ReadMe.md

In ClaraMarquardt/ehR: A collection of R functions designed to facilitate the interaction with and analysis of EHR data.

ehR

NOTE: THIS VERSION OF THE REPOSITORY IS NO LONGER ACTIVELY MAINTAINED

Please see https://github.com/sysmedlab/ehR

Install

library("devtools")  
install_github("claramarquardt/ehR",dependencies = TRUE)    
library(ehR)

Documentation - See 'function_overview.csv' for an overview of all the functions (and data sets) included in the package

Datasets & Crosswalks The package contains the following data sets and crosswalks: - dia: Simulated EHR diagnosis data for 500 patients - ed: Simulated EHR ED visit data for 500 patients - dem: Simulated EHR demographics data for 500 patients - ehR_Cohort: Simulated cohort & feature set - gagne_code: ICD9 code - gagne co-morbidity category crosswalk (http://scholar.harvard.edu/gagne/software/combined-comorbidity-score) [* note the crosswalk included in the package includes gagne categories that are assigned a 0 weight (these are not included in the here referenced, publicly available version of the crosswalk)] - zocat: ICD9 code - zocat crosswalk

Notes - [1] Requires the newest version of devtools (https://github.com/hadley/devtools) to be installed

library(devtools)  
install_github("hadley/devtools")

• [2] ggplot themes included in the package (theme_[name of theme].R) may require a number of additional fonts to be installed and registered with ggplot/ggsave

# install the necessary packages
install.packages("extrafontdb",repos="http://cran.cnr.berkeley.edu/", 
   dependencies=TRUE)
install.packages("extrafont",repos="http://cran.cnr.berkeley.edu/", 
   dependencies=TRUE)

# load the necessary packages
library(extrafont)
library(extrafontdb)

# register the fonts (this step only needs to be execute once)
font_import()
loadfonts()

# Note: There may still be problems when using the themes on a plot saved in a non-PDF format

Development

• To Contribute:

# 1. Clone the repo
git clone https://github.com/ClaraMarquardt/ehR.git

# 2. Make/Save any changes 
- Ensure that all dependencies are included in @import statements at the function top and are 
listed in the Imports (CRAN Dependency)/ Remotes (Github Dependency) fields of the DESCRIPTION file
- Recompile the package by executing the 'package_management/package_update.sh' script (Note: Prior to 
compilation all dependencies need to be (manually) installed)
- Confirm that the compilation was successful by checking the 'package_management/package_update.Rout' 
file and the 'function_overview.csv'

# 2. Create a new branch
git checkout -b [branch name]

# 3. Push all changes to the branch (assuming all changes have been committed)
git push origin [branch name]

* Note: Please see the contribution guide prior to committing 
any changes: 'package_management/contribution_guide.txt'

# 4. Test by installing from the branch
library(devtools)
install_git("git://github.com/ClaraMarquardt/ehR.git", branch = "[branch name])

• Package Management Tools

See 'package_management/' for 

- (a) a script to update the package ('package_update.sh')

- (b) a script to load the package data and functions locally (rather than as a
package) ('load_package_locally.R') 

ClaraMarquardt/ehR documentation built on May 6, 2019, 12:02 p.m.