PrevalenceResults R6 Class

Container for prevalence analysis results with standardization capabilities. Manages export/import with full provenance tracking via manifest file.

Details

Results are stored as CSV files in a directory bundle with a manifest.json file tracking provenance, standardization parameters, and execution metadata.

Active Fields

  • prevalence: Data frame with crude (unadjusted) prevalence results (read/write)

  • stdPrev: Data frame with standardized prevalence results (read/write)

  • incidence: Data frame with incidence results (read/write)

  • drugUsage: Data frame with drug usage results (read/write)

  • metaInfo: Data frame with analysis metadata (read/write)

  • standardizationApplied: List containing standardization parameters (read-only)

Private Tracking Fields (visible in print/summary only)

  • executionId: Unique execution identifier

  • exportDate: Timestamp of last export

Methods

  • initialize(): Create new PrevalenceResults object

  • export(): Save results to directory bundle with manifest

  • standardizePrevalence(): Apply direct method standardization (returns new object)

  • validate(): Check data integrity and consistency

  • summary(): Print summary statistics

  • print(): Display object overview

Active bindings

prevalence

Data frame with prevalence results

incidence

Data frame with incidence results

drugUsage

Data frame with drug usage results

metaInfo

Data frame with analysis metadata

stdPrev

Data frame with standardized prevalence results

standardizationApplied

List of standardization parameters (read-only)

Methods

Public methods

Method new()

Create new PrevalenceResults object

Usage

PrevalenceResults$new(
  prevalence = NULL,
  incidence = NULL,
  drugUsage = NULL,
  metaInfo = NULL,
  executionId = NULL
)

Arguments

prevalence

Data frame with prevalence results

incidence

Data frame with incidence results

drugUsage

Data frame with drug usage results

metaInfo

Data frame with analysis metadata

executionId

Optional character string for execution tracking (internal use)

Method export()

Export results to directory bundle with manifest

Usage

PrevalenceResults$export(outputFolder, bundleName = NULL)

Arguments

outputFolder

Character path where bundle directory will be created

bundleName

Optional name for the bundle directory. Default: auto-generated timestamp

Returns

Invisibly returns self for chaining

Method standardizePrevalence()

Apply direct method standardization

Usage

PrevalenceResults$standardizePrevalence(
  referencePopulation,
  ageMin = NULL,
  ageMax = NULL,
  ageRightTruncation = NULL
)

Arguments

referencePopulation

StandardizationReference object

ageMin

Numeric minimum age for filtering

ageMax

Numeric maximum age for filtering

ageRightTruncation

Numeric age threshold for collapsing

Returns

New PrevalenceResults object with standardized prevalence

Method validate()

Validate data integrity and relationships

Usage

PrevalenceResults$validate()

Returns

Logical TRUE if valid, otherwise stops with error

Method summary()

Print summary of results

Usage

PrevalenceResults$summary()

Returns

Invisibly returns self

Method print()

Print object

Usage

PrevalenceResults$print()

Returns

Invisibly returns self

Method show_query()

Display executed SQL query for an analysis

Usage

PrevalenceResults$show_query(analysisId)

Arguments

analysisId

Character or numeric analysis ID

Returns

Invisibly returns the SQL string

Method .addExecutedQuery()

Add executed query for an analysis (internal use)

Usage

PrevalenceResults$.addExecutedQuery(analysisId, sql_string)

Arguments

analysisId

Character or numeric analysis ID

sql_string

Character SQL query string

Returns

Invisibly returns self

Method clone()

The objects of this class are cloneable with this method.

Usage

PrevalenceResults$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.