Package 'CohortGenerator'

Title: Cohort Generation for the OMOP Common Data Model
Description: Generate cohorts and subsets using an Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) Database. Cohorts are defined using 'CIRCE' (<https://github.com/ohdsi/circe-be>) or SQL compatible with 'SqlRender' (<https://github.com/OHDSI/SqlRender>).
Authors: Anthony Sena [aut, cre], Jamie Gilbert [aut], Gowtham Rao [aut], Martijn Schuemie [aut], Observational Health Data Science and Informatics [cph]
Maintainer: Anthony Sena <[email protected]>
License: Apache License
Version: 0.11.2
Built: 2024-11-01 06:11:38 UTC
Source: https://github.com/ohdsi/cohortgenerator

Help Index

Add cohort subset definition to a cohort definition set

Description

Given a subset definition and cohort definition set, this function returns a modified cohortDefinitionSet That contains cohorts that's have parent's contained within the base cohortDefinitionSet

Also adds the columns subsetParent and isSubset that denote if the cohort is a subset and what the parent definition is.

Usage

addCohortSubsetDefinition(
  cohortDefinitionSet,
  cohortSubsetDefintion,
  targetCohortIds = NULL,
  overwriteExisting = FALSE
)

Arguments

cohortDefinitionSet

data.frame that conforms to CohortDefinitionSet
cohortSubsetDefintion

CohortSubsetDefinition instance
targetCohortIds

Cohort ids to apply subset definition to. If not set, subset definition is applied to all base cohorts in set (i.e. those that are not defined by subsetOperators). Applying to cohorts that are already subsets is permitted, however, this should be done with care and identifiers must be specified manually
overwriteExisting

Overwrite existing subset definition of the same definitionId if present

Check if a cohort definition set is using the proper data types

Description

This function checks a data.frame to verify it holds the expected format for a cohortDefinitionSet's data types and can optionally fix data types that do not match the specification.

Usage

checkAndFixCohortDefinitionSetDataTypes(
  x,
  fixDataTypes = TRUE,
  emitWarning = FALSE
)

Arguments

x

The cohortDefinitionSet data.frame to check
fixDataTypes

When TRUE, this function will attempt to fix the data types to match the specification. @seealso [createEmptyCohortDefinitionSet()].
emitWarning

When TRUE, this function will emit warning messages when problems are encountered.

Value

Returns a list() of the following form:

list( dataTypesMatch = TRUE/FALSE, x = data.frame() )

dataTypesMatch == TRUE when the supplied data.frame x matches the cohortDefinitionSet specification's data types.

If fixDataTypes == TRUE, x will hold the original data from x with the data types corrected. Otherwise x will hold the original value passed to this function.

Cohort Subset Definition

Description

Set of subset definitions

Active bindings

targetOutputPairs

list of pairs of integers - (targetCohortId, outputCohortId)

subsetOperators

list of subset operations

name

name of definition

subsetCohortNameTemplate

template string for formatting resulting cohort names

operatorNameConcatString

string used when concatenating operator names together

definitionId

numeric definition id

identifierExpression

expression that can be evaluated from

Methods

Public methods

Method new()

Usage
CohortSubsetDefinition$new(definition = NULL)
Arguments
definition

json or list representation of object to List

Method toList()

List representation of object to JSON

Usage
CohortSubsetDefinition$toList()

Method toJSON()

json serialized representation of object add Subset Operator

Usage
CohortSubsetDefinition$toJSON()

Method addSubsetOperator()

add subset to class - checks if equivalent id is present Will throw an error if a matching ID is found but reference object is different

Usage
CohortSubsetDefinition$addSubsetOperator(subsetOperator)
Arguments
subsetOperator

a SubsetOperator instance

overwrite

if a subset operator of the same ID is present, replace it with a new definition get query for a given target output pair

Method getSubsetQuery()

Returns vector of join, logic, having statements returned by subset operations

Usage
CohortSubsetDefinition$getSubsetQuery(targetOutputPair)
Arguments
targetOutputPair

Target output pair Get name of an output cohort

Method getSubsetCohortName()

Usage
CohortSubsetDefinition$getSubsetCohortName(
  cohortDefinitionSet,
  targetOutputPair
)
Arguments
cohortDefinitionSet

Cohort definition set containing base names

targetOutputPair

Target output pair Set the targetOutputPairs to be added to a cohort definition set

Method setTargetOutputPairs()

Usage
CohortSubsetDefinition$setTargetOutputPairs(targetIds)
Arguments
targetIds

list of cohort ids to apply subsetting operations to Get json file name for subset definition in folder

Method getJsonFileName()

Usage
CohortSubsetDefinition$getJsonFileName(
  subsetJsonFolder = "inst/cohort_subset_definitions/"
)
Arguments
subsetJsonFolder

path to folder to place file

Method clone()

The objects of this class are cloneable with this method.

Usage
CohortSubsetDefinition$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Cohort Subset Operator

Description

A subset of type cohort - subset a population to only those contained within defined cohort to List

Super class

CohortGenerator::SubsetOperator -> CohortSubsetOperator

Active bindings

cohortIds

Integer ids of cohorts to subset to

cohortCombinationOperator

How to combine the cohorts

negate

Inverse the subset rule? TRUE will take the patients NOT in the subset

startWindow

The time window to use evaluating the subset cohort start relative to the target cohort

endWindow

The time window to use evaluating the subset cohort end relative to the target cohort

Methods

Public methods

Inherited methods

Method toList()

List representation of object Get auto generated name

Usage
CohortSubsetOperator$toList()

Method getAutoGeneratedName()

name generated from subset operation properties

Usage
CohortSubsetOperator$getAutoGeneratedName()
Returns

character

Method clone()

The objects of this class are cloneable with this method.

Usage
CohortSubsetOperator$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Computes the checksum for a value

Description

This is used as part of the incremental operations to hash a value to store in a record keeping file. This function leverages the md5 hash from the digest package

Usage

computeChecksum(val)

Arguments

val

The value to hash. It is converted to a character to perform the hash.

