Learn R Programming
⚠️There's a newer version (1.1.1) of this package.Take me there.

omopgenerics

Package overview

The omopgenerics package provides definitions of core classes and methods used by analytic pipelines that query the OMOP common data model.

#> Warning in citation("omopgenerics"): no date field in DESCRIPTION file of
#> package 'omopgenerics'
#> Warning in citation("omopgenerics"): could not determine year for
#> 'omopgenerics' from package DESCRIPTION file
#> 
#> To cite package 'omopgenerics' in publications use:
#> 
#>   Català M, Burn E (????). _omopgenerics: Methods and Classes for the
#>   OMOP Common Data Model_. R package version 0.3.1.900,
#>   <https://darwin-eu.github.io/omopgenerics/>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {omopgenerics: Methods and Classes for the OMOP Common Data Model},
#>     author = {Martí Català and Edward Burn},
#>     note = {R package version 0.3.1.900},
#>     url = {https://darwin-eu.github.io/omopgenerics/},
#>   }

If you find the package useful in supporting your research study, please consider citing this package.

Installation

You can install the development version of OMOPGenerics from GitHub with:

install.packages("pak")
pak::pkg_install("darwin-eu/omopgenerics")

And load it using the library command:

library(omopgenerics)
library(dplyr)

Core classes and methods

CDM Reference

A cdm reference is a single R object that represents OMOP CDM data. The tables in the cdm reference may be in a database, but a cdm reference may also contain OMOP CDM tables that are in dataframes/tibbles or in arrow. In the latter case the cdm reference would typically be a subset of an original cdm reference that has been derived as part of a particular analysis.

omopgenerics contains the class definition of a cdm reference and a dataframe implementation. For creating a cdm reference using a database, see the CDMConnector package (https://darwin-eu.github.io/CDMConnector/).

A cdm object can contain four type of tables:

  • Standard tables:
omopTables()
#>  [1] "person"                "observation_period"    "visit_occurrence"     
#>  [4] "visit_detail"          "condition_occurrence"  "drug_exposure"        
#>  [7] "procedure_occurrence"  "device_exposure"       "measurement"          
#> [10] "observation"           "death"                 "note"                 
#> [13] "note_nlp"              "specimen"              "fact_relationship"    
#> [16] "location"              "care_site"             "provider"             
#> [19] "payer_plan_period"     "cost"                  "drug_era"             
#> [22] "dose_era"              "condition_era"         "metadata"             
#> [25] "cdm_source"            "concept"               "vocabulary"           
#> [28] "domain"                "concept_class"         "concept_relationship" 
#> [31] "relationship"          "concept_synonym"       "concept_ancestor"     
#> [34] "source_to_concept_map" "drug_strength"         "cohort_definition"    
#> [37] "attribute_definition"  "concept_recommended"

Each one of the tables has a required columns. For example, for the person table this are the required columns:

omopColumns(table = "person")
#>  [1] "person_id"                   "gender_concept_id"          
#>  [3] "year_of_birth"               "month_of_birth"             
#>  [5] "day_of_birth"                "birth_datetime"             
#>  [7] "race_concept_id"             "ethnicity_concept_id"       
#>  [9] "location_id"                 "provider_id"                
#> [11] "care_site_id"                "person_source_value"        
#> [13] "gender_source_value"         "gender_source_concept_id"   
#> [15] "race_source_value"           "race_source_concept_id"     
#> [17] "ethnicity_source_value"      "ethnicity_source_concept_id"
  • Cohort tables We can see the cohort-related tables and their required columns.
cohortTables()
#> [1] "cohort"           "cohort_set"       "cohort_attrition" "cohort_codelist"
cohortColumns(table = "cohort")
#> [1] "cohort_definition_id" "subject_id"           "cohort_start_date"   
#> [4] "cohort_end_date"

In addition, cohorts are defined in terms of a generatedCohortSet class. For more details on this class definition see the corresponding vignette.

