Install
library("devtools")
install_github("sysmedlab/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")
Development
- To Contribute:
# 1. Clone the repo
git clone https://github.com/sysmedlab/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/sysmedlab/ehR.git", branch = [branch name])
- To Contribute:
# 1. Clone the repo
git clone https://github.com/sysmedlab/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/sysmedlab/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')
Fork the repo:
- Follow the steps listed on GitHub Help: Fork A Repo. Make sure to add the original repo as
upstream:
git remote add upstream https://github.com/sysmedlab/ehR.git
To verify:
$ git remote -v
origin https://github.com/USERNAME/ehR.git (fetch)
origin https://github.com/USERNAME/ehR.git (push)
upstream git://github.com/sysmedlab/ehR.git (fetch)
upstream git://github.com/sysmedlab/ehR.git (push)
- To test a pull request, get a copy:
git fetch upstream pull/<id>/head:<branch> - Switch to the branch:
git checkout <branch> - After checking the PR, return to your branch
git checkout master