Package 'Achilles' reference manual

Title:	Achilles Data Source Characterization
Description:	Automated Characterization of Health Information at Large-Scale Longitudinal Evidence Systems. Creates a descriptive statistics summary for an Observational Medical Outcomes Partnership Common Data Model standardized data source. This package includes functions for executing summary queries on the specified data source and exporting reporting content for use across a variety of Observational Health Data Sciences and Informatics community applications.
Authors:	Frank DeFalco [aut, cre], Patrick Ryan [aut], Martijn Schuemie [aut], Vojtech Huser [aut], Chris Knoll [aut], Ajit Londhe [aut], Taha Abdul-Basser [aut], Anthony Molinaro [aut], Observational Health Data Science and Informatics [cph]
Maintainer:	Frank DeFalco <[email protected]>
License:	Apache License
Version:	1.7.2
Built:	2024-11-02 04:12:37 UTC
Source:	https://github.com/cran/Achilles

achilles

Description

achilles creates descriptive statistics summary for an entire OMOP CDM instance.

Usage

achilles(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema = cdmDatabaseSchema,
  scratchDatabaseSchema = resultsDatabaseSchema,
  vocabDatabaseSchema = cdmDatabaseSchema,
  tempEmulationSchema = resultsDatabaseSchema,
  sourceName = "",
  analysisIds,
  createTable = TRUE,
  smallCellCount = 5,
  cdmVersion = "5",
  createIndices = TRUE,
  numThreads = 1,
  tempAchillesPrefix = "tmpach",
  dropScratchTables = TRUE,
  sqlOnly = FALSE,
  outputFolder = "output",
  verboseMode = TRUE,
  optimizeAtlasCache = FALSE,
  defaultAnalysesOnly = TRUE,
  updateGivenAnalysesOnly = FALSE,
  excludeAnalysisIds,
  sqlDialect = NULL
)
achilles(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema = cdmDatabaseSchema,
  scratchDatabaseSchema = resultsDatabaseSchema,
  vocabDatabaseSchema = cdmDatabaseSchema,
  tempEmulationSchema = resultsDatabaseSchema,
  sourceName = "",
  analysisIds,
  createTable = TRUE,
  smallCellCount = 5,
  cdmVersion = "5",
  createIndices = TRUE,
  numThreads = 1,
  tempAchillesPrefix = "tmpach",
  dropScratchTables = TRUE,
  sqlOnly = FALSE,
  outputFolder = "output",
  verboseMode = TRUE,
  optimizeAtlasCache = FALSE,
  defaultAnalysesOnly = TRUE,
  updateGivenAnalysesOnly = FALSE,
  excludeAnalysisIds,
  sqlDialect = NULL
)

Arguments

`connectionDetails`	An R object of type `connectionDetails` created using the function `createConnectionDetails` in the `DatabaseConnector` package.
`cdmDatabaseSchema`	Fully qualified name of database schema that contains OMOP CDM schema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_instance.dbo'.
`resultsDatabaseSchema`	Fully qualified name of database schema that we can write final results to. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_results.dbo'.
`scratchDatabaseSchema`	Fully qualified name of the database schema that will store all of the intermediate scratch tables, so for example, on SQL Server, 'cdm_scratch.dbo'. Must be accessible to/from the cdmDatabaseSchema and the resultsDatabaseSchema. Default is resultsDatabaseSchema. Making this "#" will run Achilles in single-threaded mode and use temporary tables instead of permanent tables.
`vocabDatabaseSchema`	String name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.
`tempEmulationSchema`	Formerly oracleTempSchema. For databases like Oracle where you must specify the name of the database schema where you want all temporary tables to be managed. Requires create/insert permissions to this database.
`sourceName`	String name of the data source name. If blank, CDM_SOURCE table will be queried to try to obtain this.
`analysisIds`	(OPTIONAL) A vector containing the set of Achilles analysisIds for which results will be generated. If not specified, all analyses will be executed. Use `getAnalysisDetails` to get a list of all Achilles analyses and their Ids.
`createTable`	If true, new results tables will be created in the results schema. If not, the tables are assumed to already exist, and analysis results will be inserted (slower on MPP).
`smallCellCount`	To avoid patient identification, cells with small counts (<= smallCellCount) are deleted. Set to 0 for complete summary without small cell count restrictions.
`cdmVersion`	Define the OMOP CDM version used: currently supports v5 and above. Use major release number or minor number only (e.g. 5, 5.3)
`createIndices`	Boolean to determine if indices should be created on the resulting Achilles tables. Default= TRUE
`numThreads`	(OPTIONAL, multi-threaded mode) The number of threads to use to run Achilles in parallel. Default is 1 thread.
`tempAchillesPrefix`	(OPTIONAL, multi-threaded mode) The prefix to use for the scratch Achilles analyses tables. Default is "tmpach"
`dropScratchTables`	(OPTIONAL, multi-threaded mode) TRUE = drop the scratch tables (may take time depending on dbms), FALSE = leave them in place for later removal.
`sqlOnly`	Boolean to determine if Achilles should be fully executed. TRUE = just generate SQL files, don't actually run, FALSE = run Achilles
`outputFolder`	Path to store logs and SQL files
`verboseMode`	Boolean to determine if the console will show all execution steps. Default = TRUE
`optimizeAtlasCache`	Boolean to determine if the atlas cache has to be optimized. Default = FALSE
`defaultAnalysesOnly`	Boolean to determine if only default analyses should be run. Including non-default analyses is substantially more resource intensive. Default = TRUE
`updateGivenAnalysesOnly`	Boolean to determine whether to preserve the results of the analyses NOT specified with the `analysisIds` parameter. To update only analyses specified by `analysisIds`, set createTable = FALSE and updateGivenAnalysesOnly = TRUE. By default, updateGivenAnalysesOnly = FALSE, to preserve the original behavior of Achilles when supplied `analysisIds`.
`excludeAnalysisIds`	(OPTIONAL) A vector containing the set of Achilles analyses to exclude.
`sqlDialect`	(OPTIONAL) String to be used when specifying sqlOnly = TRUE and NOT supplying the `connectionDetails` parameter. if the `connectionDetails` parameter is supplied, `sqlDialect` is ignored. If the `connectionDetails` parameter is not supplied, `sqlDialect` must be supplied to enable `SqlRender` to translate properly. `sqlDialect` takes the value normally supplied to connectionDetails$dbms. Default = NULL.

