https://github.com/OHDSI/CohortMethod
Tip revision: 1c24f56f3f5e1571a16de90085ae198805f2c28d authored by Admin_mschuemi on 31 August 2023, 04:51:49 UTC
Finished updating multiple studies vignette
Finished updating multiple studies vignette
Tip revision: 1c24f56
README.md
CohortMethod
============
[![Build Status](https://github.com/OHDSI/CohortMethod/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/CohortMethod/actions?query=workflow%3AR-CMD-check)
[![codecov.io](https://codecov.io/github/OHDSI/CohortMethod/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/CohortMethod?branch=main)
CohortMethod is part of [HADES](https://ohdsi.github.io/Hades).
Introduction
============
CohortMethod is an R package for performing new-user cohort studies in an observational database in the OMOP Common Data Model.
Features
========
- Extracts the necessary data from a database in OMOP Common Data Model format.
- Uses a large set of covariates for both the propensity and outcome model, including for example all drugs, diagnoses, procedures, as well as age, comorbidity indexes, etc.
- Large scale regularized regression to fit the propensity and outcome models.
- Includes function for trimming, stratifying, matching, and weighting on propensity scores.
- Includes diagnostic functions, including propensity score distribution plots and plots showing covariate balance before and after matching and/or trimming.
- Supported outcome models are (conditional) logistic regression, (conditional) Poisson regression, and (conditional) Cox regression.
Screenshots
===========
<table>
<tr valign="bottom">
<td width = 50%>
<img src="https://github.com/OHDSI/CohortMethod/raw/main/extras/ps.png"/>
</td>
<td width = 50%>
<img src="https://github.com/OHDSI/CohortMethod/raw/main/extras/balanceScatterplot.png"/>
</td>
</tr><tr>
<td>Propensity (preference score) distribution</td><td>Covariate balance plot</td>
</tr>
</table>
Technology
============
CohortMethod is an R package, with some functions implemented in C++.
System Requirements
============
Requires R (version 3.6.0 or higher). Installation on Windows requires [RTools](https://cran.r-project.org/bin/windows/Rtools/). Libraries used in CohortMethod require Java.
Installation
=============
1. See the instructions [here](https://ohdsi.github.io/Hades/rSetup.html) for configuring your R environment, including RTools and Java.
2. In R, use the following commands to download and install CohortMethod:
```r
install.packages("remotes")
remotes::install_github("ohdsi/CohortMethod")
```
3. Optionally, run this to check if CohortMethod was correctly installed:
```r
connectionDetails <- createConnectionDetails(dbms="postgresql",
server="my_server.org",
user = "joe",
password = "super_secret")
checkCmInstallation(connectionDetails)
```
Where dbms, server, user, and password need to be changed to the settings for your database environment. Type
```r
?createConnectionDetails
```
for more details on how to configure your database connection.
User Documentation
==================
Documentation can be found on the [package website](https://ohdsi.github.io/CohortMethod).
PDF versions of the documentation are also available:
* Vignette: [Single studies using the CohortMethod package](https://raw.githubusercontent.com/OHDSI/CohortMethod/main/inst/doc/SingleStudies.pdf)
* Vignette: [Running multiple analyses at once using the CohortMethod package](https://raw.githubusercontent.com/OHDSI/CohortMethod/main/inst/doc/MultipleAnalyses.pdf)
* Package manual: [CohortMethod.pdf](https://raw.githubusercontent.com/OHDSI/CohortMethod/main/extras/CohortMethod.pdf)
Support
=======
* Developer questions/comments/feedback: <a href="http://forums.ohdsi.org/c/developers">OHDSI Forum</a>
* We use the <a href="https://github.com/OHDSI/CohortMethod/issues">GitHub issue tracker</a> for all bugs/issues/enhancements
Contributing
============
Read [here](https://ohdsi.github.io/Hades/contribute.html) how you can contribute to this package.
License
=======
CohortMethod is licensed under Apache License 2.0
Development
===========
CohortMethod is being developed in R Studio.
### Development status
CohortMethod is actively being used in several studies and is ready for use.
# Acknowledgements
- This project is supported in part through the National Science Foundation grant IIS 1251151.