README.md

In OHDSI/CohortMethod: New-User Cohort Method with Large Scale Propensity and Outcome Models

CohortMethod

CohortMethod is part of 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

Propensity (preference score) distributionCovariate balance plot

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. Libraries used in CohortMethod require Java.

Installation

1. See the instructions here 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")

1. 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.

PDF versions of the documentation are also available:

• Vignette: Single studies using the CohortMethod package
• Vignette: Running multiple analyses at once using the CohortMethod package
• Package manual: CohortMethod.pdf

Support

• Developer questions/comments/feedback: OHDSI Forum
• We use the GitHub issue tracker for all bugs/issues/enhancements

Contributing

Read here 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.

OHDSI/CohortMethod documentation built on Feb. 9, 2024, 9:01 a.m.