Help for package CodelistGenerator

Title:

Identify Relevant Clinical Codes and Evaluate Their Use

Version:

3.5.0

Description:

Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.

License:

Apache License (≥ 2)

Encoding:

UTF-8

RoxygenNote:

7.3.2

Depends:

R (≥ 4.1)

Imports:

DBI (≥ 1.1.0), dplyr (≥ 1.1.0), omopgenerics (≥ 1.1.1), rlang (≥ 1.0.0), glue (≥ 1.5.0), stringr (≥ 1.4.0), stringi (≥ 1.8.1), tidyr (≥ 1.2.0), cli (≥ 3.1.0), purrr, clock, PatientProfiles (≥ 1.3.1), vctrs, jsonlite, lifecycle

Suggests:

covr, duckdb, CDMConnector (≥ 1.7.0), visOmopResults (≥ 1.0.0), knitr, rmarkdown, testthat (≥ 3.0.0), RPostgres, odbc, spelling, tibble, gt, flextable, omock, CohortConstructor

Config/testthat/edition:

Config/testthat/parallel:

true

VignetteBuilder:

knitr

URL:

https://darwin-eu.github.io/CodelistGenerator/

Language:

en-US

NeedsCompilation:

Packaged:

2025-04-10 16:24:02 UTC; eburn

Author:

Edward Burn

[aut, cre], Marti Catala

[ctb], Xihang Chen

[aut], Nuria Mercade-Besora

[aut], Mike Du

[ctb], Danielle Newby

[ctb], Marta Alcalde-Herraiz

[ctb]

Maintainer:

Edward Burn <edward.burn@ndorms.ox.ac.uk>

Repository:

CRAN

Date/Publication:

2025-04-10 19:20:39 UTC

CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

Description

Author(s)

Maintainer: Edward Burn edward.burn@ndorms.ox.ac.uk (ORCID)

Authors:

Xihang Chen xihang.chen@ndorms.ox.ac.uk (ORCID)
Nuria Mercade-Besora nuria.mercadebesora@ndorms.ox.ac.uk (ORCID)

Other contributors:

Marti Catala marti.catalasabate@ndorms.ox.ac.uk (ORCID) [contributor]
Mike Du mike.du@ndorms.ox.ac.uk (ORCID) [contributor]
Danielle Newby danielle.newby@ndorms.ox.ac.uk (ORCID) [contributor]
Marta Alcalde-Herraiz marta.alcaldeherraiz@ndorms.ox.ac.uk (ORCID) [contributor]

Helper for consistent documentation of `.options`.

Description

Helper for consistent documentation of .options.

Arguments

.options

Named list with additional formatting options. visOmopResults::tableOptions() shows allowed arguments and their default values.

Helper for consistent documentation of `ageGroup`.

Description

Helper for consistent documentation of ageGroup.

Arguments

ageGroup

If not NULL, a list of ageGroup vectors of length two.

Get the names of all available Anatomical Therapeutic Chemical (ATC) classification codes

Description

Get the names of all available Anatomical Therapeutic Chemical (ATC) classification codes

Usage

availableATC(cdm, level = c("ATC 1st"))

Arguments

cdm

A cdm reference via CDMConnector.

level

ATC level. Can be one or more of "ATC 1st", "ATC 2nd", "ATC 3rd", "ATC 4th", and "ATC 5th".

Value

A vector containing the names of ATC codes for the chosen level(s) found in the concept table of cdm.

Examples


cdm <- mockVocabRef()
availableATC(cdm)

Get the names of all International Classification of Diseases (ICD) 10 codes

Description

Get the names of all International Classification of Diseases (ICD) 10 codes

Usage

availableICD10(cdm, level = c("ICD10 Chapter", "ICD10 SubChapter"))

Arguments

cdm

A cdm reference via CDMConnector.

level

Can be either "ICD10 Chapter", "ICD10 SubChapter", "ICD10 Hierarchy", or "ICD10 Code".

Value

A vector containing the names of all ICD-10 codes for the chosen level(s) found in the concept table of cdm.

Examples


cdm <- mockVocabRef()
availableICD10(cdm)

Get the names of all available drug ingredients

Description

Get the names of all available drug ingredients

Usage

availableIngredients(cdm)

Arguments

cdm

A cdm reference via CDMConnector.

Value

A vector containing the concept names for all ingredient level codes found in the concept table of cdm.

Examples


cdm <- mockVocabRef()
availableIngredients(cdm)

Add the achilles tables with specified analyses

Description

If the cdm reference does not contain the achilles tables, this function will create them for the analyses used by other functions in the package.

Usage

buildAchillesTables(cdm, achillesId = NULL)

Arguments

cdm

A cdm reference via CDMConnector.

achillesId

A vector of achilles ids. If NULL default analysis will be used.

Value

The cdm_reference object with the achilles tables populated.

Examples


dbName <- "GiBleed"
CDMConnector::requireEunomia(dbName)
con <- duckdb::dbConnect(duckdb::duckdb(), CDMConnector::eunomiaDir(dbName))
cdm <- CDMConnector::cdmFromCon(
  con = con, cdmSchema = "main", writeSchema = "main"
)

cdm <- buildAchillesTables(cdm = cdm)

Helper for consistent documentation of `byConcept`.

Description

Helper for consistent documentation of byConcept.

Arguments

byConcept

TRUE or FALSE. If TRUE code use will be summarised by concept.

Helper for consistent documentation of `bySex`.

Description

Helper for consistent documentation of bySex.

Arguments

bySex

TRUE or FALSE. If TRUE code use will be summarised by sex.

Helper for consistent documentation of `byYear`.

Description

Helper for consistent documentation of byYear.

Arguments

byYear

TRUE or FALSE. If TRUE code use will be summarised by year.

Helper for consistent documentation of `cdm`.

Description

Helper for consistent documentation of cdm.

Arguments

cdm

A cdm reference via CDMConnector.

Get concept ids from JSON files containing cohort definitions

Description

Get concept ids from JSON files containing cohort definitions

Usage

codesFromCohort(path, cdm, type = c("codelist"))

Arguments

path

Path to a file or folder containing JSONs of cohort definitions.

cdm

A cdm reference via CDMConnector.

type

Can be "codelist", "codelist_with_details" or "concept_set_expression".

