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

[Up] [Top]

Documentation for package ‘CohortContrast’ version 1.0.0

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