  • Achilles tables The Achilles R package generates descriptive statistics about the data contained in the OMOP CDM. Again, we can see the tables created and their required columns.
achillesTables()
#> [1] "achilles_analysis"     "achilles_results"      "achilles_results_dist"
achillesColumns(table = "achilles_results")
#> [1] "analysis_id" "stratum_1"   "stratum_2"   "stratum_3"   "stratum_4"  
#> [6] "stratum_5"   "count_value"
  • Other tables, these other tables can have any format.

Any table to be part of a cdm object has to fulfill 4 conditions:

  • All must share a common source.

  • The name of the tables must be lowercase.

  • The name of the column names of each table must be lowercase.

  • person and observation_period must be present.

Concept set

A concept set can be represented as either a codelist or a concept set expression. A codelist is a named list, with each item of the list containing specific concept IDs.

condition_codes <- list("diabetes" = c(201820, 4087682, 3655269),
                        "asthma" = 317009)
condition_codes <- newCodelist(condition_codes)
#> Warning: ! `codelist` contains numeric values, they are casted to integers.

condition_codes
#> 
#> ── 2 codelists ─────────────────────────────────────────────────────────────────
#> 
#> - asthma (1 codes)
#> - diabetes (3 codes)

Meanwhile, a concept set expression provides a high-level definition of concepts that, when applied to a specific OMOP CDM vocabulary version (by making use of the concept hierarchies and relationships), will result in a codelist.

condition_cs <- list(
  "diabetes" = dplyr::tibble(
    "concept_id" = c(201820, 4087682),
    "excluded" = c(FALSE, FALSE),
    "descendants" = c(TRUE, FALSE),
    "mapped" = c(FALSE, FALSE)
  ),
  "asthma" = dplyr::tibble(
    "concept_id" = 317009,
    "excluded" = FALSE,
    "descendants" = FALSE,
    "mapped" = FALSE
  )
)
condition_cs <- newConceptSetExpression(condition_cs)

condition_cs
#> 
#> ── 2 conceptSetExpressions ─────────────────────────────────────────────────────
#> 
#> - asthma (1 concept criteria)
#> - diabetes (2 concept criteria)

A cohort table

A cohort is a set of persons who satisfy one or more inclusion criteria for a duration of time and, when defined, this table in a cdm reference has a cohort table class. Cohort tables are then associated with attributes such as settings and attrition.

person <- tibble(
  person_id = 1, gender_concept_id = 0, year_of_birth = 1990,
  race_concept_id = 0, ethnicity_concept_id = 0
)
observation_period <- dplyr::tibble(
  observation_period_id = 1, person_id = 1,
  observation_period_start_date = as.Date("2000-01-01"),
  observation_period_end_date = as.Date("2023-12-31"),
  period_type_concept_id = 0
)
diabetes <- tibble(
  cohort_definition_id = 1, subject_id = 1,
  cohort_start_date = as.Date("2020-01-01"),
  cohort_end_date = as.Date("2020-01-10")
)

cdm <- cdmFromTables(
  tables = list(
    "person" = person,
    "observation_period" = observation_period,
    "diabetes" = diabetes
  ),
  cdmName = "example_cdm"
)
#> Warning: ! 5 column in person do not match expected column type:
#> • `person_id` is numeric but expected integer
#> • `gender_concept_id` is numeric but expected integer
#> • `year_of_birth` is numeric but expected integer
#> • `race_concept_id` is numeric but expected integer
#> • `ethnicity_concept_id` is numeric but expected integer
#> Warning: ! 3 column in observation_period do not match expected column type:
#> • `observation_period_id` is numeric but expected integer
#> • `person_id` is numeric but expected integer
#> • `period_type_concept_id` is numeric but expected integer
cdm$diabetes <- newCohortTable(cdm$diabetes)
#> Warning: ! 2 column in diabetes do not match expected column type:
#> • `cohort_definition_id` is numeric but expected integer
#> • `subject_id` is numeric but expected integer