Value

Named list with concept_ids for each concept set.

Examples


cdm <- mockVocabRef("database")
x <- codesFromCohort(cdm = cdm,
                     path =  system.file(package = "CodelistGenerator",
                     "cohorts_for_mock"))
x
CDMConnector::cdmDisconnect(cdm)

Get concept ids from JSON files containing concept sets

Description

Get concept ids from JSON files containing concept sets

Usage

codesFromConceptSet(path, cdm, type = c("codelist"))

Arguments

path

Path to a file or folder containing JSONs of concept sets.

cdm

A cdm reference via CDMConnector.

type

Can be "codelist", "codelist_with_details" or "concept_set_expression".

Value

Named list with concept_ids for each concept set.

Examples


cdm <- mockVocabRef("database")
x <- codesFromConceptSet(cdm = cdm,
                         path =  system.file(package = "CodelistGenerator",
                         "concepts_for_mock"))
x
CDMConnector::cdmDisconnect(cdm)

Get the concepts being used in patient records

Description

Get the concepts being used in patient records

Usage

codesInUse(
  cdm,
  minimumCount = 0L,
  table = c("condition_occurrence", "device_exposure", "drug_exposure", "measurement",
    "observation", "procedure_occurrence", "visit_occurrence")
)

Arguments

cdm

A cdm reference via CDMConnector.

minimumCount

Any codes with a frequency under this will be removed.

table

cdm table of interest.

Value

A list of integers indicating codes being used in the database.

Examples


cdm <- mockVocabRef("database")
x <- codesInUse(cdm = cdm)
x
CDMConnector::cdmDisconnect(cdm)

Compare overlap between two sets of codes

Description

Compare overlap between two sets of codes

Usage

compareCodelists(codelist1, codelist2)

Arguments

codelist1

Output of getCandidateCodes or a codelist

codelist2

Output of getCandidateCodes.

Value

Tibble with information on the overlap of codes in both codelists.

Examples


cdm <- mockVocabRef()
codes1 <- getCandidateCodes(
 cdm = cdm,
 keywords = "Arthritis",
 domains = "Condition",
 includeDescendants = TRUE
)
codes2 <- getCandidateCodes(
 cdm = cdm,
 keywords = c("knee osteoarthritis", "arthrosis"),
 domains = "Condition",
 includeDescendants = TRUE
)
compareCodelists(
 codelist1 = codes1,
 codelist2 = codes2
)

Helper for consistent documentation of `countBy`.

Description

Helper for consistent documentation of countBy.

Arguments

countBy

Either "record" for record-level counts or "person" for person-level counts.

Helper for consistent documentation of `domain`.

Description

Helper for consistent documentation of domain.

Arguments

domain

Character vector with one or more of the OMOP CDM domains. The results will be restricted to the given domains. Check the available ones by running getDomains(). If NULL, all supported domains are included: Condition, Drug, Procedure, Device, Observation, and Measurement.

Helper for consistent documentation of `doseForm`.

Description

Helper for consistent documentation of doseForm.

Arguments

doseForm

Only codes with the specified dose form will be returned. If NULL, descendant codes will be returned regardless of dose form. Use 'getDoseForm()' to see the available dose forms.

Helper for consistent documentation of `doseUnit`.

Description

Helper for consistent documentation of doseUnit.

Arguments

doseUnit

Only codes with the specified dose unit will be returned. If NULL, descendant codes will be returned regardless of dose unit Use 'getDoseUnit()' to see the available dose units.

Get the descendant codes of Anatomical Therapeutic Chemical (ATC) classification codes

Description

Get the descendant codes of Anatomical Therapeutic Chemical (ATC) classification codes

Usage

getATCCodes(
  cdm,
  level = c("ATC 1st"),
  name = NULL,
  nameStyle = "{concept_code}_{concept_name}",
  doseForm = NULL,
  doseUnit = NULL,
  routeCategory = NULL,
  type = "codelist"
)

Arguments

cdm

A cdm reference via CDMConnector.

level

ATC level. Can be one or more of "ATC 1st", "ATC 2nd", "ATC 3rd", "ATC 4th", and "ATC 5th".

name

ATC name of interest. For example, c("Dermatologicals", "Nervous System"), would result in a list of length two with the descendant concepts for these two particular ATC groups.

nameStyle

Name style to apply to returned list. Can be one of "{concept_code}","{concept_id}", "{concept_name}", or a combination (i.e., "{concept_code}_{concept_name}").

doseForm

Only codes with the specified dose form will be returned. If NULL, descendant codes will be returned regardless of dose form. Use 'getDoseForm()' to see the available dose forms.

doseUnit

Only codes with the specified dose unit will be returned. If NULL, descendant codes will be returned regardless of dose unit Use 'getDoseUnit()' to see the available dose units.

routeCategory

Only codes with the specified route will be returned. If NULL, descendant codes will be returned regardless of route category. Use getRoutes() to find the available route categories.

type

Can be "codelist" or "codelist_with_details".

Value

Concepts with their format based on the type argument

Examples


library(CodelistGenerator)
cdm <- mockVocabRef()
getATCCodes(cdm = cdm, level = "ATC 1st")

Generate a candidate codelist

Description

This function generates a set of codes that can be considered for creating a phenotype using the OMOP CDM.

Usage

getCandidateCodes(
  cdm,
  keywords,
  exclude = NULL,
  domains = "Condition",
  standardConcept = "Standard",
  searchInSynonyms = FALSE,
  searchNonStandard = FALSE,
  includeDescendants = TRUE,
  includeAncestor = FALSE
)

Arguments

cdm

A cdm reference via CDMConnector.

keywords

Character vector of words to search for. Where more than one word is given (e.g. "knee osteoarthritis"), all combinations of those words should be identified positions (e.g. "osteoarthritis of knee") should be identified.

exclude

Character vector of words to identify concepts to exclude.

domains

Character vector with one or more of the OMOP CDM domain. If NULL, all supported domains are included: Condition, Drug, Procedure, Device, Observation, and Measurement.

standardConcept

Character vector with one or more of "Standard", "Classification", and "Non-standard". These correspond to the flags used for the standard_concept field in the concept table of the cdm.

searchInSynonyms

Either TRUE or FALSE. If TRUE the code will also search using both the primary name in the concept table and synonyms from the concept synonym table.

searchNonStandard

Either TRUE or FALSE. If TRUE the code will also search via non-standard concepts.

includeDescendants

Either TRUE or FALSE. If TRUE descendant concepts of identified concepts will be included in the candidate codelist. If FALSE only direct mappings from ICD-10 codes to standard codes will be returned.

includeAncestor

Either TRUE or FALSE. If TRUE the direct ancestor concepts of identified concepts will be included in the candidate codelist.

