Package: omopgenerics 0.3.1.900

Martí Català

omopgenerics: Methods and Classes for the OMOP Common Data Model

Provides definitions of core classes and methods used by analytic pipelines that query the OMOP (Observational Medical Outcomes Partnership) common data model.

Authors:Martí Català [aut, cre], Edward Burn [aut], Mike Du [ctb], Yuchen Guo [ctb], Adam Black [ctb], Marta Alcalde-Herraiz [ctb]

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omopgenerics/json (API)

# Install 'omopgenerics' in R:

install.packages('omopgenerics', repos = c('https://darwin-eu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/darwin-eu/omopgenerics/issues

On CRAN:

9.49 score 12 packages 116 scripts 1.2k downloads 90 exports 25 dependencies

Last updated 1 days agofrom:34f6f64259. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 23 2024
R-4.5-win	OK	Nov 23 2024
R-4.5-linux	OK	Nov 23 2024
R-4.4-win	OK	Nov 23 2024
R-4.4-mac	OK	Nov 23 2024
R-4.3-win	OK	Nov 23 2024
R-4.3-mac	OK	Nov 23 2024

Exports:achillesColumns achillesTables assertCharacter assertChoice assertClass assertDate assertList assertLogical assertNumeric assertTable assertTrue attrition bind cdmFromTables cdmName cdmReference cdmSelect cdmSource cdmSourceType cdmTableFromSource cdmVersion checkCohortRequirements cohortCodelist cohortColumns cohortCount cohortTables combineStrata dropSourceTable dropTable emptyAchillesTable emptyCdmReference emptyCodelist emptyCodelistWithDetails emptyCohortTable emptyOmopTable emptySummarisedResult estimateTypeChoices exportCodelist exportConceptSetExpression exportSummarisedResult filter getCohortId getCohortName getPersonIdentifier importCodelist importConceptSetExpression importSummarisedResult insertFromSource insertTable isResultSuppressed isTableEmpty listSourceTables newAchillesTable newCdmReference newCdmSource newCdmTable newCodelist newCodelistWithDetails newCohortTable newConceptSetExpression newLocalSource newOmopTable newSummarisedResult omopColumns omopTableFields omopTables participants readSourceTable recordCohortAttrition resultColumns resultPackageVersion settings sourceType suppress tableName tableSource tmpPrefix toSnakeCase uniqueId uniqueTableName validateAgeGroupArgument validateCdmArgument validateCohortArgument validateCohortIdArgument validateConceptSetArgument validateNameArgument validateNameLevel validateResultArguemnt validateResultArgument validateWindowArgument

Dependencies:blob cli cpp11 DBI dbplyr dplyr fansi generics glue lifecycle magrittr pillar pkgconfig purrr R6 rlang snakecase stringi stringr tibble tidyr tidyselect utf8 vctrs withr

The cdm reference

Rendered fromcdm_reference.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2024-07-04
Started: 2024-07-04

Concept sets

Rendered fromcodelists.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2024-07-04
Started: 2024-07-04

Cohort tables

Rendered fromcohorts.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2024-08-06
Started: 2024-07-04

A summarised result

Rendered fromsummarised_result.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2024-11-01
Started: 2024-07-04

