Iris

IRIS provides a high-level descriptive summary of a population within a OMOP CDM-compliant database

This version 1.1 uses CDM v5. Unlike v1.0, this version makes use of the Measurement table to go after lab results.

In terms of database engines - we tested the package on Postgres, MS SQL with no errors. For Oracle, there is a known bug and known fix for it (see Issues on GitHub for the fix).

#How to use it?

The best way to use Iris is as R package and from within R.

##R mode

install.packages("devtools")
devtools::install_github("OHDSI/SqlRender")
devtools::install_github("ODHSI/DatabaseConnector")
devtools::install_github("OHDSI/Iris")
?Iris::execute # To get extended help

# Run study
a<-Iris::execute(dbms = "postgresql",      # Change to participant settings
              user = "joebruin",
              password = "supersecret",
              server = "myserver",
              cdmSchema = "cdm_schema",
              cdmVersion = 4)
#show timing again
a$executionTime

#show results
a$result

#write to a file
write.csv(a$result,file='iris-results.csv',row.names = F)


# Email results file
Iris::email(from = "collaborator@ohdsi.org",         # Change to participant email address
      dataDescription = "CDM4 Simulated Data") # Change to participant data description

To reload saved results in R

# Load (or reload) study results
results <- Iris::loadOhdsiStudy(verbose = TRUE)

#Sample output (for v1.0):

MEASURE     RESULT     EXPLANATION
G1     141,805,491        count of patients
G2     20,328,289,601     count of events
D2     90,024,522         count of patients with at least 1 Dx and 1 Rx
D3     112,148,500        count of patients with at least 1 Dx and 1 Proc
D4     5,939,621          count of patients with at least 1 Obs, 1 Dx and 1 Rx
D5     277,975            count of deceased patients

Relevant IRIS forum discussion is here http://forums.ohdsi.org/t/short-and-quick-way-to-describe-your-cdm-dataset/251

haivietduong/Iris

Iris