cdm$diabetes
#> # A tibble: 1 × 4
#>   cohort_definition_id subject_id cohort_start_date cohort_end_date
#>                  <dbl>      <dbl> <date>            <date>         
#> 1                    1          1 2020-01-01        2020-01-10
settings(cdm$diabetes)
#> # A tibble: 1 × 2
#>   cohort_definition_id cohort_name
#>                  <int> <chr>      
#> 1                    1 cohort_1
attrition(cdm$diabetes)
#> # A tibble: 1 × 7
#>   cohort_definition_id number_records number_subjects reason_id reason          
#>                  <int>          <int>           <int>     <int> <chr>           
#> 1                    1              1               1         1 Initial qualify…
#> # ℹ 2 more variables: excluded_records <int>, excluded_subjects <int>
cohortCount(cdm$diabetes)
#> # A tibble: 1 × 3
#>   cohort_definition_id number_records number_subjects
#>                  <int>          <int>           <int>
#> 1                    1              1               1

Summarised result

A summarised result provides a standard format for the results of an analysis performed against data mapped to the OMOP CDM.

For example this format is used when we get a summary of the cdm as a whole

summary(cdm) |> 
  dplyr::glimpse()
#> Rows: 13
#> Columns: 13
#> $ result_id        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
#> $ cdm_name         <chr> "example_cdm", "example_cdm", "example_cdm", "example…
#> $ group_name       <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ group_level      <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ strata_name      <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ strata_level     <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ variable_name    <chr> "snapshot_date", "person_count", "observation_period_…
#> $ variable_level   <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA
#> $ estimate_name    <chr> "value", "count", "count", "source_name", "version", …
#> $ estimate_type    <chr> "date", "integer", "integer", "character", "character…
#> $ estimate_value   <chr> "2024-11-01", "1", "1", "", NA, "5.3", "", "", "", ""…
#> $ additional_name  <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…

and also when we summarise a cohort

summary(cdm$diabetes) |> 
  dplyr::glimpse()
#> Rows: 6
#> Columns: 13
#> $ result_id        <int> 1, 1, 2, 2, 2, 2
#> $ cdm_name         <chr> "example_cdm", "example_cdm", "example_cdm", "example…
#> $ group_name       <chr> "cohort_name", "cohort_name", "cohort_name", "cohort_…
#> $ group_level      <chr> "cohort_1", "cohort_1", "cohort_1", "cohort_1", "coho…
#> $ strata_name      <chr> "overall", "overall", "reason", "reason", "reason", "…
#> $ strata_level     <chr> "overall", "overall", "Initial qualifying events", "I…
#> $ variable_name    <chr> "number_records", "number_subjects", "number_records"…
#> $ variable_level   <chr> NA, NA, NA, NA, NA, NA
#> $ estimate_name    <chr> "count", "count", "count", "count", "count", "count"
#> $ estimate_type    <chr> "integer", "integer", "integer", "integer", "integer"…
#> $ estimate_value   <chr> "1", "1", "1", "1", "0", "0"
#> $ additional_name  <chr> "overall", "overall", "reason_id", "reason_id", "reas…
#> $ additional_level <chr> "overall", "overall", "1", "1", "1", "1"

Copy Link

Version

Install

install.packages('omopgenerics')

Monthly Downloads

2,525

Version

1.0.0

License

Apache License (>= 2)