Value

A tibble with the information on the potential codes of interest.

Examples


cdm <- CodelistGenerator::mockVocabRef()
CodelistGenerator::getCandidateCodes(
  cdm = cdm,
  keywords = "osteoarthritis"
 )

Get the concept classes used in a given set of domains

Description

Get the concept classes used in a given set of domains

Usage

getConceptClassId(cdm, standardConcept = "Standard", domain = NULL)

Arguments

cdm

A cdm reference via CDMConnector.

standardConcept

Character vector with one or more of "Standard", "Classification", and "Non-standard". These correspond to the flags used for the standard_concept field in the concept table of the cdm.

domain

Value

The concept classes used for the requested domains.

Examples


cdm <- mockVocabRef()
getConceptClassId(cdm = cdm, domain = "drug")

Get descendant codes for a given concept

Description

Get descendant codes for a given concept

Usage

getDescendants(
  cdm,
  conceptId,
  withAncestor = FALSE,
  ingredientRange = c(0, Inf),
  doseForm = NULL
)

Arguments

cdm

A cdm reference via CDMConnector.

conceptId

concept_id to search

withAncestor

If TRUE, return column with ancestor. In case of multiple ancestors, concepts will be separated by ";".

ingredientRange

Used to restrict descendant codes to those associated with a specific number of drug ingredients. Must be a vector of length two with the first element the minimum number of ingredients allowed and the second the maximum. A value of c(2, 2) would restrict to only concepts associated with two ingredients.

doseForm

Only codes with the specified dose form will be returned. If NULL, descendant codes will be returned regardless of dose form. Use 'getDoseForm()' to see the available dose forms.

Value

The descendants of a given concept id.

Examples


cdm <- mockVocabRef()
getDescendants(cdm = cdm, conceptId = 1)

Get the domains available in the cdm

Description

Get the domains available in the cdm

Usage

getDomains(cdm, standardConcept = "Standard")

Arguments

cdm

A cdm reference via CDMConnector.

standardConcept

Character vector with one or more of "Standard", "Classification", and "Non-standard". These correspond to the flags used for the standard_concept field in the concept table of the cdm.

Value

A vector with the domains of the cdm.

Examples


cdm <- mockVocabRef()
getDomains(cdm = cdm)

Get the dose forms available for drug concepts

Description

Get the dose forms available for drug concepts

Usage

getDoseForm(cdm)

Arguments

cdm

A cdm reference via CDMConnector.

Value

The dose forms available for drug concepts.

Examples


cdm <- mockVocabRef()
getDoseForm(cdm = cdm)

Get available dose units

Description

Get the dose form categories available in the database (see https://doi.org/10.1002/pds.5809 for more details on how routes were classified).

Usage

getDoseUnit(cdm)

Arguments

cdm

A cdm reference via CDMConnector.

Value

A character vector with available routes.

Examples


library(CodelistGenerator)

cdm <- mockVocabRef()

getDoseUnit(cdm)

Get descendant codes of drug ingredients

Description

Get descendant codes of drug ingredients

Usage

getDrugIngredientCodes(
  cdm,
  name = NULL,
  nameStyle = "{concept_code}_{concept_name}",
  doseForm = NULL,
  doseUnit = NULL,
  routeCategory = NULL,
  ingredientRange = c(1, Inf),
  type = "codelist"
)

Arguments

cdm

A cdm reference via CDMConnector.

name

Names of ingredients of interest. For example, c("acetaminophen", "codeine"), would result in a list of length two with the descendant concepts for these two particular drug ingredients. Users can also specify the concept ID instead of the name (e.g., c(1125315, 42948451)) using a numeric vector.

nameStyle

Name style to apply to returned list. Can be one of "{concept_code}","{concept_id}", "{concept_name}", or a combination (i.e., "{concept_code}_{concept_name}").

doseForm

Only codes with the specified dose form will be returned. If NULL, descendant codes will be returned regardless of dose form. Use 'getDoseForm()' to see the available dose forms.

doseUnit

Only codes with the specified dose unit will be returned. If NULL, descendant codes will be returned regardless of dose unit Use 'getDoseUnit()' to see the available dose units.

routeCategory

Only codes with the specified route will be returned. If NULL, descendant codes will be returned regardless of route category. Use getRoutes() to find the available route categories.

ingredientRange

type

Can be "codelist" or "codelist_with_details".

Value

Concepts with their format based on the type argument.

Examples


cdm <- mockVocabRef()
getDrugIngredientCodes(cdm = cdm, name = "Adalimumab",
                       nameStyle = "{concept_name}")

Get corresponding standard codes for International Classification of Diseases (ICD) 10 codes

Description

Get corresponding standard codes for International Classification of Diseases (ICD) 10 codes

Usage

getICD10StandardCodes(
  cdm,
  level = c("ICD10 Chapter", "ICD10 SubChapter"),
  name = NULL,
  nameStyle = "{concept_code}_{concept_name}",
  includeDescendants = TRUE,
  type = "codelist"
)

Arguments

cdm

A cdm reference via CDMConnector.

level

Can be either "ICD10 Chapter", "ICD10 SubChapter", "ICD10 Hierarchy", or "ICD10 Code".

name

Name of chapter or sub-chapter of interest. If NULL, all will be considered.

nameStyle

Name style to apply to returned list. Can be one of "{concept_code}","{concept_id}", "{concept_name}", or a combination (i.e., "{concept_code}_{concept_name}").

includeDescendants

type

Can be "codelist" or "codelist_with_details".

Value

A named list, with each element containing the corresponding standard codes (and descendants) of ICD chapters and sub-chapters.

