reinstall the package that had the error.

2. I have found that using the github `remotes`` to install packages can be impacted if you have multiple R sessions open as one session with a library open can cause the library to be locked and this can prevent an install of a package that depends on that library.

Acknowledgments

Considerable work has been dedicated to provide the Characterization package.

citation("Characterization")

## 
## To cite package 'Characterization' in publications use:
## 
##   Reps J, Ryan P (2024). _Characterization: Characterizations of
##   Cohorts_. https://ohdsi.github.io/Characterization,
##   https://github.com/OHDSI/Characterization.
## 
## A BibTeX entry for LaTeX users is
## 
##   @Manual{,
##     title = {Characterization: Characterizations of Cohorts},
##     author = {Jenna Reps and Patrick Ryan},
##     year = {2024},
##     note = {https://ohdsi.github.io/Characterization, https://github.com/OHDSI/Characterization},
##   }