Package {CohortIncidence}

Type: Package
Title: Cohort Incidence Analysis for the OMOP Common Data Model
Version: 4.2.0
Date: 2026-07-27
Description: Provides functionality for performing cohort incidence analyses against data stored in the OMOP Common Data Model (CDM). The package generates database-specific SQL, executes analyses across supported database platforms, and returns standardized incidence estimates using configurable time-at-risk, stratification, and cohort definitions. It is intended to support reproducible observational research within the OHDSI analytics framework.
License: Apache License 2.0
VignetteBuilder: knitr
URL: https://ohdsi.github.io/CohortIncidence/
BugReports: https://github.com/OHDSI/CohortIncidence/issues
Depends: R (≥ 3.2.2), DatabaseConnector (≥ 3.0.0)
Imports: rlang, rJava(≥ 0.9-10), checkmate, jsonlite, SqlRender (≥ 1.6.0)
SystemRequirements: Java (>= 8)
NeedsCompilation: yes
Encoding: UTF-8
Suggests: testthat (≥ 3.0.0), knitr, rmarkdown, withr, readr, Eunomia, duckdb, R6
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Packaged: 2026-08-20 17:23:17 UTC; cknoll1
Author: Christopher Knoll [aut, cre]
Maintainer: Christopher Knoll <cknoll@ohdsi.org>
Repository: CRAN
Date/Publication: 2026-08-25 14:10:02 UTC

CohortIncidence: Cohort Incidence Analysis for the OMOP Common Data Model

Description

Provides functionality for performing cohort incidence analyses against data stored in the OMOP Common Data Model (CDM). The package generates database-specific SQL, executes analyses across supported database platforms, and returns standardized incidence estimates using configurable time-at-risk, stratification, and cohort definitions. It is intended to support reproducible observational research within the OHDSI analytics framework.

Author(s)

Maintainer: Christopher Knoll cknoll@ohdsi.org

Authors:

See Also

Useful links:

R6 Class Representing a CohortDefinition

Description

The CohortDefinition class, encapsulating the id, name and expression of a cohort definition.

Details

This R6 class is intended to wrap the Cohort Defintion expression used to generate the cohort, and provide the id and name attribute for this cohort.

Note, when serializing with a library such as jsonlite, first call toList() on the R6 class before calling jsonlite::toJSON().

Value

A CohortDefinition R6 object used to hold optional cohort metadata and a serialized cohort definition expression. This object is primarily metadata for the design and is not required for analysis generation.

Public fields

id

The cohort ID

name

The cohort name

expression

The cohort expression

Methods

Public methods

CohortDefinition$toList()

returns the R6 class elements as a list for use in jsonlite::toJSON()

Usage
CohortDefinition$toList()
Returns

A named list with id, name, and expression, where expression is itself a nested list representation of the cohort definition expression.

CohortDefinition$asJSON()

returns the JSON string for this R6 class

Usage
CohortDefinition$asJSON()
Returns

A JSON string representing the CohortDefinition object.

CohortDefinition$clone()

The objects of this class are cloneable with this method.

Usage
CohortDefinition$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R6 Class Representing a CohortReference

Description

The CohortReference class, encapsulating the id, name and descritpion fields that refernces a cohort definition.

Details

This class is used to reference a cohort definition by ID, while providing a way to substitute a name for this specific reference.

Note, when serializing with a library such as jsonlite, first call toList() on the R6 class before calling jsonlite::toJSON().

Value

A CohortReference R6 object that stores the cohort id, display name, and optional description used to reference a target, outcome, or subgroup cohort.

Active bindings

id

the cohort id being referenced

name

the name for the cohort to be used in this reference.

description

A description for this Cohort Reference.

Methods

Public methods

CohortReference$new()

creates a new instance, using the provided data param if provided.

Usage
CohortReference$new(data = list())
Arguments
data

the data (as a json string or list) to initialize with

Returns

A new CohortReference object initialized from a list or JSON string.