Examples


library(CodelistGenerator)
cdm <- mockVocabRef()
getICD10StandardCodes(cdm = cdm, level = c(
  "ICD10 Chapter",
  "ICD10 SubChapter"
))

Show mappings from non-standard vocabularies to standard.

Description

Show mappings from non-standard vocabularies to standard.

Usage

getMappings(
  candidateCodelist,
  cdm = NULL,
  nonStandardVocabularies = c("ATC", "ICD10CM", "ICD10PCS", "ICD9CM", "ICD9Proc",
    "LOINC", "OPCS4", "Read", "RxNorm", "RxNorm Extension", "SNOMED")
)

Arguments

candidateCodelist

Dataframe.

cdm

A cdm reference via CDMConnector.

nonStandardVocabularies

Character vector.

Value

Tibble with the information of potential standard to non-standard mappings for the codelist of interest.

Examples


cdm <- CodelistGenerator::mockVocabRef()
codes <- CodelistGenerator::getCandidateCodes(
  cdm = cdm,
  keywords = "osteoarthritis"
)
CodelistGenerator::getMappings(
  cdm = cdm,
  candidateCodelist = codes,
  nonStandardVocabularies = "READ"
)

Get available relationships between concepts

Description

Get available relationships between concepts

Usage

getRelationshipId(
  cdm,
  standardConcept1 = "standard",
  standardConcept2 = "standard",
  domains1 = "condition",
  domains2 = "condition"
)

Arguments

cdm

A cdm reference via CDMConnector.

standardConcept1

Character vector with one or more of "Standard", "Classification", and "Non-standard". These correspond to the flags used for the standard_concept field in the concept table of the cdm.

standardConcept2

Character vector with one or more of "Standard", "Classification", and "Non-standard". These correspond to the flags used for the standard_concept field in the concept table of the cdm.

domains1

Character vector with one or more of the OMOP CDM domain.

domains2

Character vector with one or more of the OMOP CDM domain.

Value

A character vector with unique concept relationship values.

Examples


cdm <- mockVocabRef()
getRelationshipId(cdm = cdm)

Get available drug routes

Description

Get the dose form categories available in the database (see https://doi.org/10.1002/pds.5809) for more details on how routes were classified).

Usage

getRouteCategories(cdm)

Arguments

cdm

A cdm reference via CDMConnector.

Value

A character vector with all available routes.

Examples


library(CodelistGenerator)

cdm <- mockVocabRef()

getRouteCategories(cdm)

Get the version of the vocabulary used in the cdm

Description

Get the version of the vocabulary used in the cdm

Usage

getVocabVersion(cdm)

Arguments

cdm

A cdm reference via CDMConnector.

Value

The vocabulary version being used in the cdm.

Examples


cdm <- mockVocabRef()
getVocabVersion(cdm = cdm)

Get the vocabularies available in the cdm

Description

Get the vocabularies available in the cdm

Usage

getVocabularies(cdm)

Arguments

cdm

A cdm reference via CDMConnector.

Value

Names of available vocabularies.

Examples


cdm <- mockVocabRef()
getVocabularies(cdm = cdm)

Helper for consistent documentation of `groupColumn`.

Description

Helper for consistent documentation of groupColumn.

Arguments

groupColumn

Variables to use as group labels. Allowed columns are: "cdm_name", "codelist_name", "domain_id", "standard_concept_name", "standard_concept_id", "estimate_name", "standard_concept", "vocabulary_id". These cannot be used in header.

Helper for consistent documentation of `groupColumn`.

Description

Helper for consistent documentation of groupColumn.

Arguments

groupColumn

Variables to use as group labels. Allowed columns are: "cdm_name", "codelist_name", "standard_concept_name", "standard_concept_id", "estimate_name", "source_concept_name", "source_concept_id", "domain_id". If results are stratified, "year", "sex", "age_group" can also be used. These cannot be used in header.

Helper for consistent documentation of `header`.

Description

Helper for consistent documentation of header.

Arguments

header

A vector specifying the elements to include in the header. The order of elements matters, with the first being the topmost header. The header vector can contain one of the following variables: "cdm_name", "codelist_name", "domain_id", "standard_concept_name", "standard_concept_id", "estimate_name", "standard_concept", "vocabulary_id". Alternatively, it can include other names to use as overall header labels.

Helper for consistent documentation of `header`.

Description

Helper for consistent documentation of header.

Arguments

header

A vector specifying the elements to include in the header. The order of elements matters, with the first being the topmost header. The header vector can contain one of the following variables: "cdm_name", "codelist_name", "standard_concept_name", "standard_concept_id", "estimate_name", "source_concept_name", "source_concept_id", "domain_id". If results are stratified, "year", "sex", "age_group" can also be used. Alternatively, it can include other names to use as overall header labels.

Helper for consistent documentation of `hide`.

Description

Helper for consistent documentation of hide.

Arguments

hide

Table columns to exclude, options are: "cdm_name", "codelist_name", "domain_id", "standard_concept_name", "standard_concept_id", "estimate_name", "standard_concept", "vocabulary_id". These cannot be used in header or groupColumn.

Helper for consistent documentation of `hide`.

Description

Helper for consistent documentation of hide.

Arguments

hide

Table columns to exclude, options are: "cdm_name", "codelist_name", "year", "sex", "age_group", "standard_concept_name", "standard_concept_id", "estimate_name", "source_concept_name", "source_concept_id", "domain_id". If results are stratified, "year", "sex", "age_group" can also be used. These cannot be used in header or groupColumn.

Helper for consistent documentation of `includeDescendants`.

Description

Helper for consistent documentation of includeDescendants.

Arguments

includeDescendants

Helper for consistent documentation of `ingredientRange`.

Description

Helper for consistent documentation of ingredientRange.

Arguments

ingredientRange

Helper for consistent documentation of `keepOriginal`.

Description

Helper for consistent documentation of keepOriginal.

Arguments

keepOriginal

Whether to keep the original codelist and append the stratify (if TRUE) or just return the stratified codelist (if FALSE).

Helper for consistent documentation of `level`.

Description

Helper for consistent documentation of level.

Arguments

level

ATC level. Can be one or more of "ATC 1st", "ATC 2nd", "ATC 3rd", "ATC 4th", and "ATC 5th".