Details

achilles creates descriptive statistics summary for an entire OMOP CDM instance.

Value

An object of type achillesResults containing details for connecting to the database containing the results

Examples

## Not run: 
connectionDetails <- createConnectionDetails(dbms = "sql server", server = "some_server")
achillesResults <- achilles(connectionDetails = connectionDetails,
  cdmDatabaseSchema = "cdm",
  resultsDatabaseSchema = "results",
  scratchDatabaseSchema = "scratch", 
  sourceName = "Some Source", 
  cdmVersion = "5.3", 
  numThreads = 10, 
  outputFolder = "output")

## End(Not run)

## Not run: 
connectionDetails <- createConnectionDetails(dbms = "sql server", server = "some_server")
achillesResults <- achilles(connectionDetails = connectionDetails,
  cdmDatabaseSchema = "cdm",
  resultsDatabaseSchema = "results",
  scratchDatabaseSchema = "scratch", 
  sourceName = "Some Source", 
  cdmVersion = "5.3", 
  numThreads = 10, 
  outputFolder = "output")

## End(Not run)

Create indicies

Description

Create indicies

Usage

createIndices(
  connectionDetails,
  resultsDatabaseSchema,
  outputFolder,
  sqlOnly = FALSE,
  verboseMode = TRUE,
  achillesTables = c("achilles_results", "achilles_results_dist")
)
createIndices(
  connectionDetails,
  resultsDatabaseSchema,
  outputFolder,
  sqlOnly = FALSE,
  verboseMode = TRUE,
  achillesTables = c("achilles_results", "achilles_results_dist")
)

Arguments

`connectionDetails`	An R object of type `connectionDetails` created using the function `createConnectionDetails` in the `DatabaseConnector` package.
`resultsDatabaseSchema`	Fully qualified name of database schema that we can write final results to. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_results.dbo'.
`outputFolder`	Path to store logs and SQL files
`sqlOnly`	TRUE = just generate SQL files, don't actually run, FALSE = run Achilles
`verboseMode`	Boolean to determine if the console will show all execution steps. Default = TRUE
`achillesTables`	Which achilles tables should be indexed? Default is both achilles_results and achilles_results_dist.

Details

Post-processing, create indices to help performance. Cannot be used with Redshift.

Value

A collection of queries that were executed to drop any existing indices and create new indicies as specified.

createTimeSeries

Description

createTimeSeries Creates a monthly multivariate time series object given a data frame in the proper format.

Usage

createTimeSeries(temporalData)
createTimeSeries(temporalData)

Arguments

temporalData

A data frame from which to create the time series

Details

createTimeSeries Requires the following:

 1. The given data frame must contain
four columns: START_DATE, COUNT_VALUE, PREVALENCE, and PROPORTION_WITHIN_YEAR. 2. START_DATE must
be in the YYYYMMDD format. 3. COUNT_VALUE, PREVALENCE, and PROPORTION_WITHIN_YEAR contain only
numeric data.

The individual monthly univariate time series can be extracted by specifying the correct column name (see example).