Value

Returns a string containing the checksum

A definition of subset functions to be applied to a set of cohorts

Description

A definition of subset functions to be applied to a set of cohorts

Usage

createCohortSubset(
  name = NULL,
  cohortIds,
  cohortCombinationOperator,
  negate,
  startWindow,
  endWindow
)

Arguments

name

optional name of operator
cohortIds

integer - set of cohort ids to subset to
cohortCombinationOperator

"any" or "all" if using more than one cohort id allow a subject to be in any cohort or require that they are in all cohorts in specified windows
negate

The opposite of this definition - include patients who do NOT meet the specified criteria
startWindow

A SubsetCohortWindow that patients must fall inside (see createSubsetCohortWindow)
endWindow

A SubsetCohortWindow that patients must fall inside (see createSubsetCohortWindow)

Value

a CohortSubsetOperator instance

Create Subset Definition

Description

Create subset definition from subset objects

Usage

createCohortSubsetDefinition(
  name,
  definitionId,
  subsetOperators,
  identifierExpression = NULL,
  operatorNameConcatString = "",
  subsetCohortNameTemplate = ""
)

Arguments

name

Name of definition
definitionId

Definition identifier
subsetOperators

list of subsetOperator instances to apply
identifierExpression

Expression (or string that converts to expression) that returns an id for an output cohort the default is dplyr::expr(targetId * 1000 + definitionId)
operatorNameConcatString

(optional) String to concatenate operator names together when outputting resulting cohort name
subsetCohortNameTemplate

(optional) SqlRender string template for formatting names of resulting subset cohorts Can use the variables @baseCohortName, @subsetDefinitionName and @operatorNames. This is applied when adding the subset definition to a cohort definition set.

Create cohort tables

Description

This function creates an empty cohort table and empty tables for cohort statistics.

Usage

createCohortTables(
  connectionDetails = NULL,
  connection = NULL,
  cohortDatabaseSchema,
  cohortTableNames = getCohortTableNames(),
  incremental = FALSE
)

Arguments

connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package. Can be left NULL if connection is provided.
connection

An object of type connection as created using the connect function in the DatabaseConnector package. Can be left NULL if connectionDetails is provided, in which case a new connection will be opened at the start of the function, and closed when the function finishes.
cohortDatabaseSchema

Schema name where your cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
cohortTableNames

The names of the cohort tables. See getCohortTableNames for more details.
incremental

When set to TRUE, this function will check to see if the cohortTableNames exists in the cohortDatabaseSchema and if they exist, it will skip creating the tables.

Create createDemographicSubset Subset

Description

Create createDemographicSubset Subset

Usage

createDemographicSubset(
  name = NULL,
  ageMin = 0,
  ageMax = 99999,
  gender = NULL,
  race = NULL,
  ethnicity = NULL
)

Arguments

name

Optional char name
ageMin

The minimum age
ageMax

The maximum age
gender

Gender demographics - concepts - 0, 8532, 8507, 0, "female", "male". Any string that is not "male" or "female" (case insensitive) is converted to gender concept 0. https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Gender&page=1&pageSize=15&query= Specific concept ids not in this set can be used but are not explicitly validated
race

Race demographics - concept ID list
ethnicity

Ethnicity demographics - concept ID list

Create an empty cohort definition set

Description

This function creates an empty cohort set data.frame for use with generateCohortSet.

Usage

createEmptyCohortDefinitionSet(verbose = FALSE)

Arguments

verbose

When TRUE, descriptions of each field in the data.frame are returned

Value

Invisibly returns an empty cohort set data.frame

Create an empty negative control outcome cohort set

Description

This function creates an empty cohort set data.frame for use with generateNegativeControlOutcomeCohorts.

Usage

createEmptyNegativeControlOutcomeCohortSet(verbose = FALSE)

Arguments

verbose

When TRUE, descriptions of each field in the data.frame are returned

Value

Invisibly returns an empty negative control outcome cohort set data.frame

Create Limit Subset

Description

Subset cohorts using specified limit criteria

Usage

createLimitSubset(
  name = NULL,
  priorTime = 0,
  followUpTime = 0,
  limitTo = "all",
  calendarStartDate = NULL,
  calendarEndDate = NULL
)

Arguments

name

Name of operation
priorTime

Required prior observation window (specified as a positive integer)
followUpTime

Required post observation window (specified as a positive integer)
limitTo

character one of: "firstEver" - only first entry in patient history "earliestRemaining" - only first entry after washout set by priorTime "latestRemaining" - the latest remaining after washout set by followUpTime "lastEver" - only last entry in patient history inside

Note, when using firstEver and lastEver with follow up and washout, patients with events outside this will be censored. The "firstEver" and "lastEver" are applied first. The "earliestRemaining" and "latestRemaining" are applied after all other limit criteria are applied (i.e. after applying prior/post time and calendar time).
calendarStartDate

End date to allow periods (e.g. 2020/1/1/)
calendarEndDate

Start date to allow period (e.g. 2015/1/1)

Create the results data model tables on a database server.

Description

Create the results data model tables on a database server.

Usage

createResultsDataModel(
  connectionDetails = NULL,
  databaseSchema,
  tablePrefix = ""
)

Arguments

connectionDetails

DatabaseConnector connectionDetails instance @seealso[DatabaseConnector::createConnectionDetails]
databaseSchema

The schema on the server where the tables will be created.
tablePrefix

(Optional) string to insert before table names for database table names

Details

Only PostgreSQL and SQLite servers are supported.