Helper for consistent documentation of `level`.

Description

Helper for consistent documentation of level.

Arguments

level

Can be either "ICD10 Chapter", "ICD10 SubChapter", "ICD10 Hierarchy", or "ICD10 Code".

Helper for consistent documentation of `minimumCount`.

Description

Helper for consistent documentation of minimumCount.

Arguments

minimumCount

Any codes with a frequency under this will be removed.

Generate example vocabulary database

Description

Generate example vocabulary database

Usage

mockVocabRef(backend = "data_frame")

Arguments

backend

'database' (duckdb) or 'data_frame'.

Value

cdm reference with mock vocabulary.

Examples


library(CodelistGenerator)
cdm <- mockVocabRef()
cdm

Helper for consistent documentation of `nameStyle`.

Description

Helper for consistent documentation of nameStyle.

Arguments

nameStyle

Name style to apply to returned list. Can be one of "{concept_code}","{concept_id}", "{concept_name}", or a combination (i.e., "{concept_code}_{concept_name}").

Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

omopgenerics: cohortCodelist, exportCodelist, exportConceptSetExpression, importCodelist, importConceptSetExpression, newCodelist, newCodelistWithDetails, newConceptSetExpression

Helper for consistent documentation of `routeCategory`.

Description

Helper for consistent documentation of routeCategory.

Arguments

routeCategory

Only codes with the specified route will be returned. If NULL, descendant codes will be returned regardless of route category. Use getRoutes() to find the available route categories.

Get the source codes being used in patient records

Description

Get the source codes being used in patient records

Usage

sourceCodesInUse(
  cdm,
  table = c("condition_occurrence", "device_exposure", "drug_exposure", "measurement",
    "observation", "procedure_occurrence", "visit_occurrence")
)

Arguments

cdm

A cdm reference via CDMConnector.

table

cdm table of interest.

Value

A list of source codes used in the database.

Examples


cdm <- mockVocabRef("database")
x <- sourceCodesInUse(cdm = cdm)
x
CDMConnector::cdmDisconnect(cdm)

Helper for consistent documentation of `standardConcept`.

Description

Helper for consistent documentation of standardConcept.

Arguments

standardConcept

Character vector with one or more of "Standard", "Classification", and "Non-standard". These correspond to the flags used for the standard_concept field in the concept table of the cdm.

Stratify a codelist by the concepts included within it.

Description

Stratify a codelist by the concepts included within it.

Usage

stratifyByConcept(x, cdm, keepOriginal = FALSE)

Arguments

x

A codelist.

cdm

A cdm reference via CDMConnector.

keepOriginal

Whether to keep the original codelist and append the stratify (if TRUE) or just return the stratified codelist (if FALSE).

Value

The codelist or a codelist with details with the required stratifications, as different elements of the list.

Examples


library(CodelistGenerator)
cdm <- mockVocabRef()
codes <- list("concepts" = c(20,21))
new_codes <- stratifyByConcept(x = codes,
                               cdm = cdm,
                               keepOriginal = TRUE)
new_codes

Stratify a codelist by dose unit.

Description

Stratify a codelist by dose unit.

Usage

stratifyByDoseUnit(x, cdm, keepOriginal = FALSE)

Arguments

x

A codelist.

cdm

A cdm reference via CDMConnector.

keepOriginal

Whether to keep the original codelist and append the stratify (if TRUE) or just return the stratified codelist (if FALSE).

Value

The codelist with the required stratifications, as different elements of the list.

Examples


library(CodelistGenerator)
cdm <- mockVocabRef()
codes <- list("concepts" = c(20,21))
new_codes <- stratifyByDoseUnit(x = codes,
                                cdm = cdm,
                                keepOriginal = TRUE)
new_codes

Stratify a codelist by route category.

Description

Stratify a codelist by route category.

Usage

stratifyByRouteCategory(x, cdm, keepOriginal = FALSE)

Arguments

x

A codelist.

cdm

A cdm reference via CDMConnector.

keepOriginal

Whether to keep the original codelist and append the stratify (if TRUE) or just return the stratified codelist (if FALSE).

Value

The codelist with the required stratifications, as different elements of the list.

Examples


library(CodelistGenerator)
cdm <- mockVocabRef()
codes <- list("concepts" = c(20,21))
new_codes <- stratifyByRouteCategory(x = codes,
                                     cdm = cdm,
                                     keepOriginal = TRUE)
new_codes

Subset a codelist to only those codes from a particular domain.

Description

Subset a codelist to only those codes from a particular domain.

Usage

subsetOnDomain(x, cdm, domain, negate = FALSE)

Arguments

x

A codelist.

cdm

A cdm reference via CDMConnector.

domain

negate

If FALSE, only concepts with the domain specified will be returned. If TRUE, concepts with the domain specified will be excluded.

Value

The codelist with only those concepts associated with the domain (if negate = FALSE) or the codelist without those concepts associated with the domain (if negate = TRUE).

Examples


library(CodelistGenerator)
cdm <- mockVocabRef()
codes <- subsetOnDomain(
              x = list("codes" = c(10,13,15)),
              cdm = cdm,
              domain = "Drug")
codes

Subset a codelist to only those with a particular dose unit.

Description

Subset a codelist to only those with a particular dose unit.

Usage

subsetOnDoseUnit(x, cdm, doseUnit, negate = FALSE)

Arguments

x

A codelist.

cdm

A cdm reference via CDMConnector.

doseUnit

Only codes with the specified dose unit will be returned. If NULL, descendant codes will be returned regardless of dose unit Use 'getDoseUnit()' to see the available dose units.

negate

If FALSE, only concepts with the dose unit specified will be returned. If TRUE, concepts with the dose unit specified will be excluded.

Value

The codelist with only those concepts associated with the dose unit (if negate = FALSE) or codelist without those concepts associated with the dose unit(if negate = TRUE).