Maintainer

Marti Catala

Last Published

February 14th, 2025

Functions in omopgenerics (1.0.0)

assertTable

Assert that an object is a table.
compute.cdm_table

Store results in a table.
combineStrata

Provide all combinations of strata levels.
cdmSource

Get the cdmSource of an object.
cdmSelect

Restrict the cdm object to a subset of tables.
cohortCodelist

Get codelist from a cohort_table object.
cohortColumns

Required columns for a generated cohort set.
emptyOmopTable

Create an empty omop table
emptyCohortTable

Create an empty cohort_table object
emptySummarisedResult

Empty summarised_result object.
cdmName

Get the name of a cdm_reference associated object
estimateTypeChoices

Choices that can be present in estimate_type column.
cdmReference

Get the cdm_reference of a cdm_table.
dropSourceTable

Drop a table from a cdm object.
dropTable

Drop a table from a cdm object. [Deprecated]
cdmVersion

Get the version of an object.
cohortCount

Get cohort counts from a cohort_table object.
checkCohortRequirements

Check whether a cohort table satisfies requirements
cohortTables

Cohort tables that a cdm reference can contain in the OMOP Common Data Model.
exportSummarisedResult

Export a summarised_result object to a csv file.
cdmFromTables

Create a cdm object from local tables
cdmDisconnect

Disconnect from a cdm object.
emptyCodelist

Empty codelist object.
emptyCdmReference

Create an empty cdm_reference
emptyAchillesTable

Create an empty achilles table
cdmTableFromSource

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.
cdmSourceType

Get the source type of a cdm_reference object.
collect.cdm_reference

Retrieves the cdm reference into a local cdm.
exportCodelist

Export a codelist object.
getCohortName

Get the cohort name of a certain cohort definition id
collect.cohort_table

To collect a cohort_table object.
emptyCodelistWithDetails

Empty codelist object.
insertTable

Insert a table to a cdm object.
isResultSuppressed

To check whether an object is already suppressed to a certain min cell count.
filterAdditional

Filter the additional_name-additional_level pair in a summarised_result
exportConceptSetExpression

Export a concept set expression.
newCdmSource

Create a cdm source object.
groupColumns

Identify variables in group_name column
pivotEstimates

Set estimates as columns
newCdmTable

Create an cdm table.
omopgenerics-package

omopgenerics: Methods and Classes for the OMOP Common Data Model
numberSubjects

Count the number of subjects that a cdm_table has.
newOmopTable

Create an omop table from a cdm table.
newLocalSource

A new local source for the cdm
listSourceTables

List tables that can be accessed though a cdm object.
importCodelist

Import a codelist.
isTableEmpty

Check if a table is empty or not
filterStrata

Filter the strata_name-strata_level pair in a summarised_result
settings.cohort_table

Get cohort settings from a cohort_table object.
settings.summarised_result

Get settings from a summarised_result object.
omopColumns

Required columns that the standard tables in the OMOP Common Data Model must have.
print.codelist_with_details

Print a codelist with details
readSourceTable

Read a table from the cdm_source and add it to to the cdm.
print.conceptSetExpression

Print a concept set expression
splitAdditional

Split additional_name and additional_level columns
getCohortId

Get the cohort definition id of a certain name
insertFromSource

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.
newCodelist

'codelist' object constructor
insertCdmTo

Insert a cdm_reference object to a different source.
validateWindowArgument

Validate a window argument. It must be a list of two elements (window start and window end), both must be integerish and window start must be lower or equal than window end.
tidyColumns

Identify tidy columns of a <summarised_result>
[[.cdm_reference

Subset a cdm reference object.
tidy.summarised_result

Turn a <summarised_result> object into a tidy tibble
strataColumns

Identify variables in strata_name column
recordCohortAttrition

Update cohort attrition.
splitAll

Split all pairs name-level into columns.
toSnakeCase

Convert a character vector to snake case
validateColumn

Validate whether a variable points to a certain exiting column in a table.
tmpPrefix

Create a temporary prefix for tables, that contains a unique prefix that starts with tmp.
validateCohortIdArgument

