README.md

In aostropolets/ConceptPrevalence: Concept Prevalence Calculation

ConceptPrevalence

Introduction

A package to calculate the counts of the standard and source concepts in an OMOP CDM and extract the current version of the mappings used

Technology

ConceptPrevalence is an R package.

Dependencies

• SqlRender
• DatabaseConnector

Getting started

In R, use the following commands to download and install:

install.packages("devtools") devtools::install_github("OHDSI/StudyProtocolSandbox/ConceptPrevalence")

library('ConceptPrevalence')

Add inputs for the site:

dbms <- 'your_dbms'

user <- 'user'

password <- 'password'

server <- Sys.getenv('server')

port <- Sys.getenv('port')

cdmName <- 'your_cdm_name'

cdmDatabaseSchema <- 'your_cdm_schema

vocabDatabaseSchema <- 'your_vocab_schema'

resultDatabaseSchema <-"your_results_schema"

connectionDetails <- DatabaseConnector::createConnectionDetails(

                              dbms = dbms,

                                                          server = server,

                                                          user = user,

                                                          password = password,

                                                          port = port
                              )

Then run the following:

ConceptPrevalence::calculate (

             connectionDetails,

             cdmName,

             cdmDatabaseSchema,

             vocabDatabaseSchema,

             resultDatabaseSchema

             )

Once the results are ready please send them to [e-mail]

License

ConceptPrevalence is licensed under Apache License 2.0

Development

ConceptPrevalence is being developed in R Studio.

aostropolets/ConceptPrevalence documentation built on Sept. 16, 2022, 12:11 p.m.