Examples


library(CodelistGenerator)
cdm <- mockVocabRef()
codes <- subsetOnDoseUnit(x = list("codes" = c(20,21)),
                          cdm = cdm,
                          doseUnit = c("milligram"))

codes

Subset a codelist to only those with a particular route category

Description

Subset a codelist to only those with a particular route category

Usage

subsetOnRouteCategory(x, cdm, routeCategory, negate = FALSE)

Arguments

x

A codelist.

cdm

A cdm reference via CDMConnector.

routeCategory

Only codes with the specified route will be returned. If NULL, descendant codes will be returned regardless of route category. Use getRoutes() to find the available route categories.

negate

If FALSE, only concepts with the routeCategory specified will be returned. If TRUE, concepts with the routeCategory specified will be excluded.

Value

The codelist with only those concepts associated with the specified route categories (if negate is FALSE) or the codelist without those concepts associated with the specified route categories (if negate is TRUE).

Examples


library(CodelistGenerator)
cdm <- mockVocabRef()
codes <- subsetOnRouteCategory(
              x = list("codes" = c(20,21)),
              cdm = cdm,
              routeCategory = "topical")
codes

Filter a codelist to keep only the codes being used in patient records

Description

Filter a codelist to keep only the codes being used in patient records

Usage

subsetToCodesInUse(
  x,
  cdm,
  minimumCount = 0L,
  table = c("condition_occurrence", "device_exposure", "drug_exposure", "measurement",
    "observation", "procedure_occurrence", "visit_occurrence")
)

Arguments

x

A codelist.

cdm

A cdm reference via CDMConnector.

minimumCount

Any codes with a frequency under this will be removed.

table

cdm table of interest.

Value

The filtered codelist with only the codes used in the database

Examples


cdm <- mockVocabRef("database")
codes <- getCandidateCodes(cdm = cdm,
                           keywords = "arthritis",
                           domains = "Condition",
                           includeDescendants = FALSE)
x <- subsetToCodesInUse(list("cs1" = codes$concept_id,
                               "cs2" = 999),
                                cdm = cdm)

x
CDMConnector::cdmDisconnect(cdm)

Summarise code use from achilles counts.

Description

Summarise code use from achilles counts.

Usage

summariseAchillesCodeUse(x, cdm, countBy = c("record", "person"))

Arguments

x

A codelist.

cdm

A cdm reference via CDMConnector.

countBy

Either "record" for record-level counts or "person" for person-level counts.

Value

A tibble with summarised counts.

Examples


cdm <- mockVocabRef("database")
oa <- getCandidateCodes(cdm = cdm, keywords = "osteoarthritis")
result_achilles <- summariseAchillesCodeUse(list(oa = oa$concept_id), cdm = cdm)
result_achilles
CDMConnector::cdmDisconnect(cdm)

Summarise code use in patient-level data.

Description

Summarise code use in patient-level data.

Usage

summariseCodeUse(
  x,
  cdm,
  countBy = c("record", "person"),
  byConcept = TRUE,
  byYear = FALSE,
  bySex = FALSE,
  ageGroup = NULL,
  dateRange = as.Date(c(NA, NA))
)

Arguments

x

A codelist.

cdm

A cdm reference via CDMConnector.

countBy

Either "record" for record-level counts or "person" for person-level counts.

byConcept

TRUE or FALSE. If TRUE code use will be summarised by concept.

byYear

TRUE or FALSE. If TRUE code use will be summarised by year.

bySex

TRUE or FALSE. If TRUE code use will be summarised by sex.

ageGroup

If not NULL, a list of ageGroup vectors of length two.

dateRange

Two dates. The first indicating the earliest cohort start date and the second indicating the latest possible cohort end date. If NULL or the first date is set as missing, the earliest observation_start_date in the observation_period table will be used for the former. If NULL or the second date is set as missing, the latest observation_end_date in the observation_period table will be used for the latter.

Value

A tibble with count results overall and, if specified, by strata.

Examples

## Not run: 
con <- DBI::dbConnect(duckdb::duckdb(),
                      dbdir = CDMConnector::eunomiaDir())
cdm <- CDMConnector::cdmFromCon(con,
                                cdmSchema = "main",
                                writeSchema = "main")
acetiminophen <- c(1125315,  1127433, 40229134,
40231925, 40162522, 19133768,  1127078)
poliovirus_vaccine <- c(40213160)
cs <- list(acetiminophen = acetiminophen,
          poliovirus_vaccine = poliovirus_vaccine)
results <- summariseCodeUse(cs,cdm = cdm)
results
CDMConnector::cdmDisconnect(cdm)

## End(Not run)

Summarise code use among a cohort in the cdm reference

Description

Summarise code use among a cohort in the cdm reference

Usage

summariseCohortCodeUse(
  x,
  cdm,
  cohortTable,
  cohortId = NULL,
  timing = "any",
  countBy = c("record", "person"),
  byConcept = TRUE,
  byYear = FALSE,
  bySex = FALSE,
  ageGroup = NULL
)

Arguments

x

A codelist.

cdm

A cdm reference via CDMConnector.

cohortTable

A cohort table from the cdm reference.

cohortId

A vector of cohort IDs to include

timing

When to assess the code use relative cohort dates. This can be "any"(code use any time by individuals in the cohort) or "entry" (code use on individuals' cohort start date).

countBy

Either "record" for record-level counts or "person" for person-level counts.

byConcept

TRUE or FALSE. If TRUE code use will be summarised by concept.

byYear

TRUE or FALSE. If TRUE code use will be summarised by year.

bySex

TRUE or FALSE. If TRUE code use will be summarised by sex.

ageGroup

If not NULL, a list of ageGroup vectors of length two.

Value

A tibble with results overall and, if specified, by strata

Examples

## Not run: 
library(CodelistGenerator)
library(duckdb)
library(DBI)
library(CDMConnector)
con <- dbConnect(duckdb(),
                 dbdir = eunomiaDir())
cdm <- cdmFromCon(con,
                 cdmSchema = "main",
                 writeSchema = "main")
cdm <- generateConceptCohortSet(cdm = cdm,
                  conceptSet = list(a = 260139,
                                    b = 1127433),
                  name = "cohorts",
                  end = "observation_period_end_date",
                  overwrite = TRUE)

results_cohort_mult <-
summariseCohortCodeUse(list(cs = c(260139,19133873)),
                      cdm = cdm,
                      cohortTable = "cohorts",
                      timing = "entry")

results_cohort_mult
CDMConnector::cdmDisconnect(cdm)

## End(Not run)

Find orphan codes related to a codelist using achilles counts and, if available, PHOEBE concept recommendations

Description

Find orphan codes related to a codelist using achilles counts and, if available, PHOEBE concept recommendations

Usage

summariseOrphanCodes(
  x,
  cdm,
  domain = c("condition", "device", "drug", "measurement", "observation", "procedure",
    "visit")
)

Arguments

x

A codelist.

cdm

A cdm reference via CDMConnector.

domain

Value

A summarised result containg the frequency of codes related to (but not in) the codelist.

