# Enrichment Analysis of Clinically Relevant Concepts in Common Data Model Cohort Data

## Documentation for package ‘CohortContrast’ version 1.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

automaticCorrelationCombineConcepts | Function for automatically combining concepts by hierarchy mapping
automaticHierarchyCombineConcepts | Function for automatically combining concepts by hierarchy mapping
checkDataMode | Check if a Data Directory Contains Summary Mode Data
checkPythonDeps | Check Python Dependencies
CohortContrast | Run CohortContrast Analysis
CohortContrastViewer | CohortContrast Viewer - Interactive Disease Cohort Visualization
cohortFromCohortTable | Read cohort from database cohort table
cohortFromCSV | Read cohort from CSV
cohortFromDataTable | Read cohort from data.frame object
cohortFromJSON | Read cohort from JSON
configurePython | Configure Python Environment for CohortContrast Viewer
createControlCohortInverse | Function for creating automatic matches based on inverse control logic
createControlCohortMatching | Function for creating automatic matches based on age and sex
generateMappingTable | Create a mapping table with predefined maximum abstraction level
getPythonInfo | Get Python Configuration Information
getTopSeparatingConcepts | Get Top Concepts That Best Separate Clusters
installPythonDeps | Install Python Dependencies
installPythonDepsOffline | Install Python Dependencies Offline
loadCohortContrastStudy | Load a Saved CohortContrast Study
matchCohortsByAge | Function for matching the control to target by age
nGramClusterSummarization | Function for summarizing ngrams from nGramDiscovery output
nGramDiscovery | Function for discovering ngrams from the extracted data from CohortContrast function
precomputeSummary | Pre-compute Summary Data for a Study
removeTemporalBias | Remove Temporal Bias from CohortContrast Analysis
resolveCohortTableOverlaps | Resolve overlaps inside the cohort table
runCohortContrastViewer | Run CohortContrast Viewer Dashboard
stopCohortContrastViewer | Stop CohortContrast Viewer Dashboard