CohortReference$toList()

returns the R6 class elements as a list for use in jsonlite::toJSON()

Usage
CohortReference$toList()
Returns

A named list with id, name, and description fields.

CohortReference$asJSON()

returns the JSON string for this R6 class

Usage
CohortReference$asJSON()
Returns

A JSON string representation of the CohortReference object.

CohortReference$clone()

The objects of this class are cloneable with this method.

Usage
CohortReference$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R6 Class Representing a Cohort Subgroup definition

Description

The CohortSubgroup class, encapsulating the id, name, description, and CohortRef.

Details

This class is used to specify a cohort subgroup to be used in the analysis. A TAR will be considered part of the subgroup if the TAR starts between the subgroup's cohort start and cohort end.

Note, when serializing with a library such as jsonlite, first call toList() on the R6 class before calling jsonlite::toJSON().

Value

A CohortSubgroup R6 object containing subgroup metadata and the CohortReference used to determine subgroup membership.

Active bindings

id

an integer uniquely identifying this subgroup

name

The name to use for this cohort reference

description

The description for this subgroup

cohort

the cohort used to represent this subgroup. Must be class CohortReference

Methods

Public methods

CohortSubgroup$new()

creates a new instance, using the provided data param if provided. The JSON takes the form: ⁠{"id":1,"name":"some name","description":"some description","cohort":{"id":99, "name":"cohort"}}⁠

Usage
CohortSubgroup$new(data = list(CohortSubgroup = list()))
Arguments
data

the data (as a json string or list) to initialize with

Returns

A new CohortSubgroup object initialized from a list or JSON string.

CohortSubgroup$toList()

returns the R6 class elements as a list for use in jsonlite::toJSON()

Usage
CohortSubgroup$toList()
Returns

A named list with a single CohortSubgroup element that contains id, name, description, and a nested cohort definition.

CohortSubgroup$asJSON()

returns the JSON string for this R6 class

Usage
CohortSubgroup$asJSON()
Returns

A JSON string representation of the CohortSubgroup object.

CohortSubgroup$clone()

The objects of this class are cloneable with this method.

Usage
CohortSubgroup$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R6 Class Representing a DataRange

Description

The DateRange class, encapsulating the startDate and endDate of a date range.

Details

This class is used to specify a DateRange, with start and end dates specified as strings formatted as YYYY-MM-DD.

Value

A DateRange R6 object storing startDate and endDate as YYYY-MM-DD strings.

Active bindings

startDate

a character with format YYYY-MM-DD to be used as the date range's start date.

endDate

a character with format YYYY-MM-DD to be used as the date range's end date.

Methods

Public methods

DateRange$new()

creates a new instance, using the provided data param if provided.

Usage
DateRange$new(data = list())
Arguments
data

the data (as a json string or list) to initialize with

Returns

A new DateRange object initialized from a list or JSON string.

DateRange$toList()

returns the R6 class elements as a list for use in jsonlite::toJSON()

Usage
DateRange$toList()
Returns

A named list with startDate and endDate fields.

DateRange$asJSON()

returns the JSON string for this R6 class

Usage
DateRange$asJSON()
Returns

A JSON string representation of the DateRange object.

DateRange$clone()

The objects of this class are cloneable with this method.

Usage
DateRange$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R6 Class Representing a IncidenceAnalysis

Description

The IncidenceAnalysis class, encapsulating the targets, outcomes and tars.

Details

The targets, outcomes and tars fields are referencing IDs of the targetDef, outcomeDef and tarDefs R6 classes.

Note, when serializing with a library such as jsonlite, first call toList() on the R6 class before calling jsonlite::toJSON().

Value

A IncidenceAnalysis R6 object that stores the analysis combination as three integer ID vectors: targets, outcomes, and time-at-risk definitions.

Active bindings

targets

A vector of target IDs from target definitions. Must be a vector.

outcomes

A vector of outcome IDs from outcome definitions. Must be a vector.

tars

A vector of TAR IDs from time-at-risk definitions. Must be a vector.