Examples


cdm <- mockVocabRef("database")
codes <- getCandidateCodes(cdm = cdm,
keywords = "Musculoskeletal disorder",
domains = "Condition",
includeDescendants = FALSE)

orphan_codes <- summariseOrphanCodes(x = list("msk" = codes$concept_id),
cdm = cdm)

orphan_codes
CDMConnector::cdmDisconnect(cdm)

Find unmapped concepts related to codelist

Description

Find unmapped concepts related to codelist

Usage

summariseUnmappedCodes(
  x,
  cdm,
  table = c("condition_occurrence", "device_exposure", "drug_exposure", "measurement",
    "observation", "procedure_occurrence")
)

Arguments

x

A codelist.

cdm

A cdm reference via CDMConnector.

table

Names of clinical tables in which to search for unmapped codes. Can be one or more of "condition_occurrence", "device_exposure", "drug_exposure", "measurement", "observation", and "procedure_occurrence".

Value

A summarised result of unmapped concepts related to given codelist.

Examples


cdm <- mockVocabRef("database")
codes <- list("Musculoskeletal disorder" = 1)
cdm <- omopgenerics::insertTable(cdm, "condition_occurrence",
dplyr::tibble(person_id = 1,
              condition_occurrence_id = 1,
              condition_concept_id = 0,
              condition_start_date  = as.Date("2000-01-01"),
              condition_type_concept_id  = NA,
              condition_source_concept_id = 7))
summariseUnmappedCodes(x = list("osteoarthritis" = 2), cdm = cdm,
table = "condition_occurrence")

CDMConnector::cdmDisconnect(cdm)

Format the result of summariseAchillesCodeUse into a table

Description

Format the result of summariseAchillesCodeUse into a table

Usage

tableAchillesCodeUse(
  result,
  type = "gt",
  header = c("cdm_name", "estimate_name"),
  groupColumn = character(),
  hide = character(),
  .options = list()
)

Arguments

result

A ⁠<summarised_result>⁠ with results of the type "achilles_code_use".

type

Type of desired formatted table. To see supported formats use visOmopResults::tableType().

header

groupColumn

hide

.options

Named list with additional formatting options. visOmopResults::tableOptions() shows allowed arguments and their default values.

Value

A table with a formatted version of the summariseCohortCodeUse result.

Examples


cdm <- mockVocabRef("database")
oa <- getCandidateCodes(cdm = cdm, keywords = "osteoarthritis")
result_achilles <- summariseAchillesCodeUse(list(oa = oa$concept_id), cdm = cdm)
tableAchillesCodeUse(result_achilles)
CDMConnector::cdmDisconnect(cdm)

Format the result of summariseCodeUse into a table.

Description

Format the result of summariseCodeUse into a table.

Usage

tableCodeUse(
  result,
  type = "gt",
  header = c("cdm_name", "estimate_name"),
  groupColumn = character(),
  hide = character(),
  .options = list()
)

Arguments

result

A ⁠<summarised_result>⁠ with results of the type "code_use".

type

Type of desired formatted table. To see supported formats use visOmopResults::tableType().

header

A vector specifying the elements to include in the header. The order of elements matters, with the first being the topmost header. The header vector can contain one of the following variables: "cdm_name", "codelist_name", "standard_concept_name", "standard_concept_id", "estimate_name", "source_concept_name", "source_concept_id", "domain_id". If results are stratified, "year", "sex", "age_group" can also be used. Alternatively, it can include other names to use as overall header labels.

groupColumn

hide

.options

Named list with additional formatting options. visOmopResults::tableOptions() shows allowed arguments and their default values.

Value

A table with a formatted version of the summariseCodeUse result.

Examples

## Not run: 
con <- DBI::dbConnect(duckdb::duckdb(),
                      dbdir = CDMConnector::eunomiaDir())
cdm <- CDMConnector::cdmFromCon(con,
                                cdmSchema = "main",
                                writeSchema = "main")
acetiminophen <- c(1125315,  1127433, 40229134,
40231925, 40162522, 19133768,  1127078)
poliovirus_vaccine <- c(40213160)
cs <- list(acetiminophen = acetiminophen,
          poliovirus_vaccine = poliovirus_vaccine)
results <- summariseCodeUse(cs,cdm = cdm)
tableCodeUse(results)
CDMConnector::cdmDisconnect(cdm)

## End(Not run)

Format the result of summariseCohortCodeUse into a table.

Description

Format the result of summariseCohortCodeUse into a table.

Usage

tableCohortCodeUse(
  result,
  type = "gt",
  header = c("cdm_name", "estimate_name"),
  groupColumn = character(),
  hide = c("timing"),
  .options = list(),
  timing = lifecycle::deprecated()
)

Arguments

result

A ⁠<summarised_result>⁠ with results of the type "cohort_code_use".

type

Type of desired formatted table. To see supported formats use visOmopResults::tableType().

header

A vector specifying the elements to include in the header. The order of elements matters, with the first being the topmost header. The header vector can contain one of the following variables: "cdm_name", "codelist_name", "standard_concept_name", "standard_concept_id", "estimate_name", "source_concept_name", "source_concept_id", "domain_id". If results are stratified, "year", "sex", "age_group" can also be used. Alternatively, it can include other names to use as overall header labels.

groupColumn

hide

.options

Named list with additional formatting options. visOmopResults::tableOptions() shows allowed arguments and their default values.

timing

deprecated.

Value

A table with a formatted version of the summariseCohortCodeUse result.