A definition of subset functions to be applied to a set of cohorts

Description

A definition of subset functions to be applied to a set of cohorts

Usage

createSubsetCohortWindow(startDay, endDay, targetAnchor)

Arguments

startDay

The start day for the window
endDay

The end day for the window
targetAnchor

To anchor using the target cohort's start date or end date

Value

a SubsetCohortWindow instance

Demographic Subset Operator

Description

Operators for subsetting a cohort by demographic criteria

Value

char vector Get auto generated name

Super class

CohortGenerator::SubsetOperator -> DemographicSubsetOperator

Active bindings

ageMin

Int between 0 and 99999 - minimum age

ageMax

Int between 0 and 99999 - maximum age

gender

vector of gender concept IDs

race

character string denoting race

ethnicity

character string denoting ethnicity

Methods

Public methods

Inherited methods

Method toList()

List representation of object Map gender concepts to names

Usage
DemographicSubsetOperator$toList()

Method mapGenderConceptsToNames()

Usage
DemographicSubsetOperator$mapGenderConceptsToNames(
  mapping = list(`8507` = "males", `8532` = "females", `0` = "unknown gender")
)
Arguments
mapping

optional list of mappings for concept id to nouns

Method getAutoGeneratedName()

name generated from subset operation properties

Usage
DemographicSubsetOperator$getAutoGeneratedName()
Returns

character

Method toJSON()

json serialized representation of object

Usage
DemographicSubsetOperator$toJSON()

Method isEqualTo()

Compare Subset to another

Usage
DemographicSubsetOperator$isEqualTo(criteria)
Arguments
criteria

DemographicSubsetOperator instance

Method getGender()

Gender getter - used when constructing SQL to default NULL to an empty string

Usage
DemographicSubsetOperator$getGender()

Method getRace()

Race getter - used when constructing SQL to default NULL to an empty string

Usage
DemographicSubsetOperator$getRace()

Method getEthnicity()

Ethnicity getter - used when constructing SQL to default NULL to an empty string

Usage
DemographicSubsetOperator$getEthnicity()

Method clone()

The objects of this class are cloneable with this method.

Usage
DemographicSubsetOperator$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Drop cohort statistics tables

Description

This function drops the cohort statistics tables.

Usage

dropCohortStatsTables(
  connectionDetails = NULL,
  connection = NULL,
  cohortDatabaseSchema,
  cohortTableNames = getCohortTableNames(),
  dropCohortTable = FALSE
)

Arguments

connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package. Can be left NULL if connection is provided.
connection

An object of type connection as created using the connect function in the DatabaseConnector package. Can be left NULL if connectionDetails is provided, in which case a new connection will be opened at the start of the function, and closed when the function finishes.
cohortDatabaseSchema

Schema name where your cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
cohortTableNames

The names of the cohort tables. See getCohortTableNames for more details.
dropCohortTable

Optionally drop cohort table in addition to stats tables (defaults to FALSE)

Export the cohort statistics tables to the file system

Description

This function retrieves the data from the cohort statistics tables and writes them to the inclusion statistics folder specified in the function call. NOTE: inclusion rule names are handled in one of two ways:

1. You can specify the cohortDefinitionSet parameter and the inclusion rule names will be extracted from the data.frame. 2. You can insert the inclusion rule names into the database using the insertInclusionRuleNames function of this package.

The first approach is preferred as to avoid the warning emitted.

Usage

exportCohortStatsTables(
  connectionDetails,
  connection = NULL,
  cohortDatabaseSchema,
  cohortTableNames = getCohortTableNames(),
  cohortStatisticsFolder,
  snakeCaseToCamelCase = TRUE,
  fileNamesInSnakeCase = FALSE,
  incremental = FALSE,
  databaseId = NULL,
  minCellCount = 5,
  cohortDefinitionSet = NULL,
  tablePrefix = ""
)

Arguments

connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package. Can be left NULL if connection is provided.
connection

An object of type connection as created using the connect function in the DatabaseConnector package. Can be left NULL if connectionDetails is provided, in which case a new connection will be opened at the start of the function, and closed when the function finishes.
cohortDatabaseSchema

Schema name where your cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
cohortTableNames

The names of the cohort tables. See getCohortTableNames for more details.
cohortStatisticsFolder

The path to the folder where the cohort statistics folder where the results will be written
snakeCaseToCamelCase

Should column names in the exported files convert from snake_case to camelCase? Default is FALSE
fileNamesInSnakeCase

Should the exported files use snake_case? Default is FALSE
incremental

If incremental = TRUE, results are written to update values instead of overwriting an existing results
databaseId

Optional - when specified, the databaseId will be added to the exported results
minCellCount

To preserve privacy: the minimum number of subjects contributing to a count before it can be included in the results. If the count is below this threshold, it will be set to '-minCellCount'.
cohortDefinitionSet

The cohortDefinitionSet argument must be a data frame with the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

sql

The OHDSI-SQL used to generate the cohort

Optionally, this data frame may contain:

json

The Circe JSON representation of the cohort
tablePrefix

Optional - allows to append a prefix to the exported file names.

Generate a set of cohorts

Description

This function generates a set of cohorts in the cohort table.

Usage

generateCohortSet(
  connectionDetails = NULL,
  connection = NULL,
  cdmDatabaseSchema,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  cohortDatabaseSchema = cdmDatabaseSchema,
  cohortTableNames = getCohortTableNames(),
  cohortDefinitionSet = NULL,
  stopOnError = TRUE,
  incremental = FALSE,
  incrementalFolder = NULL
)

Arguments

connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package. Can be left NULL if connection is provided.
connection

An object of type connection as created using the connect function in the DatabaseConnector package. Can be left NULL if connectionDetails is provided, in which case a new connection will be opened at the start of the function, and closed when the function finishes.
cdmDatabaseSchema

Schema name where your patient-level data in OMOP CDM format resides. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.
tempEmulationSchema

Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created.
cohortDatabaseSchema

Schema name where your cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
cohortTableNames

The names of the cohort tables. See getCohortTableNames for more details.
cohortDefinitionSet

The cohortDefinitionSet argument must be a data frame with the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

sql

The OHDSI-SQL used to generate the cohort

Optionally, this data frame may contain:

json

The Circe JSON representation of the cohort
stopOnError

If an error happens while generating one of the cohorts in the cohortDefinitionSet, should we stop processing the other cohorts? The default is TRUE; when set to FALSE, failures will be identified in the return value from this function.
incremental

Create only cohorts that haven't been created before?
incrementalFolder

If incremental = TRUE, specify a folder where records are kept of which definition has been executed.