Methods

Public methods

IncidenceAnalysis$new()

creates a new instance, using the provided data param if provided.

Usage
IncidenceAnalysis$new(data = list())
Arguments
data

the data (as a json string or list) to initialize with

Returns

A new IncidenceAnalysis object initialized from a list or JSON string representation of one analysis combination.

IncidenceAnalysis$toList()

returns the R6 class elements as a list for use in jsonlite::toJSON()

Usage
IncidenceAnalysis$toList()

IncidenceAnalysis$asJSON()

returns the JSON string for this R6 class

Usage
IncidenceAnalysis$asJSON()

IncidenceAnalysis$clone()

The objects of this class are cloneable with this method.

Usage
IncidenceAnalysis$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R6 Class Representing a IncidenceDesign

Description

This class encapsulates the other R6 Class elements that define an IncidenceDesign

Details

The IncidenceDesign class encapsulates the following:

Value

A IncidenceDesign R6 object that stores the full cohort incidence analysis design, including cohort definitions, target definitions, outcomes, time-at-risk definitions, analyses, subgroups, strata settings, and study window metadata used to generate SQL.

Active bindings

cohortDefs

A list of cohort definitions. Must be a list of CohortDefinition

conceptSets

A list of concept set expressions. Currently unused.

targetDefs

A list of cohort references to be used as target cohorts. Must be a list of CohortReference

outcomeDefs

A list of outcome definitions. Must be a list of Outcome

timeAtRiskDefs

A list of time-at-risk definitions. Must be a list of TimeAtRisk

analysisList

A list of analyses, containing the T-O-TAR combinations to perform. Must be a list of IncidenceAnalysis

subgroups

A list of subgroups. Must be a list of CohortSubgroup

strataSettings

The strata settings for this design. Must be a class StrataSettings

studyWindow

a study window for this design. Must be a list of class DateRange

firstAtRisk

a boolean indicating to limit TAR to first per person.

firstPostOutcome

a boolean indicating to limit TAR to first per person.

Methods

Public methods

IncidenceDesign$new()

creates a new instance, using the provided data param if provided.

Usage
IncidenceDesign$new(data = list())
Arguments
data

the data (as a json string or list) to initialize with

Returns

A new IncidenceDesign object initialized from a list or JSON string representation of the full design.

IncidenceDesign$toList()

returns the R6 class elements as a list for use in jsonlite::toJSON()

Usage
IncidenceDesign$toList()

IncidenceDesign$asJSON()

returns the JSON string for this R6 class

Usage
IncidenceDesign$asJSON(...)
Arguments
...

paramaters that are passed forward to rjsonlite::toJSON()

IncidenceDesign$clone()

The objects of this class are cloneable with this method.

Usage
IncidenceDesign$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R6 Class Representing an Outcome definition

Description

The Outcome class, encapsulating the id, name, outcome cohortId, exclusion cohortId, and clean window.

Details

This class is used to specify an outcome definition. The outcome id is distinct from the outcome cohort ID in that you can define multiple outcomes that use the same outcome cohort with different clean windows or exclusion cohort.

Note, when serializing with a library such as jsonlite, first call toList() on the R6 class before calling jsonlite::toJSON().

Value

An Outcome R6 object describing one outcome definition, including the outcome cohort id, clean window, and optional exclusion cohort id.

Active bindings

id

an integer uniquely identifying this outcome definition

name

the name given to this outcome definition

cohortId

The outcome cohort ID for this outcome.

cleanWindow

The clean window for this outcome.

excludeCohortId

The cohort that will be used to exclude time at risk.

Methods

Public methods

Outcome$new()

creates a new instance, using the provided data param if provided.

Usage
Outcome$new(data = list())
Arguments
data

the data (as a json string or list) to initialize with

Returns

A new Outcome object initialized from a list or JSON string.

