DatabaseConnector - Connecting to Various Database Platforms

An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server', 'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', 'Google BigQuery', 'Snowflake', 'Spark', 'SQLite', and 'InterSystems IRIS'). Also includes support for fetching data as 'Andromeda' objects. Uses either 'Java Database Connectivity' ('JDBC') or other 'DBI' drivers to connect to databases.

Last updated 1 months ago

hadesopenjdk

12.63 score 56 stars 11 dependents 772 scripts 3.8k downloads

SqlRender - Rendering Parameterized SQL and Translation to Dialects

A rendering tool for parameterized SQL that also translates into different SQL dialects. These dialects include 'Microsoft SQL Server', 'Oracle', 'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', 'Snowflake', 'Azure Synapse Analytics Dedicated', 'Apache Spark', 'SQLite', and 'InterSystems IRIS'.

Last updated 3 months ago

hadesopenjdk

12.38 score 82 stars 12 dependents 488 scripts 3.5k downloads

PatientLevelPrediction - Develop Clinical Prediction Models Using the Common Data Model

A user friendly way to create patient level prediction models using the Observational Medical Outcomes Partnership Common Data Model. Given a cohort of interest and an outcome of interest, the package can use data in the Common Data Model to build a large set of features. These features can then be used to fit a predictive model with a number of machine learning algorithms. This is further described in Reps (2017) <doi:10.1093/jamia/ocy032>.

Last updated 1 days ago

hadesopenjdk

10.85 score 190 stars 297 scripts 304 downloads

FeatureExtraction - Generating Features for a Cohort

An R interface for generating features for a cohort using data in the Common Data Model. Features can be constructed using default or custom made feature definitions. Furthermore it's possible to aggregate features and get the summary statistics.

Last updated 5 months ago

hadesopenjdk

10.30 score 62 stars 1 dependents 209 scripts 770 downloads

CohortConstructor - Build and Manipulate Study Cohorts Using a Common Data Model

Create and manipulate study cohorts in data mapped to the Observational Medical Outcomes Partnership Common Data Model.

Last updated 2 days ago

9.70 score 2 stars 2 dependents 207 scripts 602 downloads

ParallelLogger - Support for Parallel Computation, Logging, and Function Automation

Support for parallel computation with progress bar, and option to stop or proceed on errors. Also provides logging to console and disk, and the logging persists in the parallel threads. Additional functions support function call automation with delayed execution (e.g. for executing functions in parallel).

Last updated 6 months ago

hades

9.18 score 12 stars 11 dependents 87 scripts 2.2k downloads

Andromeda - Asynchronous Disk-Based Representation of Massive Data

Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.

Last updated 7 months ago

hades

9.18 score 11 stars 7 dependents 57 scripts 1.4k downloads

Cyclops - Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis

This model fitting tool incorporates cyclic coordinate descent and majorization-minimization approaches to fit a variety of regression models found in large-scale observational healthcare data. Implementations focus on computational optimization and fine-scale parallelization to yield efficient inference in massive datasets. Please see: Suchard, Simpson, Zorych, Ryan and Madigan (2013) <doi:10.1145/2414416.2414791>.

Last updated 3 months ago

hadescpp

9.05 score 39 stars 4 dependents 73 scripts 1.4k downloads

EmpiricalCalibration - Routines for Performing Empirical Calibration of Observational Study Estimates

Routines for performing empirical calibration of observational study estimates. By using a set of negative control hypotheses we can estimate the empirical null distribution of a particular observational study setup. This empirical null distribution can be used to compute a calibrated p-value, which reflects the probability of observing an estimated effect size when the null hypothesis is true taking both random and systematic error into account. A similar approach can be used to calibrate confidence intervals, using both negative and positive controls. For more details, see Schuemie et al. (2013) <doi:10.1002/sim.5925> and Schuemie et al. (2018) <doi:10.1073/pnas.1708282114>.

Last updated 22 days ago

hadescpp

8.51 score 10 stars 1 dependents 151 scripts 768 downloads

CohortGenerator - Cohort Generation for the OMOP Common Data Model

Generate cohorts and subsets using an Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) Database. Cohorts are defined using 'CIRCE' (<https://github.com/ohdsi/circe-be>) or SQL compatible with 'SqlRender' (<https://github.com/OHDSI/SqlRender>).

Last updated 5 months ago

hadesopenjdk

7.91 score 13 stars 165 scripts 491 downloads

CohortSymmetry - Sequence Symmetry Analysis Using the Observational Medical Outcomes Partnership Common Data Model

Calculating crude sequence ratio, adjusted sequence ratio and confidence intervals using data mapped to the Observational Medical Outcomes Partnership Common Data Model.

Last updated 7 days ago

7.53 score 1 stars 73 scripts 414 downloads

omock - Creation of Mock Observational Medical Outcomes Partnership Common Data Model

Creates mock data for testing and package development for the Observational Medical Outcomes Partnership common data model. The package offers functions crafted with pipeline-friendly implementation, enabling users to effortlessly include only the necessary tables for their testing needs.