Value

A multivariate time series object

Examples

# Example 1:
temporalData <- data.frame(START_DATE = seq.Date(as.Date("20210101", "%Y%m%d"),
                                                 as.Date("20231201",
  "%Y%m%d"), by = "month"), COUNT_VALUE = round(runif(36, 1, 1000)), PREVALENCE = round(runif(36,
  0, 10), 2), PROPORTION_WITHIN_YEAR = round(runif(36, 0, 1), 2), stringsAsFactors = FALSE)
dummyTs <- createTimeSeries(temporalData)
dummyTs.cv <- dummyTs[, "COUNT_VALUE"]
dummyTs.pv <- dummyTs[, "PREVALENCE"]
dummyTs.pwy <- dummyTs[, "PROPORTION_WITHIN_YEAR"]

## Not run: 
# Example 2:
pneumonia <- 255848
temporalData <- getTemporalData(connectionDetails = connectionDetails, cdmDatabaseSchema = "cdm",
  resultsDatabaseSchema = "results", conceptId = pneumonia)
pneumoniaTs <- createTimeSeries(temporalData)
pneumoniaTs.cv <- pneumoniaTs[, "COUNT_VALUE"]
pneumoniaTs.pv <- pneumoniaTs[, "PREVALENCE"]
pneumoniaTs.pwy <- pneumoniaTs[, "PROPORTION_WITHIN_YEAR"]

## End(Not run)

# Example 1:
temporalData <- data.frame(START_DATE = seq.Date(as.Date("20210101", "%Y%m%d"),
                                                 as.Date("20231201",
  "%Y%m%d"), by = "month"), COUNT_VALUE = round(runif(36, 1, 1000)), PREVALENCE = round(runif(36,
  0, 10), 2), PROPORTION_WITHIN_YEAR = round(runif(36, 0, 1), 2), stringsAsFactors = FALSE)
dummyTs <- createTimeSeries(temporalData)
dummyTs.cv <- dummyTs[, "COUNT_VALUE"]
dummyTs.pv <- dummyTs[, "PREVALENCE"]
dummyTs.pwy <- dummyTs[, "PROPORTION_WITHIN_YEAR"]

## Not run: 
# Example 2:
pneumonia <- 255848
temporalData <- getTemporalData(connectionDetails = connectionDetails, cdmDatabaseSchema = "cdm",
  resultsDatabaseSchema = "results", conceptId = pneumonia)
pneumoniaTs <- createTimeSeries(temporalData)
pneumoniaTs.cv <- pneumoniaTs[, "COUNT_VALUE"]
pneumoniaTs.pv <- pneumoniaTs[, "PREVALENCE"]
pneumoniaTs.pwy <- pneumoniaTs[, "PROPORTION_WITHIN_YEAR"]

## End(Not run)

Drop all possible scratch tables

Description

Drop all possible scratch tables

Usage

dropAllScratchTables(
  connectionDetails,
  scratchDatabaseSchema,
  tempAchillesPrefix = "tmpach",
  numThreads = 1,
  tableTypes = c("achilles"),
  outputFolder,
  verboseMode = TRUE,
  defaultAnalysesOnly = TRUE
)
dropAllScratchTables(
  connectionDetails,
  scratchDatabaseSchema,
  tempAchillesPrefix = "tmpach",
  numThreads = 1,
  tableTypes = c("achilles"),
  outputFolder,
  verboseMode = TRUE,
  defaultAnalysesOnly = TRUE
)

Arguments

`connectionDetails`	An R object of type `connectionDetails` created using the function `createConnectionDetails` in the `DatabaseConnector` package.
`scratchDatabaseSchema`	string name of database schema that Achilles scratch tables were written to.
`tempAchillesPrefix`	The prefix to use for the "temporary" (but actually permanent) Achilles analyses tables. Default is "tmpach"
`numThreads`	The number of threads to use to run this function. Default is 1 thread.
`tableTypes`	The types of Achilles scratch tables to drop: achilles
`outputFolder`	Path to store logs and SQL files
`verboseMode`	Boolean to determine if the console will show all execution steps. Default = TRUE
`defaultAnalysesOnly`	Boolean to determine if only default analyses should be run. Including non-default analyses is substantially more resource intensive. Default = TRUE

Details

Drop all possible Achilles scratch tables

Value

No return value, called to drop interim scratch tables.

exportConditionEraToJson

Description

exportConditionEraToJson Exports Achilles Condition Era report into a JSON form for reports.

Usage

exportConditionEraToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportConditionEraToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates individual files for Condition Era report found in Achilles.Web

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportConditionEraToJson(connectionDetails,
                         cdmDatabaseSchema = "cdm4_sim",
                         outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportConditionEraToJson(connectionDetails,
                         cdmDatabaseSchema = "cdm4_sim",
                         outputPath = "your/output/path")

## End(Not run)

exportConditionToJson

Description

exportConditonToJson Exports Achilles Condition report into a JSON form for reports.

Usage

exportConditionToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportConditionToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates individual files for Condition report found in Achilles.Web

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportConditionToJson(connectionDetails,
                      cdmDatabaseSchema = "cdm4_sim",
                      outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportConditionToJson(connectionDetails,
                      cdmDatabaseSchema = "cdm4_sim",
                      outputPath = "your/output/path")

## End(Not run)

exportDashboardToJson

Description

exportDashboardToJson Exports Achilles Dashboard report into a JSON form for reports.