Outcome$toList()

returns the R6 class elements as a list for use in jsonlite::toJSON()

Usage
Outcome$toList()
Returns

A named list with id, name, cohortId, cleanWindow, and excludeCohortId fields.

Outcome$asJSON()

returns the JSON string for this R6 class

Usage
Outcome$asJSON()
Returns

A JSON string representation of the Outcome object.

Outcome$clone()

The objects of this class are cloneable with this method.

Usage
Outcome$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R6 Class Representing the Stratification Settings of a IncidenceDesign

Description

The StrataSettings class, encapsulating the age, gender and start-year + age breaks settings.

Details

This class is used to specify the stratification settings for an analysis. The settings can indicate the statistics should be grouped by the age, gender, or start year, and any combination of those selections.

Example: age = TRUE and gender = TRUE will produce statisics by age, by gender, and by age and gender.

Value

A StrataSettings R6 object that stores the age, gender, year, and age-break stratification options used during analysis.

Note, when serializing with a library such as jsonlite, first call toList() on the R6 class before calling jsonlite::toJSON().

Active bindings

byAge

enables stratification by age

byGender

enables stratification by gender

byYear

enables stratification by start year of TAR

ageBreaks

a list of age breaks with at least 1 member

ageBreakList

a list of age breaks

Methods

Public methods

StrataSettings$new()

creates a new instance, using the provided data param if provided.

Usage
StrataSettings$new(data = list())
Arguments
data

the data (as a json string or list) to initialize with

Returns

A new StrataSettings object initialized from a list or JSON string.

StrataSettings$toList()

returns the R6 class elements as a list for use in jsonlite::toJSON()

Usage
StrataSettings$toList()
Returns

A named list containing the logical flags and age break lists used by the design.

StrataSettings$asJSON()

returns the JSON string for this R6 class

Usage
StrataSettings$asJSON()
Returns

A JSON string representation of the StrataSettings object.

StrataSettings$clone()

The objects of this class are cloneable with this method.

Usage
StrataSettings$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R6 Class Representing an Time-at-Risk (TAR) definition

Description

The TimeAtRisk class, encapsulating the id, startWith, startOffset, endWith and endOffset

Details

This class is used to specify a time-at-risk (TAR) definition. A TAR is defined by choosing the start/end date of a cohort to start with (plus an offset), and a start/end date of the cohort to end with (plus an offset).

Note, when serializing with a library such as jsonlite, first call toList() on the R6 class before calling jsonlite::toJSON().

Value

A TimeAtRisk R6 object describing the TAR start and end anchors plus offsets used to compute person-time.

Active bindings

id

an integer uniquely identifying this time at risk

startWith

the cohort date to start the time-at-risk. Can be either "start" or "end".

startOffset

The number of days added to the date specified in startWith.

endWith

the cohort date to start the time-at-risk. Can be either "start" or "end".

endOffset

The number of days added to the date specified in startWith.

Methods

Public methods

TimeAtRisk$new()

creates a new instance, using the provided data param if provided. The JSON takes the form:⁠{"id":1,"start":{"dateField":"start","offset":1},"end":{"dateField":"start","offset":30}}⁠

Usage
TimeAtRisk$new(data = list())
Arguments
data

the data (as a json string or list) to initialize with

Returns

A new TimeAtRisk object initialized from a list or JSON string.

TimeAtRisk$toList()

returns the R6 class elements as a list for use in jsonlite::toJSON()

Usage
TimeAtRisk$toList()
Returns

A named list with id, start, and end fields, where start and end are nested lists containing dateField and offset.

TimeAtRisk$asJSON()

returns the JSON string for this R6 class

Usage
TimeAtRisk$asJSON()
Returns

A JSON string representation of the TimeAtRisk object.

TimeAtRisk$clone()

The objects of this class are cloneable with this method.