Value

A data.frame consisting of the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

generationStatus

The status of the generation task which may be one of the following:

COMPLETE

The generation completed successfully

FAILED

The generation failed (see logs for details)

SKIPPED

If using incremental == 'TRUE', this status indicates that the cohort's generation was skipped since it was previously completed.

startTime

The start time of the cohort generation. If the generationStatus == 'SKIPPED', the startTime will be NA.

endTime

The end time of the cohort generation. If the generationStatus == 'FAILED', the endTime will be the time of the failure. If the generationStatus == 'SKIPPED', endTime will be NA.

Generate a set of negative control outcome cohorts

Description

This function generate a set of negative control outcome cohorts. For more information please see [Chapter 12 - Population Level Estimation](https://ohdsi.github.io/TheBookOfOhdsi/PopulationLevelEstimation.html) for more information how these cohorts are utilized in a study design.

Usage

generateNegativeControlOutcomeCohorts(
  connectionDetails = NULL,
  connection = NULL,
  cdmDatabaseSchema,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  cohortDatabaseSchema = cdmDatabaseSchema,
  cohortTable = getCohortTableNames()$cohortTable,
  negativeControlOutcomeCohortSet,
  occurrenceType = "all",
  incremental = FALSE,
  incrementalFolder = NULL,
  detectOnDescendants = FALSE
)

Arguments

connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package. Can be left NULL if connection is provided.
connection

An object of type connection as created using the connect function in the DatabaseConnector package. Can be left NULL if connectionDetails is provided, in which case a new connection will be opened at the start of the function, and closed when the function finishes.
cdmDatabaseSchema

Schema name where your patient-level data in OMOP CDM format resides. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.
tempEmulationSchema

Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created.
cohortDatabaseSchema

Schema name where your cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
cohortTable

Name of the cohort table.
negativeControlOutcomeCohortSet

The negativeControlOutcomeCohortSet argument must be a data frame with the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

outcomeConceptId

The concept_id in the condition domain to use for the negative control outcome.
occurrenceType

The occurrenceType will detect either: the first time an outcomeConceptId occurs or all times the outcomeConceptId occurs for a person. Values accepted: 'all' or 'first'.
incremental

Create only cohorts that haven't been created before?
incrementalFolder

If incremental = TRUE, specify a folder where records are kept of which definition has been executed.
detectOnDescendants

When set to TRUE, detectOnDescendants will use the vocabulary to find negative control outcomes using the outcomeConceptId and all descendants via the concept_ancestor table. When FALSE, only the exact outcomeConceptId will be used to detect the outcome.

Value

Invisibly returns an empty negative control outcome cohort set data.frame

Count the cohort(s)

Description

Computes the subject and entry count per cohort. Note the cohortDefinitionSet parameter is optional - if you specify the cohortDefinitionSet, the cohort counts will be joined to the cohortDefinitionSet to include attributes like the cohortName.

Usage

getCohortCounts(
  connectionDetails = NULL,
  connection = NULL,
  cohortDatabaseSchema,
  cohortTable = "cohort",
  cohortIds = c(),
  cohortDefinitionSet = NULL,
  databaseId = NULL
)

Arguments

connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package. Can be left NULL if connection is provided.
connection

An object of type connection as created using the connect function in the DatabaseConnector package. Can be left NULL if connectionDetails is provided, in which case a new connection will be opened at the start of the function, and closed when the function finishes.
cohortDatabaseSchema

Schema name where your cohort table resides. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
cohortTable

The name of the cohort table.
cohortIds

The cohort Id(s) used to reference the cohort in the cohort table. If left empty and no 'cohortDefinitionSet' argument is specified, all cohorts in the table will be included. If you specify the 'cohortIds' AND 'cohortDefinitionSet', the counts will reflect the 'cohortIds' from the 'cohortDefinitionSet'.
cohortDefinitionSet

The cohortDefinitionSet argument must be a data frame with the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

sql

The OHDSI-SQL used to generate the cohort

Optionally, this data frame may contain:

json

The Circe JSON representation of the cohort
databaseId

Optional - when specified, the databaseId will be added to the exported results

Value

A data frame with cohort counts

Get a cohort definition set

Description

This function supports the legacy way of retrieving a cohort definition set from the file system or in a package. This function supports the legacy way of storing a cohort definition set in a package with a CSV file, JSON files, and SQL files in the 'inst' folder.

Usage

getCohortDefinitionSet(
  settingsFileName = "Cohorts.csv",
  jsonFolder = "cohorts",
  sqlFolder = "sql/sql_server",
  cohortFileNameFormat = "%s",
  cohortFileNameValue = c("cohortId"),
  subsetJsonFolder = "inst/cohort_subset_definitions/",
  packageName = NULL,
  warnOnMissingJson = TRUE,
  verbose = FALSE
)

Arguments

settingsFileName

The name of the CSV file that will hold the cohort information including the cohortId and cohortName
jsonFolder

The name of the folder that will hold the JSON representation of the cohort if it is available in the cohortDefinitionSet
sqlFolder

The name of the folder that will hold the SQL representation of the cohort.
cohortFileNameFormat

Defines the format string for naming the cohort JSON and SQL files. The format string follows the standard defined in the base sprintf function.
cohortFileNameValue

Defines the columns in the cohortDefinitionSet to use in conjunction with the cohortFileNameFormat parameter.
subsetJsonFolder

Defines the folder to store the subset JSON
packageName

The name of the package containing the cohort definitions.
warnOnMissingJson

Provide a warning if a .JSON file is not found for a cohort in the settings file
verbose

When TRUE, extra logging messages are emitted

Value

Returns a cohort set data.frame

Get Cohort Inclusion Rules from a cohort definition set

Description

This function returns a data frame of the inclusion rules defined in a cohort definition set.

