Function reference • picard

Core Classes

Main R6 classes for package functionality

CohortDef: CohortDef R6 Class

CohortManifest: CohortManifest R6 Class

ConceptSetDef: ConceptSetDef R6 Class

ConceptSetManifest: ConceptSetManifest R6 Class

ContributorLine: ContributorLine R6 Class

DbConfigBlock: DbConfigBlock R6 Class

ExecOptions: ExecOptions R6 Class

ExecutionSettings: ExecutionSettings

StudyMeta: StudyMeta R6 Class

UlyssesStudy: UlyssesStudy R6 Class

Creation Functions

Functions for creating objects and structures (make*)

makeExecOptions(): Make ExecOptions for Ulysses

makePrintFriendlyFile(): Generate Print-Friendly Cohort Documentation from JSON

makeSrcFile(): Create a Source Utility File

makeSrcSqlFile(): Create a SqlRender SQL File

makeStudyMeta(): Make Study Meta for Ulysses

makeTaskFile(): Function initializing an R file for an analysis task

makeUlyssesStudySettings(): Make Ulysses Study Settings

Initialization Functions

Functions for initializing components (init*)

initAgentMode(): Initialize or Restore Agent Mode for Cloned Repository

initializeRenv(): Initialize Renv for Project

Build Functions

Functions for building study components (build*)

buildComplementCohort(): Build a Complement Cohort Definition

buildStudyHub(): Build Study Hub

buildSubsetCohortDemographic(): Build a Subset Cohort Definition (Demographic)

buildSubsetCohortTemporal(): Build a Subset Cohort Definition (Temporal)

buildUnionCohort(): Build a Union Cohort Definition

Create Functions

Functions for creating new objects (create*)

createAgentBranch(): Create Feature Branch for Agent Work

createBlankCohortsLoadFile(): Create Blank Cohorts Load File

createBlankConceptSetsLoadFile(): Create Blank Concept Sets Load File

createExecutionSettings(): Create an ExecutionSettings object and set its attributes

createExecutionSettingsFromConfig(): Create ExecutionSettings from Config Block

createPullRequest(): Create Pull Request Metadata

Execution Functions

Functions for executing study tasks (exec*)

execStudyPipeline(): Production Study Pipeline Execution

Configuration Functions

Functions for configuration and setup (set*)

getTaskRunSummary(): Get Task Run Summary

setAtlasConnection(): Set Atlas Connection

setContributor(): Set Ulysses Contributor

setDbConfigBlock(): set the config block for a database

setOutputFolder(): Set Output Folder for Task

Loading Functions

Functions for loading and importing data (load*)

loadCohortManifest(): Load Cohort Manifest from Database or Cohort Files

loadConceptSetManifest(): Load Concept Set Manifest

Utility Functions

Other utility and helper functions

agentSaveWork(): Save Work for Agents (Automated, No Prompts)

cleanColumnNames(): Clean Column Names to Standard Format

clearPendingPR(): Clear Pending PR Reference

displayTaskStatusReport(): Display Task Status Report

documentDependencies(): Document Dependencies

formatFloats(): Format Float Columns

formatPercentages(): Format Percentage Columns

generateCohorts(): Generate Cohorts for Pipeline Execution

importAndBind(): Import and Bind Results by Version and Task

importAtlasCohorts(): Import CIRCE Cohort Definitions from ATLAS

importAtlasConceptSets(): Import CIRCE Concept Sets from ATLAS

launchCohortsLoadEditor(): Launch Interactive Cohort Load File Editor

launchConceptSetsLoadEditor(): Launch Interactive Concept Set Load Editor

orchestratePipelineExport(): Orchestrate Pipeline Export with Merging and QC

pivotForComparison(): Pivot Data Wide for Comparison

placeHolderExecOptions(): set the execOptions as placeholder.

prepareDisseminationData(): Prepare Dissemination Data with Chained Transformations

recordTaskExecution(): Record Task Execution Status

resetCohortManifest(): Reset Cohort Manifest Database

resetConceptSetManifest(): Reset Concept Set Manifest Database

restoreEnvironment(): Restore Environment from Lockfile

reviewExportSchema(): Review Export File Schema

saveWork(): Sync Local Work to Remote Branch

shouldRerunTask(): Check if Task Needs to be Rerun

snapshotEnvironment(): Snapshot Current Environment State

standardizeDataTypes(): Standardize Data Types

templateAtlasCredentials(): Template for setting Atlas Credentials

testStudyPipeline(): Test Study Pipeline

testStudyTask(): Test a Single Study Task

updateStudyVersion(): Function to update the study version

validateCohortResults(): Validate Cohort Results Completeness

validateConfigYaml(): Validate config.yml File Structure

validateStudyTask(): Validate Study Task Script

validateUlyssesStructure(): Validate Ulysses Repository Structure

visualizeCohortDependencies(): Visualize Cohort Dependencies in a Report

zipAndArchive(): Zip and Archive results from a study execution