Usage
TimeAtRisk$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Builds the BuilderOptions jObject with the specified paramaters

Description

Builds the BuilderOptions jObject with the specified paramaters

Usage

buildOptions(
  cohortTable,
  outcomeCohortTable = cohortTable,
  subgroupCohortTable = cohortTable,
  sourceName,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  vocabularySchema = cdmDatabaseSchema,
  useTempTables = FALSE,
  refId
)

Arguments

cohortTable

The name of table with cohorts

outcomeCohortTable

The name of table with outcome cohorts, defaults to cohortTable param.

subgroupCohortTable

The name of table with subgroup cohorts, defaults to cohortTable param.

sourceName

A value to inject to the results table for the source name.

cdmDatabaseSchema

the name of schema containing data in CDM format

resultsDatabaseSchema

the name of schema where results would be placed

vocabularySchema

the name of schema with vocabulary tables, defaults to cdmDatabaseSchema param

useTempTables

use temp tables instead of a results schema.

refId

A number tagged to the results for retrieval purposes.

Value

a BuilderOptions object used in buildQuery.

Builds SQL code to run analyses according given Cohort Characterization design

Description

Builds SQL code to run analyses according given Cohort Characterization design

Usage

buildQuery(incidenceDesign, buildOptions)

Arguments

incidenceDesign

A string object containing valid JSON that represents cohort incidence design

buildOptions

the parameters to use in building the analysis queries, created by buildOptions()

Value

SQL code in MS Sql Server dialect, if it's required to run analysis on another DBMS you have to use translateSql function in the SqlRender package.

Creates R6 object for CohortReference

Description

Creates R6 object for CohortReference

Usage

createCohortRef(id, name, description)

Arguments

id

the cohort id that is being referenced

name

the name to use for this reference

description

an optional description to use for this reference.

Value

A CohortReference R6 object that stores the cohort identifier, display name, and optional description used to reference a cohort definition in the design.

Creates R6 object for CohortSubgroup

Description

Creates R6 object for CohortSubgroup

Usage

createCohortSubgroup(id, name, description, cohortRef)

Arguments

id

the unique identifier for this subgroup

name

The subgroup name

description

The subgroup description

cohortRef

A cohort reference, as an R6 Class CohortReference

Value

A CohortSubgroup R6 object containing subgroup metadata and the CohortReference used to determine subgroup membership.

Creates R6 object for DateRange

Description

Creates R6 object for DateRange

Usage

createDateRange(startDate, endDate)

Arguments

startDate

a character vector representing a date in YYYY-MM-DD format

endDate

a character vector representing a date in YYYY-MM-DD format

Value

A DateRange R6 object containing the start and end date strings in YYYY-MM-DD format.

Creates R6 object for IncidenceAnalysis

Description

Creates R6 object for IncidenceAnalysis

Usage

createIncidenceAnalysis(targets, outcomes, tars)

Arguments

targets

A list or vector of target IDs from target definitions.

outcomes

A list or vector of outcome IDs from outcome definitions.

tars

A list or vector of TAR IDs from time-at-risk definitions.

Value

An IncidenceAnalysis R6 object containing the target, outcome, and TAR identifier vectors used to define one analysis combination.

Creates R6 object for IncidenceDesign

Description

Creates R6 object for IncidenceDesign

Usage

createIncidenceDesign(
  cohortDefs,
  targetDefs,
  outcomeDefs,
  tars,
  analysisList,
  conceptSets,
  subgroups,
  strataSettings,
  studyWindow,
  firstAtRisk,
  firstPostOutcome
)

Arguments

cohortDefs

The set of cohort definitions. Optional metadata used when building a design, not required for analysis execution.

targetDefs

A list of target definitions, each element must be class CohortReference.

outcomeDefs

A list of outcome definitions, each element must be class Outcome

tars

A list of TAR definitions, each element must be class TimeAtRisk

analysisList

A list of analysis definitions, each element must be class IncidenceAnalysis

conceptSets

A list of concept sets, currently unused.

subgroups

A list of cohort subgroups, each element must be class Subgroup.

strataSettings

The strata settings used in the anlaysis, must be class StrataSettings.

studyWindow

Limits time at risk to the specified study window. Must be class DateRange.

firstAtRisk

Limits time at risk to the first per person. Must be boolean.

firstPostOutcome

Limits outcomes to first outcome within clean window of the first TAR or after. Must be boolean.