Usage

getCohortInclusionRules(cohortDefinitionSet)

Arguments

cohortDefinitionSet

The cohortDefinitionSet argument must be a data frame with the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

sql

The OHDSI-SQL used to generate the cohort

Optionally, this data frame may contain:

json

The Circe JSON representation of the cohort

Get Cohort Inclusion Stats Table Data

Description

This function returns a data frame of the data in the Cohort Inclusion Tables. Results are organized in to a list with 5 different data frames:

  • cohortInclusionTable

  • cohortInclusionResultTable

  • cohortInclusionStatsTable

  • cohortSummaryStatsTable

  • cohortCensorStatsTable

These can be optionally specified with the outputTables. See exportCohortStatsTables function for saving data to csv.

Usage

getCohortStats(
  connectionDetails,
  connection = NULL,
  cohortDatabaseSchema,
  databaseId = NULL,
  snakeCaseToCamelCase = TRUE,
  outputTables = c("cohortInclusionTable", "cohortInclusionResultTable",
    "cohortInclusionStatsTable", "cohortInclusionStatsTable", "cohortSummaryStatsTable",
    "cohortCensorStatsTable"),
  cohortTableNames = getCohortTableNames()
)

Arguments

connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package. Can be left NULL if connection is provided.
connection

An object of type connection as created using the connect function in the DatabaseConnector package. Can be left NULL if connectionDetails is provided, in which case a new connection will be opened at the start of the function, and closed when the function finishes.
cohortDatabaseSchema

Schema name where your cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
databaseId

Optional - when specified, the databaseId will be added to the exported results
snakeCaseToCamelCase

Convert column names from snake case to camel case.
outputTables

Character vector. One or more of "cohortInclusionTable", "cohortInclusionResultTable", "cohortInclusionStatsTable", "cohortInclusionStatsTable", "cohortSummaryStatsTable" or "cohortCensorStatsTable". Output is limited to these tables. Cannot export, for, example, the cohort table. Defaults to all stats tables.
cohortTableNames

The names of the cohort tables. See getCohortTableNames for more details.

Used to get a list of cohort table names to use when creating the cohort tables

Description

This function creates a list of table names used by createCohortTables to specify the table names to create. Use this function to specify the names of the main cohort table and cohort statistics tables.

Usage

getCohortTableNames(
  cohortTable = "cohort",
  cohortSampleTable = cohortTable,
  cohortInclusionTable = paste0(cohortTable, "_inclusion"),
  cohortInclusionResultTable = paste0(cohortTable, "_inclusion_result"),
  cohortInclusionStatsTable = paste0(cohortTable, "_inclusion_stats"),
  cohortSummaryStatsTable = paste0(cohortTable, "_summary_stats"),
  cohortCensorStatsTable = paste0(cohortTable, "_censor_stats")
)

Arguments

cohortTable

Name of the cohort table.
cohortSampleTable

Name of the cohort table for sampled cohorts (defaults to the same as the cohort table).
cohortInclusionTable

Name of the inclusion table, one of the tables for storing inclusion rule statistics.
cohortInclusionResultTable

Name of the inclusion result table, one of the tables for storing inclusion rule statistics.
cohortInclusionStatsTable

Name of the inclusion stats table, one of the tables for storing inclusion rule statistics.
cohortSummaryStatsTable

Name of the summary stats table, one of the tables for storing inclusion rule statistics.
cohortCensorStatsTable

Name of the censor stats table, one of the tables for storing inclusion rule statistics.

Value

A list of the table names as specified in the parameters to this function.

Get database migrations instance

Description

Returns ResultModelManager DataMigrationsManager instance.

Usage

getDataMigrator(connectionDetails, databaseSchema, tablePrefix = "")

Arguments

connectionDetails

DatabaseConnector connection details object
databaseSchema

String schema where database schema lives
tablePrefix

(Optional) Use if a table prefix is used before table names (e.g. "cg_")

Value

Instance of ResultModelManager::DataMigrationManager that has interface for converting existing data models

Get a list of tasks required when running in incremental mode

Description

This function will attempt to check the recordKeepingFile to determine if a list of operations have completed by comparing the keys passed into the function with the checksum supplied

Usage

getRequiredTasks(..., checksum, recordKeepingFile)

Arguments

...

Parameter values used to identify the key in the incremental record keeping file
checksum

The checksum representing the operation to check
recordKeepingFile

A file path to a CSV file containing the record keeping information.

Value

Returns a list of outstanding tasks based on inspecting the full contents of the record keeping file

Get specifications for CohortGenerator results data model

Description

Get specifications for CohortGenerator results data model

Usage

getResultsDataModelSpecifications()

Value

A tibble data frame object with specifications

Get cohort subset definitions from a cohort definition set

Description

Get the subset definitions (if any) applied to a cohort definition set. Note that these subset definitions are a copy of those applied to the cohort set. Modifying these definitions will not modify the base cohort set. To apply a modification, reapply the subset definition to the cohort definition set data.frame with addCohortSubsetDefinition with 'overwriteExisting = TRUE'.

Usage

getSubsetDefinitions(cohortDefinitionSet)

Arguments

cohortDefinitionSet

A valid cohortDefinitionSet

Value

list of cohort subset definitions or empty list

Used to insert the inclusion rule names from a cohort definition set when generating cohorts that include cohort statistics

Description

This function will take a cohortDefinitionSet that inclusions the Circe JSON representation of each cohort, parse the InclusionRule property to obtain the inclusion rule name and sequence number and insert the values into the cohortInclusionTable. This function is only required when generating cohorts that include cohort statistics.

