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

ExecutionSettings: ExecutionSettings

StudyMeta: StudyMeta R6 Class

UlyssesStudy: UlyssesStudy R6 Class

Creation Functions

Functions for creating objects and structures (make*)

makeBlock(): Make a database config block

makeDisseminationScript(): Create a Dissemination Script Template

makeInputBuilderScript(): Create a Pre-Pipeline Builder Script

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

initCohortManifest(): Initialize a New Cohort Manifest

initConceptSetManifest(): Initialize a New Concept Set Manifest

initializeRenv(): Initialize Renv for Project

Build Functions

Functions for building study components (build*)

buildStudyHub(): Build Study Hub

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

createDisseminationEnv(): Create a Dissemination Environment Object

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

createExecutionSettingsFromConfig(): Create ExecutionSettings from Config Block

createPullRequest(): Create Pull Request Metadata

createSubsetEndWindow(): Create a Subset End Window Operator

createSubsetStartWindow(): Create a Subset Start Window Operator

Execution Functions

Functions for executing study tasks (exec*)

execStudyPipeline(): Production Study Pipeline Execution

Configuration Functions

Functions for configuration and setup (set*)

getAtlasConnection(): Get Atlas Connection

getTaskRunSummary(): Get Task Run Summary

setContributor(): Set Ulysses Contributor

setDbConfigBlock(): set the config block for a database

setOutputFolder(): Set Output Folder for Task

setupAtlasSecretsKeyring(): Set up Atlas/WebAPI keyring credentials

setupDbSecretsKeyring(): Set up keyring-based credentials for a database server

Loading Functions

Functions for loading and importing data (load*)

loadCohortManifest(): Load Cohort Manifest from SQLite Database

loadConceptSetManifest(): Load Concept Set Manifest

Utility Functions

Other utility and helper functions

addBlock(): Add a config block to an existing config.yml

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

editSecrets(): Edit the secrets.yml file

findStudyProjectRoot(): Find the root of a Picard study repository

formatFloats(): Format Float Columns

formatPercentages(): Format Percentage Columns

generateCohorts(): Generate Cohorts for Pipeline Execution

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

migrateCohortManifest(): Migrate Old CohortManifest SQLite to New Schema

migrateConceptSetManifest(): Migrate Old ConceptSetManifest SQLite to New Schema

normalizeCohortManifestPaths(): Normalize Legacy Cohort Manifest File Paths

normalizeConceptSetManifestPaths(): Normalize Legacy Concept Set Manifest File Paths

pivotForComparison(): Pivot Data Wide for Comparison

plotCohortGraph(): Plot Cohort Dependency Graph

prepareDisseminationData(): Prepare Dissemination Data with Chained Transformations

publishStudyHubPosit(): Publish Study Hub to Posit Connect

recordTaskExecution(): Record Task Execution Status

resetCohortManifest(): Reset Cohort Manifest

resetConceptSetManifest(): Reset Concept Set Manifest

restoreEnvironment(): Restore Environment from Lockfile

reviewExportSchema(): Review Export File Schema

reviewKeyringCredentials(): Review keyring credentials for picard service

runPostProcessing(): Run Post-Processing Pipeline with Merging and QC

runTestPostProcessing(): Run Post-Processing Pipeline for test mode

saveWork(): Sync Local Work to Remote Branch

shouldRerunTask(): Check if Task Needs to be Rerun

snapshotEnvironment(): Snapshot Current Environment State

sourceDisseminationScripts(): Source Dissemination Scripts

sourceInputBuilderScripts(): Source Pre-Pipeline Input Builder Scripts

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