Usage

exportDashboardToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportDashboardToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates individual files for Dashboard report found in Achilles.Web. NOTE: This function reads the results from the other exports and aggregates them into a single file. If other reports are not genreated, this function will fail.

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportDashboardToJson(connectionDetails,
                      cdmDatabaseSchema = "cdm4_sim",
                      outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportDashboardToJson(connectionDetails,
                      cdmDatabaseSchema = "cdm4_sim",
                      outputPath = "your/output/path")

## End(Not run)

exportDataDensityToJson

Description

exportDataDensityToJson Exports Achilles Data Density report into a JSON form for reports.

Usage

exportDataDensityToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportDataDensityToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates individual files for Data Density report found in Achilles.Web

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportDataDensityToJson(connectionDetails,
                        cdmDatabaseSchema = "cdm4_sim",
                        outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportDataDensityToJson(connectionDetails,
                        cdmDatabaseSchema = "cdm4_sim",
                        outputPath = "your/output/path")

## End(Not run)

exportDeathToJson

Description

exportDeathToJson Exports Achilles Death report into a JSON form for reports.

Usage

exportDeathToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportDeathToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates individual files for Death report found in Achilles.Web

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportDeathToJson(connectionDetails,
                  cdmDatabaseSchema = "cdm4_sim",
                  outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportDeathToJson(connectionDetails,
                  cdmDatabaseSchema = "cdm4_sim",
                  outputPath = "your/output/path")

## End(Not run)

exportDrugEraToJson

Description

exportDrugEraToJson Exports Achilles Drug Era report into a JSON form for reports.

Usage

exportDrugEraToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportDrugEraToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates individual files for Drug Era report found in Achilles.Web

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportDrugEraToJson(connectionDetails,
                    cdmDatabaseSchema = "cdm4_sim",
                    outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportDrugEraToJson(connectionDetails,
                    cdmDatabaseSchema = "cdm4_sim",
                    outputPath = "your/output/path")

## End(Not run)

exportDrugToJson

Description

exportDrugToJson Exports Achilles Drug report into a JSON form for reports.

Usage

exportDrugToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportDrugToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates individual files for Drug report found in Achilles.Web

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportDrugToJson(connectionDetails,
                 cdmDatabaseSchema = "cdm4_sim",
                 outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportDrugToJson(connectionDetails,
                 cdmDatabaseSchema = "cdm4_sim",
                 outputPath = "your/output/path")

## End(Not run)

exportMeasurementToJson

Description

exportMeasurementToJson Exports Measurement report into a JSON form for reports.

Usage

exportMeasurementToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportMeasurementToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates individual files for Measurement report found in Achilles.Web

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportMeasurementToJson(connectionDetails,
                        cdmDatabaseSchema = "cdm4_sim",
                        outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportMeasurementToJson(connectionDetails,
                        cdmDatabaseSchema = "cdm4_sim",
                        outputPath = "your/output/path")

## End(Not run)

exportMetaToJson

Description

exportMetaToJson Exports Achilles META report into a JSON form for reports.

Usage

exportMetaToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportMetaToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates individual files for Achilles META report found in Achilles.Web

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportMetaToJson(connectionDetails,
                 cdmDatabaseSchema = "cdm4_sim",
                 outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportMetaToJson(connectionDetails,
                 cdmDatabaseSchema = "cdm4_sim",
                 outputPath = "your/output/path")

## End(Not run)

exportObservationPeriodToJson

Description

exportObservationPeriodToJson Exports Achilles Observation Period report into a JSON form for reports.

Usage

exportObservationPeriodToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportObservationPeriodToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates individual files for Observation Period report found in Achilles.Web

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportObservationPeriodToJson(connectionDetails,
                              cdmDatabaseSchema = "cdm4_sim",
                              outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportObservationPeriodToJson(connectionDetails,
                              cdmDatabaseSchema = "cdm4_sim",
                              outputPath = "your/output/path")

## End(Not run)

exportObservationToJson

Description

exportObservationToJson Exports Achilles Observation report into a JSON form for reports.

Usage

exportObservationToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportObservationToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates individual files for Observation report found in Achilles.Web

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportObservationToJson(connectionDetails,
                        cdmDatabaseSchema = "cdm4_sim",
                        outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportObservationToJson(connectionDetails,
                        cdmDatabaseSchema = "cdm4_sim",
                        outputPath = "your/output/path")

## End(Not run)

exportPerformanceToJson exportPerformanceToJson

Description

exportPerformanceToJson Exports Achilles performance report into a JSON form for reports.

Usage

exportPerformanceToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportPerformanceToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates performance report including how long each Achilles result took to generate.