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).
sourceType

Get the source type of an object.
settingsColumns

Identify settings columns of a <summarised_result>
validateCohortArgument

Validate a cohort table input.
validateCdmTable

Validate if a table is a valid cdm_table object.
newCodelistWithDetails

'codelist' object constructor
print.cdm_reference

Print a CDM reference object
print.codelist

Print a codelist
getPersonIdentifier

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.
newCdmReference

cdm_reference objects constructor
filterGroup

Filter the group_name-group_level pair in a summarised_result
newCohortTable

cohort_table objects constructor.
filterSettings

Filter a <summarised_result> using the settings
newConceptSetExpression

'conceptSetExpression' object constructor
newAchillesTable

Create an achilles table from a cdm_table.
importConceptSetExpression

Import a concept set expression.
validateOmopTable

Validate an omop_table
validateNewColumn

Validate a new column of a table
reexports

Objects exported from other packages
numberRecords

Count the number of records that a cdm_table has.
newSummarisedResult

'summarised_results' object constructor
importSummarisedResult

Import a set of summarised results.
validateNameLevel

Validate if two columns are valid Name-Level pair.
splitGroup

Split group_name and group_level columns
resultColumns

Required columns that the result tables must have.
validateCdmArgument

Validate if an object in a valid cdm_reference.
validateAgeGroupArgument

Validate the ageGroup argument. It must be a list of two integerish numbers lower age and upper age, both of the must be greater or equal to 0 and lower age must be lower or equal to the upper age. If not named automatic names will be given in the output list.
splitStrata

Split strata_name and strata_level columns
tableName

Get the table name of a cdm_table.
tableSource

Get the table source of a cdm_table.
omopTables

Standard tables that a cdm reference can contain in the OMOP Common Data Model.
omopTableFields

Return a table of omop cdm fields informations
summary.summarised_result

Summary a summarised_result
uniteStrata

Unite one or more columns in strata_name-strata_level format
uniqueTableName

Create a unique table name
summary.cohort_table

Summary a generated cohort set
uniqueId

Get a unique Identifier with a certain number of characters and a prefix.
validateAchillesTable

Validate if a cdm_table is a valid achilles table.
validateConceptSetArgument

Validate conceptSet argument. It can either be a list, a codelist, a conceptSetExpression or a codelist with details. The output will always be a codelist.
resultPackageVersion

Check if different packages version are used for summarise_results object
validateNameStyle

Validate nameStyle argument. If any of the element in ... has length greater than 1 it must be contained in nameStyle. Note that snake case notation is used.
validateNameArgument

Validate name argument. It must be a snake_case character vector. You can add the a cdm object to check name is not already used in that cdm.
settings

Get settings from an object.
[[<-.cdm_reference

Assign a table to a cdm reference.
suppress.summarised_result

Function to suppress counts in result objects
validateStrataArgument

To validate a strata list. It makes sure that elements are unique and point to columns in table.
uniteAdditional

Unite one or more columns in additional_name-additional_level format
suppress

Function to suppress counts in result objects
uniteGroup

Unite one or more columns in group_name-group_level format
validateResultArgument

Validate if a an object is a valid 'summarised_result' object.
summary.cdm_reference

Summary a cdm reference
achillesColumns

Required columns for each of the achilles result tables
assertLogical

Assert that an object is a logical.
assertClass

Assert that an object has a certain class.
achillesTables

Names of the tables that contain the results of achilles analyses
assertDate

Assert Date
addSettings

Add settings columns to a <summarised_result> object
assertCharacter

Assert that an object is a character and fulfill certain conditions.
additionalColumns

Identify variables in additional_name column
assertList

Assert that an object is a list.
bind

Bind two or more objects of the same class.
bind.summarised_result

Bind two or summarised_result objects
bind.cohort_table

Bind two or more cohort tables
$<-.cdm_reference

Assign an table to a cdm reference.
assertNumeric

Assert that an object is a numeric.
attrition.cohort_table

Get cohort attrition from a cohort_table object.
$.cdm_reference

Subset a cdm reference object.
assertChoice

Assert that an object is within a certain oprtions.
assertTrue

Assert that an expression is TRUE.
attrition

Get attrition from an object.