Value

An IncidenceDesign R6 object containing the design metadata, cohort definitions, target definitions, outcome definitions, time-at-risk definitions, analyses, subgroups, strata settings, and study window used to generate SQL. The object can be serialized to JSON for analysis execution.

Creates R6 object for Outcome

Description

Creates R6 object for Outcome

Usage

createOutcomeDef(id, name, cohortId = 0, cleanWindow = 0, excludeCohortId)

Arguments

id

the unique identifier for this outcome definition

name

an optional name for this outcome definition

cohortId

the cohort id reference for this outcome

cleanWindow

the number of days to extend the outcome cohort’s end date. See executeAnalysis() for details on how this is applied.

excludeCohortId

a cohort ID from the outcomeCohrotTable that is used to exclude time at risk. See executeAnalysis() for details on how this is applied.

Value

An Outcome R6 object describing one outcome definition, including the outcome id, cohort id, clean window, and optional exclusion cohort id.

Creates R6 object for StrataSettings

Description

Creates R6 object for StrataSettings

Usage

createStrataSettings(
  byAge = FALSE,
  byGender = FALSE,
  byYear = FALSE,
  ageBreaks,
  ageBreakList
)

Arguments

byAge

a boolean indicating to stratify by age, defaults to FALSE

byGender

a boolean indicating to stratify by gender, defaults to FALSE

byYear

a boolean indicating to stratify by year, defaults to FALSE

ageBreaks

a vector of integers indicating the age group bounds.

ageBreakList

a list of ageBreaks, used to specify multiple age break strata.

Value

A StrataSettings R6 object containing the three stratification flags plus optional age break definitions. The serialized form matches org.ohdsi.cohortincidence.design.StratifySettings JSON.

Creates R6 object for TimeAtRisk

Description

Creates R6 object for TimeAtRisk

Usage

createTimeAtRiskDef(
  id,
  startWith = "start",
  startOffset = 0,
  endWith = "end",
  endOffset = 0
)

Arguments

id

the unique identifier for this outcome definition

startWith

Specifies the field (start or end) to offset from for the TAR start. Allowed values: 'start', 'end'

startOffset

The number of days to offset for the TAR start, defaults to 0.

endWith

Specifies the field (start or end) to offset from for the TAR end. Allowed values: 'start', 'end'

endOffset

The number of days to offset for the TAR start, defaults to 0.

Value

A TimeAtRisk R6 object describing the TAR start and end anchors plus their offsets. The serialized form contains a start and end field, each with a dateField and offset.

Executes IR analysis given a design, options, and connection settings.

Description

Executes IR analysis given a design, options, and connection settings.

Usage

executeAnalysis(
  connectionDetails = NULL,
  connection = NULL,
  incidenceDesign,
  buildOptions,
  sourceName = "default"
)

Arguments

connectionDetails

An R object of type connectionDetails created using the function createConnectionDetails in the DatabaseConnector package. Either the connection or connectionDetails argument should be specified.

connection

A connection to the server containing the schema as created using the connect function in the DatabaseConnector package. Either the connection or connectionDetails argument should be specified.

incidenceDesign

A string object containing valid JSON that represents cohort incidence design

buildOptions

the parameters to use in building the analysis queries, created by buildOptions()

sourceName

the source name to attach to the results

Details

This method performs the entire cohort incidence analysis in one step without the need for creating any permenant tables.