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportPerformanceToJson(connectionDetails,
                        cdmDatabaseSchema = "cdm4_sim",
                        outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportPerformanceToJson(connectionDetails,
                        cdmDatabaseSchema = "cdm4_sim",
                        outputPath = "your/output/path")

## End(Not run)

exportPersonToJson

Description

exportPersonToJson Exports Achilles Person report into a JSON form for reports.

Usage

exportPersonToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportPersonToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates individual files for Person report found in Achilles.Web

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportPersonToJson(connectionDetails,
                   cdmDatabaseSchema = "cdm4_sim",
                   outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportPersonToJson(connectionDetails,
                   cdmDatabaseSchema = "cdm4_sim",
                   outputPath = "your/output/path")

## End(Not run)

exportProcedureToJson

Description

exportProcedureToJson Exports Achilles Procedure report into a JSON form for reports.

Usage

exportProcedureToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportProcedureToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates individual files for Procedure report found in Achilles.Web

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportProcedureToJson(connectionDetails,
                      cdmDatabaseSchema = "cdm4_sim",
                      outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportProcedureToJson(connectionDetails,
                      cdmDatabaseSchema = "cdm4_sim",
                      outputPath = "your/output/path")

## End(Not run)

exportResultsToCSV

Description

exportResultsToCSV exports all results to a CSV file

Usage

exportResultsToCSV(
  connectionDetails,
  resultsDatabaseSchema,
  analysisIds = c(),
  minCellCount = 5,
  exportFolder
)
exportResultsToCSV(
  connectionDetails,
  resultsDatabaseSchema,
  analysisIds = c(),
  minCellCount = 5,
  exportFolder
)

Arguments

`connectionDetails`	An R object of type `connectionDetails` created using the function `createConnectionDetails` in the `DatabaseConnector` package.
`resultsDatabaseSchema`	Fully qualified name of database schema that we can write final results to. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_results.dbo'.
`analysisIds`	(OPTIONAL) A vector containing the set of Achilles analysisIds for which results will be generated. If not specified, all analyses will be executed. Use `getAnalysisDetails` to get a list of all Achilles analyses and their Ids.
`minCellCount`	To avoid patient identification, cells with small counts (<= minCellCount) are deleted. Set to 0 for complete summary without small cell count restrictions.
`exportFolder`	Path to store results

Details

exportResultsToCSV writes a CSV file with all results to the export folder.

Value

No return value. Called to export CSV file to the file system.

exportToAres

Description

exportToAres Exports Achilles statistics for ARES

Usage

exportToAres(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  vocabDatabaseSchema,
  outputPath,
  reports = c()
)
exportToAres(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  vocabDatabaseSchema,
  outputPath,
  reports = c()
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the OMOP CDM.
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`vocabDatabaseSchema`	string name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.
`outputPath`	A folder location to save the JSON files. Default is current working folder
`reports`	vector of reports to run, c() defaults to all reports See `showReportTypes` for a list of all report types

Details

Creates export files

Value

none

exportToJson

Description

exportToJson Exports Achilles statistics into a JSON form for reports.

Usage

exportToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  reports = getAllReports(),
  vocabDatabaseSchema = cdmDatabaseSchema,
  compressIntoOneFile = FALSE
)
exportToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  reports = getAllReports(),
  vocabDatabaseSchema = cdmDatabaseSchema,
  compressIntoOneFile = FALSE
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the OMOP CDM.
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	A folder location to save the JSON files. Default is current working folder
`reports`	A character vector listing the set of reports to generate. Default is all reports.
`vocabDatabaseSchema`	string name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.
`compressIntoOneFile`	Boolean indicating if the JSON files should be compressed into one zip file. Please note that in Windows, the zip application must be stored in the system environment, e.g. Sys.setenv("R_ZIPCMD", "some_path_to_zip"). Due to recursion, the actual Achilles files and folders will be embedded in any parent directories that the source folder has. See `showReportTypes` for a list of all report types

Details

Creates individual files for each report found in Achilles.Web

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportToJson(connectionDetails, cdmDatabaseSchema = "cdm4_sim", outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportToJson(connectionDetails, cdmDatabaseSchema = "cdm4_sim", outputPath = "your/output/path")

## End(Not run)

exportVisitDetailToJson

Description

exportVisitDetailToJson Exports Achilles VISIT_DETAIL report into a JSON form for reports.

Usage

exportVisitDetailToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportVisitDetailToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates individual files for VISIT_DETAIL report found in Achilles.Web

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportVisitDetailToJson(connectionDetails,
                        cdmDatabaseSchema = "cdm4_sim",
                        outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportVisitDetailToJson(connectionDetails,
                        cdmDatabaseSchema = "cdm4_sim",
                        outputPath = "your/output/path")

## End(Not run)

exportVisitToJson

Description

exportVisitToJson Exports Achilles Visit report into a JSON form for reports.