Last updated 26 days ago

7.51 score 2 stars 1 dependents 45 scripts 352 downloads

PhenotypeR - Assess Study Cohorts Using a Common Data Model

Phenotype study cohorts in data mapped to the Observational Medical Outcomes Partnership Common Data Model. Diagnostics are run at the database, code list, cohort, and population level to assess whether study cohorts are ready for research.

Last updated 18 days ago

7.38 score 2 stars 57 scripts 442 downloads

ResultModelManager - Result Model Manager

Database data model management utilities for R packages in the Observational Health Data Sciences and Informatics program <https://ohdsi.org>. 'ResultModelManager' provides utility functions to allow package maintainers to migrate existing SQL database models, export and import results in consistent patterns.

Last updated 6 months ago

openjdk

7.38 score 4 stars 3 dependents 9 scripts 731 downloads

OmopSketch - Characterise Tables of an OMOP Common Data Model Instance

Summarises key information in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. Assess suitability to perform specific epidemiological studies and explore the different domains to obtain feasibility counts and trends.

Last updated 6 days ago

7.16 score 1 stars 1 dependents 16 scripts 393 downloads

Eunomia - Standard Dataset Manager for Observational Medical Outcomes Partnership Common Data Model Sample Datasets

Facilitates access to sample datasets from the 'EunomiaDatasets' repository (<https://github.com/ohdsi/EunomiaDatasets>).

Last updated 11 months ago

hadesopenjdk

6.73 score 43 stars 139 scripts 744 downloads

Characterization - Implement Descriptive Studies Using the Common Data Model

An end-to-end framework that enables users to implement various descriptive studies for a given set of target and outcome cohorts for data mapped to the Observational Medical Outcomes Partnership Common Data Model.

Last updated 9 days ago

openjdk

6.13 score 3 stars

OmopViewer - Visualise OMOP Results using 'shiny' Applications

Visualise results obtained from analysing data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model using 'shiny' applications.

Last updated 3 months ago

6.13 score 3 stars 4 scripts 190 downloads

EvidenceSynthesis - Synthesizing Causal Evidence in a Distributed Research Network

Routines for combining causal effect estimates and study diagnostics across multiple data sites in a distributed study, without sharing patient-level data. Allows for normal and non-normal approximations of the data-site likelihood of the effect parameter.

Last updated 6 months ago

hadesopenjdk

5.87 score 8 stars 31 scripts 471 downloads

CirceR - Construct Cohort Inclusion and Restriction Criteria Expressions

Wraps the 'CIRCE' (<https://github.com/ohdsi/circe-be>) 'Java' library allowing cohort definition expressions to be edited and converted to 'Markdown' or 'SQL'.

Last updated 11 months ago

hadesopenjdk

4.58 score 6 stars 64 scripts 620 downloads

LocalControl - Nonparametric Methods for Generating High Quality Comparative Effectiveness Evidence

Implements novel nonparametric approaches to address biases and confounding when comparing treatments or exposures in observational studies of outcomes. While designed and appropriate for use in studies involving medicine and the life sciences, the package can be used in other situations involving outcomes with multiple confounders. The package implements a family of methods for non-parametric bias correction when comparing treatments in observational studies, including survival analysis settings, where competing risks and/or censoring may be present. The approach extends to bias-corrected personalized predictions of treatment outcome differences, and analysis of heterogeneity of treatment effect-sizes across patient subgroups. For further details, please see: Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl: An R Package for Comparative Safety and Effectiveness Research. Journal of Statistical Software. 2020. p. 1–32. Available from <doi:10.18637/jss.v096.i04>.

Last updated 4 months ago

cpp

4.56 score 1 stars 12 scripts 372 downloads

OhdsiReportGenerator - Observational Health Data Sciences and Informatics Report Generator

Extract results into R from the Observational Health Data Sciences and Informatics result database (see <https://ohdsi.github.io/Strategus/results-schema/index.html>) and generate reports/presentations via 'quarto' that summarize results in HTML format. Learn more about 'OhdsiReportGenerator' at <https://ohdsi.github.io/OhdsiReportGenerator/>.

Last updated 10 days ago

openjdk

4.54 score 2 scripts

CohortExplorer - Explorer of Profiles of Patients in a Cohort

This software tool is designed to extract data from a randomized subset of individuals within a cohort and make it available for exploration in a shiny application environment. It retrieves date-stamped, event-level records from one or more data sources that represent patient data in the Observational Medical Outcomes Partnership (OMOP) data model format. This tool features a user-friendly interface that enables users to efficiently explore the extracted profiles, thereby facilitating applications, such as reviewing structured profiles.

Last updated 1 years ago

openjdk

4.18 score 3 stars 3 scripts 256 downloads

CohortAlgebra - Use of Interval Algebra to Create New Cohort(s) from Existing Cohorts

This software tool is designed to generate new cohorts utilizing data from previously instantiated cohorts. It employs interval algebra operators such as UNION, INTERSECT, and MINUS to manipulate the data within the instantiated cohorts and create new cohorts.

Last updated 13 days ago

openjdk

4.00 score 1 stars 673 downloads

DatabaseConnectorJars - JAR Dependencies for the 'DatabaseConnector' Package

Provides external JAR dependencies for the 'DatabaseConnector' package.

Last updated 2 years ago

hadesopenjdk

3.00 score 1 stars 193 downloads