Usage

insertInclusionRuleNames(
  connectionDetails = NULL,
  connection = NULL,
  cohortDefinitionSet,
  cohortDatabaseSchema,
  cohortInclusionTable = getCohortTableNames()$cohortInclusionTable
)

Arguments

connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package. Can be left NULL if connection is provided.
connection

An object of type connection as created using the connect function in the DatabaseConnector package. Can be left NULL if connectionDetails is provided, in which case a new connection will be opened at the start of the function, and closed when the function finishes.
cohortDefinitionSet

The cohortDefinitionSet argument must be a data frame with the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

sql

The OHDSI-SQL used to generate the cohort

Optionally, this data frame may contain:

json

The Circe JSON representation of the cohort
cohortDatabaseSchema

Schema name where your cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
cohortInclusionTable

Name of the inclusion table, one of the tables for storing inclusion rule statistics.

Value

A data frame containing the inclusion rules by cohort and sequence ID

Used to check if a string is in lower camel case

Description

This function is used check if a string conforms to the lower camel case format.

Usage

isCamelCase(x)

Arguments

x

The string to evaluate

Value

TRUE if the string is in lower camel case

Is the data.frame a cohort definition set?

Description

This function checks a data.frame to verify it holds the expected format for a cohortDefinitionSet.

Usage

isCohortDefinitionSet(x)

Arguments

x

The data.frame to check

Value

Returns TRUE if the input is a cohortDefinitionSet or returns FALSE with warnings on any violations

Is the data.frame formatted for uploading to a database?

Description

This function is used to check a data.frame to ensure all column names are in snake case format.

Usage

isFormattedForDatabaseUpload(x, warn = TRUE)

Arguments

x

A data frame
warn

When TRUE, display a warning of any columns are not in snake case format

Value

Returns TRUE if all columns are snake case format. If warn == TRUE, the function will emit a warning on the column names that are not in snake case format.

Used to check if a string is in snake case

Description

This function is used check if a string conforms to the snake case format.

Usage

isSnakeCase(x)

Arguments

x

The string to evaluate

Value

TRUE if the string is in snake case

Is a task required when running in incremental mode

Description

This function will attempt to check the recordKeepingFile to determine if an individual operation has completed by comparing the keys passed into the function with the checksum supplied

Usage

isTaskRequired(..., checksum, recordKeepingFile, verbose = TRUE)

Arguments

...

Parameter values used to identify the key in the incremental record keeping file
checksum

The checksum representing the operation to check
recordKeepingFile

A file path to a CSV file containing the record keeping information.
verbose

When TRUE, this function will output if a particular operation has completed based on inspecting the recordKeepingFile.

Value

Returns TRUE if the operation has completed according to the contents of the record keeping file.

Limit Subset Operator

Description

operator to apply limiting subset operations (e.g. washout periods, calendar ranges or earliest entries)

Get auto generated name

Super class

CohortGenerator::SubsetOperator -> LimitSubsetOperator

Active bindings

priorTime

minimum washout time in days

followUpTime

minimum required follow up time in days

limitTo

character one of: "firstEver" - only first entry in patient history "earliestRemaining" - only first entry after washout set by priorTime "latestRemaining" - the latest remaining after washout set by followUpTime "lastEver" - only last entry in patient history inside

Note, when using firstEver and lastEver with follow up and washout, patients with events outside this will be censored.

calendarStartDate

The calendar start date for limiting by date

calendarEndDate

The calendar end date for limiting by date

Methods

Public methods

Inherited methods

Method getAutoGeneratedName()

name generated from subset operation properties

Usage
LimitSubsetOperator$getAutoGeneratedName()
Returns

character To List

Method toList()

List representation of object

Usage
LimitSubsetOperator$toList()

Method clone()

The objects of this class are cloneable with this method.

Usage
LimitSubsetOperator$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Migrate Data model

Description

Migrate data from current state to next state

It is strongly advised that you have a backup of all data (either sqlite files, a backup database (in the case you are using a postgres backend) or have kept the csv/zip files from your data generation.

Usage

migrateDataModel(connectionDetails, databaseSchema, tablePrefix = "")

Arguments

connectionDetails

DatabaseConnector connection details object
databaseSchema

String schema where database schema lives
tablePrefix

(Optional) Use if a table prefix is used before table names (e.g. "cg_")

Used to read a .csv file

Description

This function is used to centralize the function for reading .csv files across the HADES ecosystem. This function will automatically convert from snake_case in the file to camelCase in the data.frame returned as is the standard described in: https://ohdsi.github.io/Hades/codeStyle.html#Interfacing_between_R_and_SQL

Usage

readCsv(file, warnOnCaseMismatch = TRUE, colTypes = readr::cols())

Arguments

file

The .csv file to read.
warnOnCaseMismatch

When TRUE, raise a warning if column headings in the .csv are not in snake_case format
colTypes

Corresponds to the 'col_types' in the 'readr::read_csv' function. One of 'NULL', a [readr::cols()] specification, or a string. See 'vignette("readr")' for more details.

If 'NULL', all column types will be inferred from 'guess_max' rows of the input, interspersed throughout the file. This is convenient (and fast), but not robust. If the guessed types are wrong, you'll need to increase 'guess_max' or supply the correct types yourself.

Column specifications created by [list()] or [cols()] must contain one column specification for each column.

Alternatively, you can use a compact string representation where each character represents one column: - c = character - i = integer - n = number - d = double - l = logical - f = factor - D = date - T = date time - t = time - ? = guess - _ or - = skip

By default, reading a file without a column specification will print a message showing what 'readr' guessed they were. To remove this message, set 'show_col_types = FALSE' or set 'options(readr.show_col_types = FALSE)'.

Value

A tibble with the .csv contents

Record a task as complete

Description

This function will record a task as completed in the recordKeepingFile

Usage

recordTasksDone(..., checksum, recordKeepingFile, incremental = TRUE)

Arguments

...