Usage

exportVisitToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)
exportVisitToJson(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  outputPath,
  vocabDatabaseSchema = cdmDatabaseSchema
)

Arguments

`connectionDetails`	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
`cdmDatabaseSchema`	Name of the database schema that contains the vocabulary files
`resultsDatabaseSchema`	Name of the database schema that contains the Achilles analysis files. Default is cdmDatabaseSchema
`outputPath`	folder location to save the JSON files. Default is current working folder
`vocabDatabaseSchema`	name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

Details

Creates individual files for Visit report found in Achilles.Web

Value

none

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportVisitToJson(connectionDetails,
                  cdmDatabaseSchema = "cdm4_sim",
                  outputPath = "your/output/path")

## End(Not run)
## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sql server",
                                                                server = "yourserver")
exportVisitToJson(connectionDetails,
                  cdmDatabaseSchema = "cdm4_sim",
                  outputPath = "your/output/path")

## End(Not run)

Get all analysis details

Description

Get all analysis details

Usage

getAnalysisDetails()
getAnalysisDetails()

Details

Get a list of all analyses with their analysis IDs and strata.

Value

A data.frame with the analysis details.

Get the seasonality score for a given monthly time series

Description

The seasonality score of a monthly time series is computed as its departure from a uniform distribution.

Usage

getSeasonalityScore(tsData)
getSeasonalityScore(tsData)

Arguments

tsData

A time series object.

Details

The degree of seasonality of a monthly time series is based on its departure from a uniform distribution. If the number of cases for a given concept is uniformly distributed across all time periods (in this case, all months), then its monthly proportion would be approximately constant. In this case, the time series would be considered "strictly non-seasonal" and its "seasonality score" would be zero. Similarly, if all cases recur at a single point in time (that is, in a single month), such a time series would be considered "strictly seasonal" and its seasonality score would be 1. All other time series would have a seasonality score between 0 and 1. Currently, only monthly time series are supported.

Value

A numeric value between 0 and 1 (inclusive) representing the seasonality of a time series.

getTemporalData

Description

getTemporalData Retrieve specific monthly analyses data to support temporal characterization.

Usage

getTemporalData(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  analysisIds = NULL,
  conceptId = NULL
)
getTemporalData(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  analysisIds = NULL,
  conceptId = NULL
)

Arguments

`connectionDetails`	An R object of type `connectionDetails` created using the function `createConnectionDetails` in the `DatabaseConnector` package.
`cdmDatabaseSchema`	Fully qualified name of database schema that contains OMOP CDM schema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_instance.dbo'.
`resultsDatabaseSchema`	Fully qualified name of database schema that we can write final results to. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_results.dbo'.
`analysisIds`	(OPTIONAL) A vector containing the set of Achilles analysisIds for which results will be returned. The following are supported: `202,402,602,702,802,1802,2102`. If not specified, data for all analysis will be returned. Ignored if `conceptId` is given.
`conceptId`	(OPTIONAL) A SNOMED concept_id from the `CONCEPT` table for which a monthly Achilles analysis exists. If not specified, all concepts for a given analysis will be returned.

Details

getTemporalData Assumes achilles has been run.

Currently supported
Achilles monthly analyses are: 202 - Visit Occurrence 402 - Condition occurrence 602 - Procedure
Occurrence 702 - Drug Exposure 802 - Observation 1802 - Measurement 2102 - Device

Value

A data frame of query results from DatabaseConnector

Examples

## Not run: 
pneumonia <- 255848
monthlyResults <- getTemporalData(connectionDetails = connectionDetails,
                                  cdmDatabaseSchema = "cdm",

  resultsDatabaseSchema = "results", conceptId = pneumonia)

## End(Not run)

## Not run: 
pneumonia <- 255848
monthlyResults <- getTemporalData(connectionDetails = connectionDetails,
                                  cdmDatabaseSchema = "cdm",

  resultsDatabaseSchema = "results", conceptId = pneumonia)

## End(Not run)

Determine whether or not a time series is stationary in the mean

Description

Uses the Augmented Dickey-Fuller test to determine when the time series has a unit root.

Usage

isStationary(tsData)
isStationary(tsData)

Arguments

tsData

A time series object.

Details

A time series must have a minimum of three complete years of data. For details on the implementation of the Augmented Dickey-Fuller test, see the tseries package on cran.

Value

A boolean indicating whether or not the given time series is stationary.

listMissingAnalyses

Description

listMissingAnalyses Find and return analyses that exist in getAnalysisDetails, but not in achilles_results or achilles_results_dist

Usage

listMissingAnalyses(connectionDetails, resultsDatabaseSchema)
listMissingAnalyses(connectionDetails, resultsDatabaseSchema)

Arguments

`connectionDetails`	An R object of type `connectionDetails` created using the function `createConnectionDetails` in the `DatabaseConnector` package.
`resultsDatabaseSchema`	Fully qualified name of database schema that contains achilles_results and achilles_results_dist tables.

