jamieweaver / ohdsirtools

An R package of support tools that didn’t fit other categories, including tools for maintaining R libraries.

OhdsiRTools

Introduction

An R package with tools to be used in the other OHDSI R packages

Features

• Auto code formatting
• Auto checking of R code
• Functions for parallel computation
• Functions for logging
• Functions used for automating analyses
• Functions for retrieving cohort definition and concept set metadata, status, and composition (SQL/JSON/CSV) from ATLAS

Examples

# Auto-format all R files in a package:
formatRFolder()

# Identify problems in R code in a package:
checkUsagePackage("OhdsiRTools")

# Run a function in parallel:
fun <- function(x) {
  return (x^2)
}

cluster <- makeCluster(numberOfThreads = 3)
result <- clusterApply(cluster, 1:10, fun)
stopCluster(cluster)

# Insert cohort definition JSON and SQL into a study package:
insertCohortDefinitionInPackage(123, "MyocardialInfarction", baseUrl = "http://server.org:80/WebAPI")

# Insert concept set concept Ids into a study package:
insertConceptSetConceptIdsInPackage(baseUrl = "http://server.org:80/WebAPI", fileName = "conceptsetids.csv")

# Get a formatted cohort definition name (no bracketed prefixes) from Atlas:
getCohortDefinitionName(baseUrl = "http://server.org:80/WebAPI", definitionId = 123, formatName = TRUE)

# Get a formatted concept set name (no bracketed prefixes) from Atlas:
getConceptSetName(baseUrl = "http://server.org:80/WebAPI", setId = 123, formatName = TRUE)

# Get all concept Ids from a concept set from Atlas:
getConceptSetConceptIds(baseUrl = "http://server.org:80/WebAPI", setId = 123)

# Get a data frame filled with generation statuses of multiple cohort definitions across multiple CDM sources in Atlas:
getCohortGenerationStatuses(baseUrl = "http://server.org:80/WebAPI", definitionIds = c(1234), sourceKeys = c("blah"))

Technology

OhdsiRTools is an R package.

System Requirements

Requires R (version 3.1.0 or higher)

Dependencies

None

Getting Started

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

install.packages("devtools")
library(devtools)
install_github("ohdsi/OhdsiRTools")

Getting Involved

• Vignette: Logging using OhdsiRTools
• Vignette: Parallel execution using OhdsiRTools
• Package manual: OhdsiRTools.pdf
• Developer questions/comments/feedback: OHDSI Forum
• We use the GitHub issue tracker for all bugs/issues/enhancements

License

OhdsiRTools is licensed under Apache License 2.0

Development

OhdsiRTools is being developed in R Studio.

Development status

Ready for use

Acknowledgements

• This project is supported in part through the National Science Foundation grant IIS 1251151.