Parameter values used to identify the key in the incremental record keeping file
checksum

The checksum representing the operation to check
recordKeepingFile

A file path to a CSV file containing the record keeping information.
incremental

When TRUE, this function will record tasks otherwise it will return without attempting to perform any action

Run a cohort generation and export results

Description

Run a cohort generation and export results

Usage

runCohortGeneration(
  connectionDetails,
  cdmDatabaseSchema,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  cohortDatabaseSchema = cdmDatabaseSchema,
  cohortTableNames = getCohortTableNames(),
  cohortDefinitionSet = NULL,
  negativeControlOutcomeCohortSet = NULL,
  occurrenceType = "all",
  detectOnDescendants = FALSE,
  stopOnError = TRUE,
  outputFolder,
  databaseId = 1,
  minCellCount = 5,
  incremental = FALSE,
  incrementalFolder = NULL
)

Arguments

connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package.
cdmDatabaseSchema

Schema name where your patient-level data in OMOP CDM format resides. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.
tempEmulationSchema

Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created.
cohortDatabaseSchema

Schema name where your cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
cohortTableNames

The names of the cohort tables. See getCohortTableNames for more details.
cohortDefinitionSet

The cohortDefinitionSet argument must be a data frame with the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

sql

The OHDSI-SQL used to generate the cohort

Optionally, this data frame may contain:

json

The Circe JSON representation of the cohort
negativeControlOutcomeCohortSet

The negativeControlOutcomeCohortSet argument must be a data frame with the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

outcomeConceptId

The concept_id in the condition domain to use for the negative control outcome.
occurrenceType

For negative controls outcomes, the occurrenceType will detect either: the first time an outcomeConceptId occurs or all times the outcomeConceptId occurs for a person. Values accepted: 'all' or 'first'.
detectOnDescendants

For negative controls outcomes, when set to TRUE, detectOnDescendants will use the vocabulary to find negative control outcomes using the outcomeConceptId and all descendants via the concept_ancestor table. When FALSE, only the exact outcomeConceptId will be used to detect the outcome.
stopOnError

If an error happens while generating one of the cohorts in the cohortDefinitionSet, should we stop processing the other cohorts? The default is TRUE; when set to FALSE, failures will be identified in the return value from this function.
outputFolder

Name of the folder where all the outputs will written to.
databaseId

A unique ID for the database. This will be appended to most tables.
minCellCount

To preserve privacy: the minimum number of subjects contributing to a count before it can be included in the results. If the count is below this threshold, it will be set to '-minCellCount'.
incremental

Create only cohorts that haven't been created before?
incrementalFolder

If incremental = TRUE, specify a folder where records are kept of which definition has been executed.

Details

Run a cohort generation for a set of cohorts and negative control outcomes. This function will also export the results of the run to the 'outputFolder'.

Sample Cohort Definition Set

Description

Create 1 or more sample of size n of a cohort definition set

Subsetted cohorts can be sampled, as with any other subset form. However, subsetting a sampled cohort is not recommended and not currently supported at this time. In the case where n > cohort count the entire cohort is copied unmodified

As different databases have different forms of randomness, the random selection is computed in R, based on the count for each cohort. This is, therefore, db platform independent

Note, this function assumes cohorts have already been generated.

Lifecycle Note: This functionality is considered experimental and not intended for use inside analytic packages

Usage

sampleCohortDefinitionSet(
  cohortDefinitionSet,
  cohortIds = cohortDefinitionSet$cohortId,
  connectionDetails = NULL,
  connection = NULL,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  cohortDatabaseSchema,
  outputDatabaseSchema = cohortDatabaseSchema,
  cohortTableNames = getCohortTableNames(),
  n = NULL,
  sampleFraction = NULL,
  seed = 64374,
  seedArgs = NULL,
  identifierExpression = "cohortId * 1000 + seed",
  incremental = FALSE,
  incrementalFolder = NULL
)

Arguments

cohortDefinitionSet

The cohortDefinitionSet argument must be a data frame with the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

sql

The OHDSI-SQL used to generate the cohort

Optionally, this data frame may contain:

json

The Circe JSON representation of the cohort
cohortIds

Optional subset of cohortIds to generate. By default this function will sample all cohorts
connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package. Can be left NULL if connection is provided.
connection

An object of type connection as created using the connect function in the DatabaseConnector package. Can be left NULL if connectionDetails is provided, in which case a new connection will be opened at the start of the function, and closed when the function finishes.
tempEmulationSchema

Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created.
cohortDatabaseSchema

Schema name where your cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
outputDatabaseSchema

optional schema to output cohorts to (if different from cohortDatabaseSchema)
cohortTableNames

The names of the cohort tables. See getCohortTableNames for more details.
n

Sample size. Ignored if sample fraction is set
sampleFraction

Fraction of cohort to sample
seed

Vector of seeds to give to the R pseudorandom number generator
seedArgs

optional arguments to pass to set.seed
identifierExpression

Optional string R expression used to compute output cohort id. Can only use variables cohortId and seed. Default is "cohortId * 1000 + seed", which is substituted and evaluated
incremental

Create only cohorts that haven't been created before?
incrementalFolder

If incremental = TRUE, specify a folder where records are kept of which definition has been executed.

Value

sampledCohortDefinitionSet - a data.frame like object that contains the resulting identifiers and modified names of cohorts

Save the cohort definition set to the file system

Description

This function saves a cohortDefinitionSet to the file system and provides options for specifying where to write the individual elements: the settings file will contain the cohort information as a CSV specified by the settingsFileName, the cohort JSON is written to the jsonFolder and the SQL is written to the sqlFolder. We also provide a way to specify the json/sql file name format using the cohortFileNameFormat and cohortFileNameValue parameters.

Usage

saveCohortDefinitionSet(
  cohortDefinitionSet,
  settingsFileName = "inst/Cohorts.csv",
  jsonFolder = "inst/cohorts",
  sqlFolder = "inst/sql/sql_server",
  cohortFileNameFormat = "%s",
  cohortFileNameValue = c("cohortId"),
  subsetJsonFolder = "inst/cohort_subset_definitions/",
  verbose = FALSE
)

Arguments

cohortDefinitionSet

The cohortDefinitionSet argument must be a data frame with the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

sql

The OHDSI-SQL used to generate the cohort

Optionally, this data frame may contain:

json

The Circe JSON representation of the cohort
settingsFileName

The name of the CSV file that will hold the cohort information including the cohortId and cohortName
jsonFolder

The name of the folder that will hold the JSON representation of the cohort if it is available in the cohortDefinitionSet
sqlFolder

The name of the folder that will hold the SQL representation of the cohort.
cohortFileNameFormat

Defines the format string for naming the cohort JSON and SQL files. The format string follows the standard defined in the base sprintf function.
cohortFileNameValue

Defines the columns in the cohortDefinitionSet to use in conjunction with the cohortFileNameFormat parameter.
subsetJsonFolder

Defines the folder to store the subset JSON
verbose

When TRUE, logging messages are emitted to indicate export progress.