Value

A dataframe which is a subset of getAnalysisDetails

Examples

## Not run: 
Achilles::listMissingAnalyses(connectionDetails = connectionDetails,
                              resultsDatabaseSchema = "results")

## End(Not run)

## Not run: 
Achilles::listMissingAnalyses(connectionDetails = connectionDetails,
                              resultsDatabaseSchema = "results")

## End(Not run)

Optimize atlas cache

Description

Optimize atlas cache

Usage

optimizeAtlasCache(
  connectionDetails,
  resultsDatabaseSchema,
  vocabDatabaseSchema = resultsDatabaseSchema,
  outputFolder = "output",
  sqlOnly = FALSE,
  verboseMode = TRUE,
  tempAchillesPrefix = "tmpach"
)
optimizeAtlasCache(
  connectionDetails,
  resultsDatabaseSchema,
  vocabDatabaseSchema = resultsDatabaseSchema,
  outputFolder = "output",
  sqlOnly = FALSE,
  verboseMode = TRUE,
  tempAchillesPrefix = "tmpach"
)

Arguments

`connectionDetails`	An R object of type `connectionDetails` created using the function `createConnectionDetails` in the `DatabaseConnector` package.
`resultsDatabaseSchema`	Fully qualified name of database schema that we can write final results to. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_results.dbo'.
`vocabDatabaseSchema`	String name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.
`outputFolder`	Path to store logs and SQL files
`sqlOnly`	TRUE = just generate SQL files, don't actually run, FALSE = run Achilles
`verboseMode`	Boolean to determine if the console will show all execution steps. Default = TRUE
`tempAchillesPrefix`	The prefix to use for the "temporary" (but actually permanent) Achilles analyses tables. Default is "tmpach"

Details

Post-processing, optimize data for atlas cache in separate table to help performance.

Value

The SQL statement executed to update cache tables is returned.

performTemporalCharacterization

Description

performTemporalCharacterization Perform temporal characterization on a concept or family of concepts belonging to a supported Achilles analysis.

Usage

performTemporalCharacterization(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  analysisIds = NULL,
  conceptId = NULL,
  outputFile = "temporal-characterization.csv"
)
performTemporalCharacterization(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  analysisIds = NULL,
  conceptId = NULL,
  outputFile = "temporal-characterization.csv"
)

Arguments

`connectionDetails`	An R object of type `connectionDetails` created using the function `createConnectionDetails` in the `DatabaseConnector` package.
`cdmDatabaseSchema`	Fully qualified name of database schema that contains OMOP CDM schema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_instance.dbo'.
`resultsDatabaseSchema`	Fully qualified name of database schema that we can write final results to. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_results.dbo'.
`analysisIds`	(OPTIONAL) A vector containing the set of Achilles analysisIds for which results will be returned. The following are supported: `202,402,602,702,802,1802,2102`. If not specified, data for all analysis will be returned. Ignored if `conceptId` is given.
`conceptId`	(OPTIONAL) A SNOMED concept_id from the `CONCEPT` table for which a monthly Achilles analysis exists. If not specified, all concepts for a given analysis will be returned.
`outputFile`	CSV file where temporal characterization will be written. Default is temporal-characterization.csv.

Details

performTemporalAnalyses Assumes achilles has been run.

Currently supported Achilles analyses for temporal analyses are:
202  - Visit Occurrence
402  - Condition occurrence
602  - Procedure Occurrence
702  - Drug Exposure
802  - Observation
1802 - Measurement
2102 - Device

Value

A csv file with temporal analyses for each time series

Examples

## Not run: 
# Example 1:
pneumonia <- 255848
performTemporalCharacterization(
	connectionDetails     = connectionDetails,
	cdmDatabaseSchema     = "cdm",
	resultsDatabaseSchema = "results",
	conceptId             = pneumonia,
 outputFolder          = "output/pneumoniaTemporalChar.csv")

# Example 2:
performTemporalCharacterization(
	connectionDetails     = connectionDetails,
	cdmDatabaseSchema     = "cdm",
	resultsDatabaseSchema = "results",
	analysisIds           = c(402,702),
 outputFolder          = "output/conditionAndDrugTemporalChar.csv")

# Example 3:
performTemporalCharacterization(
	connectionDetails     = connectionDetails,
	cdmDatabaseSchema     = "cdm",
	resultsDatabaseSchema = "results",
 outputFolder          = "output/CompleteTemporalChar.csv")

## End(Not run)

## Not run: 
# Example 1:
pneumonia <- 255848
performTemporalCharacterization(
	connectionDetails     = connectionDetails,
	cdmDatabaseSchema     = "cdm",
	resultsDatabaseSchema = "results",
	conceptId             = pneumonia,
 outputFolder          = "output/pneumoniaTemporalChar.csv")

# Example 2:
performTemporalCharacterization(
	connectionDetails     = connectionDetails,
	cdmDatabaseSchema     = "cdm",
	resultsDatabaseSchema = "results",
	analysisIds           = c(402,702),
 outputFolder          = "output/conditionAndDrugTemporalChar.csv")

# Example 3:
performTemporalCharacterization(
	connectionDetails     = connectionDetails,
	cdmDatabaseSchema     = "cdm",
	resultsDatabaseSchema = "results",
 outputFolder          = "output/CompleteTemporalChar.csv")

## End(Not run)

runMissingAnalyses

Description

runMissingAnalyses Automatically find and compute analyses that haven't been executed.

