This repo contains the model script and the cohort definitions used for a comparison of PLP and mlr3 R-based package using the SynPUF 5% dataset.
Cohort definition was performed using the ATLAS platform. The data was imported into a locally running ATLAS and the cohort definition option was used. The "cohort_target.sql" file include the target population definition used in the study. In addition "cohort_outcome_death.sql" file describes our outcome cohort within the target population.
We loaded the target and outcome cohorts data in a postgresql database. But any database format that OMOP CDM support can be used to store the SynPUF 5% dataset.
"PLPvsMLR3.Rproj" (and its dependent files, NAMESPACE, and DESCRIPTION) include the required R/R-studio settings for the project and can be directly imported into the R-studio.
RStudio version 2022.07.2 Build 576 with R version 4.3.1 was used.
MLR3 version 0.16.1
PatientLevelPrediction version 6.3.5