Re-exporting functions from omopgnerics

Rendered fromreexport.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2024-10-16
Started: 2024-02-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Subset a cdm reference object.	[[.cdm_reference
Assign a table to a cdm reference.	[[<-.cdm_reference
Subset a cdm reference object.	$.cdm_reference
Assign an table to a cdm reference.	$<-.cdm_reference
Required columns for each of the achilles result tables	achillesColumns
Names of the tables that contain the results of achilles analyses	achillesTables
Assert that an object is a character and fulfill certain conditions.	assertCharacter
Assert that an object is within a certain oprtions.	assertChoice
Assert that an object has a certain class.	assertClass
Assert Date	assertDate
Assert that an object is a list.	assertList
Assert that an object is a logical.	assertLogical
Assert that an object is a numeric.	assertNumeric
Assert that an object is a table.	assertTable
Assert that an expression is TRUE.	assertTrue
Get attrition from an object.	attrition
Get cohort attrition from a cohort_table object.	attrition.cohort_table
Bind two or more objects of the same class.	bind
Bind two or more cohort tables	bind.cohort_table
Bind two or summarised_result objects	bind.summarised_result
Create a cdm object from local tables	cdmFromTables
Get the name of a cdm_reference associated object	cdmName
Get the 'cdm_reference' of a 'cdm_table'.	cdmReference
Restrict the cdm object to a subset of tables.	cdmSelect
Get the cdmSource of an object.	cdmSource
Get the source type of a cdm_reference object.	cdmSourceType
This is an internal developer focused function that creates a cdm_table from a table that shares the source but it is not a cdm_table. Please use insertTable if you want to insert a table to a cdm_reference object.	cdmTableFromSource
Get the version of an object.	cdmVersion
Check whether a cohort table satisfies requirements	checkCohortRequirements
Get codelist from a cohort_table object.	cohortCodelist
Required columns for a generated cohort set.	cohortColumns
Get cohort counts from a cohort_table object.	cohortCount
Cohort tables that a cdm reference can contain in the OMOP Common Data Model.	cohortTables
Retrieves the cdm reference into a local cdm.	collect.cdm_reference
To collect a 'cohort_table' object.	collect.cohort_table
Provide all combinations of strata levels.	combineStrata
Store results in a table.	compute.cdm_table
Drop a table from a cdm object.	dropSourceTable
Drop a table from a cdm object.	dropTable
Create an empty achilles table	emptyAchillesTable
Create an empty cdm_reference	emptyCdmReference
Empty 'codelist' object.	emptyCodelist
Empty 'codelist' object.	emptyCodelistWithDetails
Create an empty cohort_table object	emptyCohortTable
Create an empty omop table	emptyOmopTable
Empty 'summarised_result' object.	emptySummarisedResult
Choices that can be present in 'estimate_type' column.	estimateTypeChoices
Export a codelist object.	exportCodelist
Export a concept set expression.	exportConceptSetExpression
Export a summarised_result object to a csv file.	exportSummarisedResult
Get the cohort definition id of a certain name	getCohortId
Get the cohort name of a certain cohort definition id	getCohortName
Get the column name with the person identifier from a table (either subject_id or person_id), it will throw an error if it contains both or neither.	getPersonIdentifier
Import a codelist.	importCodelist
Import a concept set expression.	importConceptSetExpression
Import a set of summarised results.	importSummarisedResult
Convert a table that is not a cdm_table but have the same original source to a cdm_table. This Table is not meant to be used to insert tables in the cdm, please use insertTable instead.	insertFromSource
Insert a table to a cdm object.	insertTable
isResultSuppressed	isResultSuppressed
Check if a table is empty or not	isTableEmpty
List tables that can be accessed though a cdm object.	listSourceTables
Create an achilles table from a cdm_table.	newAchillesTable
'cdm_reference' objects constructor	newCdmReference
Create a cdm source object.	newCdmSource
Create an cdm table.	newCdmTable
'codelist' object constructor	newCodelist
'codelist' object constructor	newCodelistWithDetails
'cohort_table' objects constructor.	newCohortTable
'conceptSetExpression' object constructor	newConceptSetExpression
A new local source for the cdm	newLocalSource
Create an omop table from a cdm table.	newOmopTable
'summarised_results' object constructor	newSummarisedResult
Required columns that the standard tables in the OMOP Common Data Model must have.	omopColumns
Return a table of omop cdm fields informations	omopTableFields
Standard tables that a cdm reference can contain in the OMOP Common Data Model.	omopTables
It returns the participants that contributed to a particular analysis	participants
Print a CDM reference object	print.cdm_reference
Print a codelist	print.codelist
Print a codelist with details	print.codelist_with_details
Print a concept set expression	print.conceptSetExpression
Read a table from the cdm_source and add it to to the cdm.	readSourceTable
Update cohort attrition.	recordCohortAttrition
Required columns that the result tables must have.	resultColumns
Check if different packages version are used for summarise_results object	resultPackageVersion
Get settings from an object.	settings
Get cohort settings from a cohort_table object.	settings.cohort_table
Get settings from a summarised_result object.	settings.summarised_result
Get the source type of an object.	sourceType
Summary a cdm reference	summary.cdm_reference
Summary a generated cohort set	summary.cohort_table
Summary a summarised_result	summary.summarised_result
Function to suppress counts in result objects	suppress
Function to suppress counts in result objects	suppress.summarised_result
Get the table name of a 'cdm_table'.	tableName
Get the table source of a 'cdm_table'.	tableSource
Create a temporary prefix for tables, that contains a unique prefix that starts with tmp.	tmpPrefix
Convert a character vector to snake case	toSnakeCase
Get a unique Identifier with a certain number of characters and a prefix.	uniqueId
Create a unique table name	uniqueTableName
validateAgeGroupArgument	validateAgeGroupArgument
validateCdmArgument	validateCdmArgument
Validate a cohort table input.	validateCohortArgument
Validate cohortId argument. CohortId can either be a cohort_definition_id value, a cohort_name or a tidyselect expression referinc to cohort_names. If you want to support tidyselect expressions please use the function as: 'validateCohortIdArgument({{cohortId}}, cohort)'.	validateCohortIdArgument
Validate conceptSet argument.	validateConceptSetArgument
Validate name argument.	validateNameArgument
Validate if two columns are valid Name-Level pair.	validateNameLevel
validateResultArgument	validateResultArguemnt
validateResultArgument	validateResultArgument
validateWindowArgument	validateWindowArgument