Highly customisable R-package for detecting event sequences in OMOP CDM by using pairwise statistical testing of all two-event sequences.
Related publication: Kadri Künnapuu, Solomon Ioannou, Kadri Ligi, Raivo Kolde, Sven Laur, Jaak Vilo, Peter R Rijnbeek, Sulev Reisberg, Trajectories: a framework for detecting temporal clinical event sequences from health data standardized to the Observational Medical Outcomes Partnership (OMOP) Common Data Model, JAMIA Open, Volume 5, Issue 1, April 2022, ooac021,


R-package TrajectoryMarkovAnalysis specializes in modeling patient trajectories using Markov chains. The package supports discrete and continuous time Markov models, Kaplan-Meier plots, Markov trees and synthetic data generation. The package is based on OMOP CDM.​


Package Cohort2Trajectory creates patient orientated treatment trajectories from cohorts defined in OHDSI ATLAS. The package can be used with access to OMOP CDM database. The package creates discrete and continuous time trajectories (and outputs them as .csv file) which describe patients’ treatment through time. Package can be run with GUI or CLI.


TrajectoryViz is an R package for visualizing patient level event sequences, to complement the sunburst plot based analyses. The patient level sequences can be filtered, shown with the gaps or without, and aligned by different events. All these visualisations are interactive allowing both quantifying the interesting aspects or zooming into interesting patterns. To make the visualization compatible with any OMOP formatted database TrajectoryViz relies on Cohort2Trajectory package in R.

Interactive chart of Estonian specialist medical care

The interactive chart is based on 6.5 million claims from specialist medical care in 2013-2019. The data is grouped by age, gender and main diagnosis. The chart is created in co-operation with Estonian Health Insurance Fund.