Save cohort subset definitions to json

Description

This is generally used as part of saveCohortDefinitionSet

Usage

saveCohortSubsetDefinition(
  subsetDefinition,
  subsetJsonFolder = "inst/cohort_subset_definitions/"
)

Arguments

subsetDefinition

The subset definition object @seealso[CohortSubsetDefinition]
subsetJsonFolder

Defines the folder to store the subset JSON

Used in incremental mode to save values to a file

Description

When running in incremental mode, we may need to update results in a CSV file. This function will replace the data in fileName based on the key parameters

Usage

saveIncremental(data, fileName, ...)

Arguments

data

The data to record in the file
fileName

A CSV holding results in the same structure as the data parameter
...

Parameter values used to identify the key in the results file

Time Window For Cohort Subset Operator

Description

Representation of a time window to use when subsetting a target cohort with a subset cohort

Active bindings

startDay

Integer

endDay

Integer

targetAnchor

Boolean

Methods

Public methods

Method toList()

List representation of object To JSON

Usage
SubsetCohortWindow$toList()

Method toJSON()

json serialized representation of object Is Equal to

Usage
SubsetCohortWindow$toJSON()

Method isEqualTo()

Compare SubsetCohortWindow to another

Usage
SubsetCohortWindow$isEqualTo(criteria)
Arguments
criteria

SubsetCohortWindow instance

Method clone()

The objects of this class are cloneable with this method.

Usage
SubsetCohortWindow$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Abstract base class for subsets.

Description

Abstract Base Class for subsets. Subsets should inherit from this and implement their own requirements.

Active bindings

name

name of subset operation - should describe what the operation does e.g. "Males under the age of 18", "Exposed to Celecoxib"

Methods

Public methods

Method new()

Usage
SubsetOperator$new(definition = NULL)
Arguments
definition

json character or list - definition of subset operator

Returns

instance of object Class Name

Method classname()

Class name of object Get auto generated name

Usage
SubsetOperator$classname()

Method getAutoGeneratedName()

Not intended to be used - should be implemented in subclasses Return query builder instance

Usage
SubsetOperator$getAutoGeneratedName()

Method getQueryBuilder()

Return query builder instance Public Fields

Usage
SubsetOperator$getQueryBuilder(id)
Arguments
id

- integer that should be unique in the sql (e.g. increment it by one for each subset operation in set)

Method publicFields()

Publicly settable fields of object Is Equal to

Usage
SubsetOperator$publicFields()

Method isEqualTo()

Compare Subsets - are they identical or not? Checks all fields and settings

Usage
SubsetOperator$isEqualTo(subsetOperatorB)
Arguments
subsetOperatorB

A subset to test equivalence to To list

Method toList()

convert to List representation To Json

Usage
SubsetOperator$toList()

Method toJSON()

convert to json serialized representation

Usage
SubsetOperator$toJSON()
Returns

list representation of object as json character

Method clone()

The objects of this class are cloneable with this method.

Usage
SubsetOperator$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

CohortSubsetOperator

DemographicSubsetOperator

LimitSubsetOperator

Upload results to the database server.

Description

Requires the results data model tables have been created using the createResultsDataModel function.

Usage

uploadResults(
  connectionDetails,
  schema,
  resultsFolder,
  forceOverWriteOfSpecifications = FALSE,
  purgeSiteDataBeforeUploading = TRUE,
  tablePrefix = "",
  ...
)

Arguments

connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package.
schema

The schema on the server where the tables have been created.
resultsFolder

The folder holding the results in .csv files
forceOverWriteOfSpecifications

If TRUE, specifications of the phenotypes, cohort definitions, and analysis will be overwritten if they already exist on the database. Only use this if these specifications have changed since the last upload.
purgeSiteDataBeforeUploading

If TRUE, before inserting data for a specific databaseId all the data for that site will be dropped. This assumes the resultsFolder file contains the full data for that data site.
tablePrefix

(Optional) string to insert before table names for database table names
...

See ResultModelManager::uploadResults

Used to write a .csv file

Description

This function is used to centralize the function for writing .csv files across the HADES ecosystem. This function will automatically convert from camelCase in the data.frame to snake_case column names in the resulting .csv file as is the standard described in: https://ohdsi.github.io/Hades/codeStyle.html#Interfacing_between_R_and_SQL

This function may also raise warnings if the data is stored in a format that will not work with the HADES standard for uploading to a results database. Specifically file names should be in snake_case format, all column headings are in snake_case format and where possible the file name should not be plural. See isFormattedForDatabaseUpload for a helper function to check a data.frame for rules on the column names

Usage

writeCsv(
  x,
  file,
  append = FALSE,
  warnOnCaseMismatch = TRUE,
  warnOnFileNameCaseMismatch = TRUE,
  warnOnUploadRuleViolations = TRUE
)

Arguments

x

A data frame or tibble to write to disk.
file

The .csv file to write.
append

When TRUE, append the values of x to an existing file.
warnOnCaseMismatch

When TRUE, raise a warning if columns in the data.frame are NOT in camelCase format.
warnOnFileNameCaseMismatch

When TRUE, raise a warning if the file name specified is not in snake_case format.
warnOnUploadRuleViolations

When TRUE, this function will provide warning messages that may indicate if the data is stored in a format in the .csv that may cause problems when uploading to a database.

Value

Returns the input x invisibly.