Showing 13 of total 13 results (show query)
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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.
Maintained by Martijn Schuemie. Last updated 2 months ago.
56 stars 12.63 score 772 scripts 11 dependentsohdsi
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'.
Maintained by Martijn Schuemie. Last updated 17 days ago.
82 stars 12.52 score 488 scripts 13 dependentsohdsi
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>.
Maintained by Egill Fridgeirsson. Last updated 22 days ago.
190 stars 10.85 score 297 scriptsohdsi
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.
Maintained by Ger Inberg. Last updated 9 days ago.
62 stars 10.64 score 209 scripts 2 dependentsohdsi
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.
Maintained by Martijn Schuemie. Last updated 7 months ago.
11 stars 9.29 score 57 scripts 8 dependentsohdsi
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).
Maintained by Martijn Schuemie. Last updated 2 days ago.
12 stars 9.28 score 87 scripts 12 dependentsohdsi
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>.
Maintained by Marc A. Suchard. Last updated 4 months ago.
39 stars 9.05 score 73 scripts 4 dependentsohdsi
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>.
Maintained by Martijn Schuemie. Last updated 1 months ago.
10 stars 8.51 score 151 scripts 1 dependentsohdsi
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>).
Maintained by Anthony Sena. Last updated 6 months ago.
13 stars 7.91 score 165 scriptsohdsi
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>).
Maintained by Frank DeFalco. Last updated 11 months ago.
43 stars 6.73 score 139 scriptsohdsi
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.
Maintained by Martijn Schuemie. Last updated 7 months ago.
8 stars 5.87 score 31 scriptsohdsi
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'.
Maintained by Chris Knoll. Last updated 11 months ago.
6 stars 4.58 score 64 scriptsohdsi
DatabaseConnectorJars:JAR Dependencies for the 'DatabaseConnector' Package
Provides external JAR dependencies for the 'DatabaseConnector' package.
Maintained by Martijn Schuemie. Last updated 3 years ago.
1 stars 3.00 score