Examples

## Not run: 
con <- DBI::dbConnect(duckdb::duckdb(),
                      dbdir = CDMConnector::eunomiaDir())
cdm <- CDMConnector::cdmFromCon(con,
                                  cdmSchema = "main",
                                  writeSchema = "main")
cdm <- CDMConnector::generateConceptCohortSet(cdm = cdm,
conceptSet = list(a = 260139,
                  b = 1127433),
                  name = "cohorts",
                  end = "observation_period_end_date",
                  overwrite = TRUE)

results_cohort_mult <-
summariseCohortCodeUse(list(cs = c(260139,19133873)),
                      cdm = cdm,
                      cohortTable = "cohorts",
                      timing = "entry")

tableCohortCodeUse(results_cohort_mult)
CDMConnector::cdmDisconnect(cdm)

## End(Not run)

Helper for consistent documentation of `table`.

Description

Helper for consistent documentation of table.

Arguments

table

cdm table of interest.

Format the result of summariseOrphanCodes into a table

Description

Format the result of summariseOrphanCodes into a table

Usage

tableOrphanCodes(
  result,
  type = "gt",
  header = c("cdm_name", "estimate_name"),
  groupColumn = character(),
  hide = character(),
  .options = list()
)

Arguments

result

A ⁠<summarised_result>⁠ with results of the type "orphan_codes".

type

Type of desired formatted table. To see supported formats use visOmopResults::tableType().

header

groupColumn

hide

.options

Named list with additional formatting options. visOmopResults::tableOptions() shows allowed arguments and their default values.

Value

A table with a formatted version of the summariseOrphanCodes result.

Examples


cdm <- mockVocabRef("database")
codes <- getCandidateCodes(cdm = cdm,
keywords = "Musculoskeletal disorder",
domains = "Condition",
includeDescendants = FALSE)

orphan_codes <- summariseOrphanCodes(x = list("msk" = codes$concept_id),
cdm = cdm)

tableOrphanCodes(orphan_codes)

CDMConnector::cdmDisconnect(cdm)

Format the result of summariseUnmappedCodeUse into a table

Description

Format the result of summariseUnmappedCodeUse into a table

Usage

tableUnmappedCodes(
  result,
  type = "gt",
  header = c("cdm_name", "estimate_name"),
  groupColumn = character(),
  hide = character(),
  .options = list()
)

Arguments

result

A ⁠<summarised_result>⁠ with results of the type "umapped_codes".

type

Type of desired formatted table. To see supported formats use visOmopResults::tableType().

header

groupColumn

hide

.options

Named list with additional formatting options. visOmopResults::tableOptions() shows allowed arguments and their default values.

Value

A table with a formatted version of the summariseUnmappedCodes result.

Examples


cdm <- mockVocabRef("database")
codes <- list("Musculoskeletal disorder" = 1)
cdm <- omopgenerics::insertTable(cdm, "condition_occurrence",
dplyr::tibble(person_id = 1,
              condition_occurrence_id = 1,
              condition_concept_id = 0,
              condition_start_date  = as.Date("2000-01-01"),
              condition_type_concept_id  = NA,
              condition_source_concept_id = 7))
unmapped_codes <- summariseUnmappedCodes(x = list("osteoarthritis" = 2),
cdm = cdm, table = "condition_occurrence")
tableUnmappedCodes(unmapped_codes)

cdm <- omopgenerics::insertTable(
 cdm,
 "measurement",
 dplyr::tibble(
   person_id = 1,
   measurement_id = 1,
   measurement_concept_id = 0,
   measurement_date  = as.Date("2000-01-01"),
   measurement_type_concept_id  = NA,
   measurement_source_concept_id = 7
 )
)
table <- summariseUnmappedCodes(x = list("cs" = 2),
                               cdm = cdm,
                               table = c("measurement"))
tableUnmappedCodes(unmapped_codes)

CDMConnector::cdmDisconnect(cdm)

Helper for consistent documentation of `type`.

Description

Helper for consistent documentation of type.

Arguments

type

Can be "codelist", "codelist_with_details" or "concept_set_expression".

Helper for consistent documentation of `type`.

Description

Helper for consistent documentation of type.

Arguments

type

Can be "codelist" or "codelist_with_details".

Helper for consistent documentation of `type`.

Description

Helper for consistent documentation of type.

Arguments

type

Type of desired formatted table. To see supported formats use visOmopResults::tableType().

Helper for consistent documentation of `x`.

Description

Helper for consistent documentation of x.

Arguments

x

A codelist.

CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

Description

Author(s)

See Also

Helper for consistent documentation of .options.

Description

Arguments

Helper for consistent documentation of ageGroup.

Description

Arguments

Get the names of all available Anatomical Therapeutic Chemical (ATC) classification codes

Description

Usage

Arguments

Value

Examples

Get the names of all International Classification of Diseases (ICD) 10 codes

Description

Usage

Arguments

Value

Examples

Get the names of all available drug ingredients

Description

Usage

Arguments

Value

Examples

Add the achilles tables with specified analyses

Description

Usage

Arguments

Value

Examples

Helper for consistent documentation of byConcept.

Description

Arguments

Helper for consistent documentation of bySex.

Description

Arguments

Helper for consistent documentation of byYear.

Description

Arguments

Helper for consistent documentation of cdm.

Description

Arguments

Get concept ids from JSON files containing cohort definitions

Description

Usage

Arguments

Value

Examples

Get concept ids from JSON files containing concept sets

Description

Usage

Arguments

Value

Examples

Get the concepts being used in patient records

Description

Usage

Arguments

Value

Examples

Compare overlap between two sets of codes

Description

Usage

Arguments

Value

Examples

Helper for consistent documentation of countBy.

Description

Arguments

Helper for consistent documentation of domain.

Description

Arguments

Helper for consistent documentation of doseForm.

Description

Arguments

Helper for consistent documentation of doseUnit.

Helper for consistent documentation of `.options`.

Helper for consistent documentation of `ageGroup`.

Helper for consistent documentation of `byConcept`.

Helper for consistent documentation of `bySex`.

Helper for consistent documentation of `byYear`.

Helper for consistent documentation of `cdm`.

Helper for consistent documentation of `countBy`.

Helper for consistent documentation of `domain`.

Helper for consistent documentation of `doseForm`.

Helper for consistent documentation of `doseUnit`.