Usage

runMissingAnalyses(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema = cdmDatabaseSchema,
  scratchDatabaseSchema = resultsDatabaseSchema,
  vocabDatabaseSchema = cdmDatabaseSchema,
  tempEmulationSchema = resultsDatabaseSchema,
  outputFolder = "output",
  defaultAnalysesOnly = TRUE
)
runMissingAnalyses(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema = cdmDatabaseSchema,
  scratchDatabaseSchema = resultsDatabaseSchema,
  vocabDatabaseSchema = cdmDatabaseSchema,
  tempEmulationSchema = resultsDatabaseSchema,
  outputFolder = "output",
  defaultAnalysesOnly = TRUE
)

Arguments

`connectionDetails`	An R object of type `connectionDetails` created using the function `createConnectionDetails` in the `DatabaseConnector` package.
`cdmDatabaseSchema`	Fully qualified name of database schema that contains OMOP CDM schema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_instance.dbo'.
`resultsDatabaseSchema`	Fully qualified name of database schema that we can write final results to. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_results.dbo'.
`scratchDatabaseSchema`	Fully qualified name of the database schema that will store all of the intermediate scratch tables, so for example, on SQL Server, 'cdm_scratch.dbo'. Must be accessible to/from the cdmDatabaseSchema and the resultsDatabaseSchema. Default is resultsDatabaseSchema. Making this "#" will run Achilles in single-threaded mode and use temporary tables instead of permanent tables.
`vocabDatabaseSchema`	String name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.
`tempEmulationSchema`	Formerly tempEmulationSchema. For databases like Oracle where you must specify the name of the database schema where you want all temporary tables to be managed. Requires create/insert permissions to this database.
`outputFolder`	Path to store logs and SQL files
`defaultAnalysesOnly`	Boolean to determine if only default analyses should be run. Including non-default analyses is substantially more resource intensive. Default = TRUE

Value

No return value. Run to execute analyses currently missing from results.

Examples

## Not run: 
Achilles::runMissingAnalyses(connectionDetails = connectionDetails,
                             cdmDatabaseSchema = "cdm",
                             resultsDatabaseSchema = "results",

  outputFolder = "/tmp")

## End(Not run)

## Not run: 
Achilles::runMissingAnalyses(connectionDetails = connectionDetails,
                             cdmDatabaseSchema = "cdm",
                             resultsDatabaseSchema = "results",

  outputFolder = "/tmp")

## End(Not run)

showReportTypes

Description

showReportTypes Displays the Report Types that can be passed as vector values to exportToJson.

Usage

showReportTypes()
showReportTypes()

Details

exportToJson supports the following report types: "CONDITION","CONDITION_ERA", "DASHBOARD", "DATA_DENSITY", "DEATH", "DRUG", "DRUG_ERA", "META", "OBSERVATION", "OBSERVATION_PERIOD", "PERSON", "PROCEDURE","VISIT"

Value

none (opens the allReports vector in a View() display)

Examples

## Not run: 
showReportTypes()

## End(Not run)
## Not run: 
showReportTypes()

## End(Not run)

For a monhtly time series, compute sum and proportion by month across all years

Description

For a monhtly time series, compute sum and proportion by month across all years

Usage

sumAcrossYears(tsData)
sumAcrossYears(tsData)

Arguments

tsData

A time series object

Value

A data frame reporting the monthly sum across all years and the proportion this sum contributes to the total.

Trim a monthly time series object to so that partial years are removed

Description

Trim a monthly time series object to so that partial years are removed

Usage

tsCompleteYears(tsData)
tsCompleteYears(tsData)

Arguments

tsData

A time series object

Details

This function is only supported for monthly time series

Value

A time series with partial years removed.

Package 'Achilles'

Help Index

achilles

Description

Usage

Arguments

Details

Value

Examples

Create indicies

Description

Usage

Arguments

Details

Value

createTimeSeries

Description

Usage

Arguments

Details

Value

Examples

Drop all possible scratch tables

Description

Usage

Arguments

Details

Value

exportConditionEraToJson

Description

Usage

Arguments

Details

Value

Examples

exportConditionToJson

Description

Usage

Arguments

Details

Value

Examples

exportDashboardToJson

Description

Usage

Arguments

Details

Value

Examples

exportDataDensityToJson

Description

Usage

Arguments

Details

Value

Examples

exportDeathToJson

Description

Usage

Arguments

Details

Value

Examples

exportDrugEraToJson

Description

Usage

Arguments

Details

Value

Examples

exportDrugToJson

Description

Usage

Arguments

Details

Value

Examples

exportMeasurementToJson

Description

Usage