The process for calculating the cohort incidence is as follows:

The resut contains the following dataframes:

incidence_summary:

Name Description
REF_ID The reference id specified in buildOptions() to track results to the analysis execution.
SOURCE_NAME The name of the source for these results
TARGET_COHORT_DEFIITION_ID The cohort ID of the target population
TAR_ID The TAR identifier
SUBGROUP_ID The subgroup identifier
OUTCOME_ID The outcome identifier
AGE_GROUP_ID The age ID for this strata representing the age band specified in the strata settings
GENDER_ID The gender concept ID for this gender strata
GENDER_NAME The name of the gender
START_YEAR The year strata, defined by using the year the TAR started
PERSONS_AT_RISK_PE Distinct persons at risk before removing excluded time from TAR
PERSONS_AT_RISK Distinct persons at risk after removing excluded time from TAR. A person must have at least 1 day TAR to be included.
PERSON_DAYS_PE Total TAR (in days) before excluded time was removed from TAR.
PERSON_DAYS Total TAR (in days) after excluded time was removed from TAR.
PERSON_OUTCOMES_PE Distinct persons with outcome before removing excluded time from TAR
PERSON_OUTCOMES Distinct persons with outcome after removing excluded time from TAR. A person must have at least 1 day TAR to be included.
OUTCOMES_PE Number of cases before excluding TAR.
OUTCOMES Number of cases after excluding TAR.
INCIDENCE_PROPORTION_P100P The Incidence Proportion (per 100 people), calculated by person_outcomes / persons_at_risk * 100
INCIDENCE_RATE_P100PY The Incidence Rate (per 100 person years), calculated by outcomes / person_days / 365.25 * 100
target_def:
Name Description
----- --------
REF_ID The reference id specified in buildOptions() to track results to the analysis execution.
TARGET_COHORT_DEFIITION_ID The cohort ID of the target population
TARGET_NAME The name of the target cohort

outcome_def:

Name Description
REF_ID The reference id specified in buildOptions() to track results to the analysis execution.
OUTCOME_ID The outcome identifier
OUTCOME_COHORT_DEFINITION_ID The cohort ID of the outcome population
OUTCOME_NAME The outcome name
CLEAN_WINDOW The clean window for this outcome definition
EXCLUDED_COHORT_DEFINITION_ID The cohort used to exclude TAR

tar_def:

Name Description
REF_ID The reference id specified in buildOptions() to track results to the analysis execution.
TAR_ID The TAR identifier
TAR_START_WITH Indicates if the TAR starts with the 'start' or 'end' of the target cohort episode
TAR_START_OFFSET The days added to the date field specified in TAR_START_WITH
TAR_END_WITH Indicates if the TAR ends with the 'start' or 'end' of the target cohort episode
TAR_END_OFFSET The days added to the date field specified in TAR_END_WITH

age_group_def:

Name Description
REF_ID The reference id specified in buildOptions() to track results to the analysis execution.
AGE_GROUP_ID The age ID for this strata representing the age band specified in the strata settings
AGE_GROUP_NAME The name for this age group
MIN_AGE The minimum age for this group
MAX_AGE the max age for this group

subgroup_def:

Name Description
REF_ID The reference id specified in buildOptions() to track results to the analysis execution.
SUBGROUP_NAME The name of the subgroup

Value

A named list of data.frame objects containing the IR results. The list includes incidence_summary, target_def, outcome_def, tar_def, age_group_def, and subgroup_def, each representing one result table produced during execution.

Gets the sql that drops the results tables

Description

Gets the sql that drops the results tables

Usage

getCleanupSql(useTempTables = FALSE)

Arguments

useTempTables

if TRUE, then temp table notation will be used.

Value

SQL code in MS Sql Server dialect. If analysis will run on another DBMS, translate the SQL with SqlRender::translateSql() before execution.

Gets the results schema DDL for Incidence Analysis

Description

Gets the results schema DDL for Incidence Analysis

Usage

getResultsDdl(useTempTables = FALSE)

Arguments

useTempTables

if TRUE, then temp table notation will be used.

Value

SQL code in MS Sql Server dialect, if it's required to run analysis on another DBMS you have to use translateSql function in the SqlRender package.