Package 'CodelistGenerator'

Title: Identify Relevant Clinical Codes and Evaluate Their Use
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.
Authors: Edward Burn [aut, cre] , Marti Catala [ctb] , Xihang Chen [aut] , Nuria Mercade-Besora [aut] , Mike Du [ctb] , Danielle Newby [ctb]
Maintainer: Edward Burn <[email protected]>
License: Apache License (>= 2)
Version: 3.3.0
Built: 2024-11-11 09:19:46 UTC
Source: https://github.com/darwin-eu/codelistgenerator

Help Index

Get all ATC codes from the cdm

Description

Get all ATC codes from the cdm

Usage

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

Arguments

cdm

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 list of all ATC codes for the chosen level(s) found in the concept table of cdm.

Examples

cdm <- mockVocabRef()
availableATC(cdm)

Get all ICD codes from the cdm

Description

Get all ICD codes from the cdm

Usage

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

Arguments

cdm

cdm_reference via CDMConnector
level

Can be either "ICD10 Chapter" or "ICD10 SubChapter"

Value

A vector list of all ICD10 codes for the chosen level(s) found in the concept table of cdm.

Examples

cdm <- mockVocabRef()
availableICD10(cdm)

Get all ingredients codes from the cdm

Description

Get all ingredients codes from the cdm

Usage

availableIngredients(cdm)

Arguments

cdm

cdm_reference via CDMConnector

Value

A vector list of all ingredient level codes found in the concept table of cdm.

Examples

cdm <- mockVocabRef()
availableIngredients(cdm)

Get concept ids from a provided path to cohort json files

Description

Get concept ids from a provided path to cohort json files

Usage

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

Arguments

path

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

A cdm reference created with CDMConnector
type

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

Value

Named list with concept_ids for each concept set

Get concept ids from a provided path to json files

Description

Get concept ids from a provided path to json files

Usage

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

Arguments

path

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

A cdm reference created with 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)

Use achilles counts to get codes used in the database

Description

Use achilles counts to get codes used in the database

Usage

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

Arguments

cdm

cdm_reference via CDMConnector
minimumCount

Any codes with a frequency under this will be removed.
table

cdm table

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 two codelists

Description

Compare two codelists

Usage

compareCodelists(codelist1, codelist2)

Arguments

codelist1

Output of getCandidateCodes
codelist2

Output of getCandidateCodes

Value

tibble

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
)

Equivalence from dose from concept IDs to route categories.

Description

Equivalence from dose from concept IDs to route categories.

Usage

doseFormToRoute

Format

A data frame with two variables: dose_form_concept_id and route_category.

Get descendant codes for ATC levels

Description

Get descendant codes for ATC levels

Usage

getATCCodes(
  cdm,
  level = c("ATC 1st"),
  name = NULL,
  doseForm = NULL,
  doseUnit = NULL,
  routeCategory = NULL,
  type = "codelist"
)

Arguments

cdm

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.
doseForm

Only descendants codes with the specified dose form will be returned. If NULL, descendant codes will be returned regardless of dose form.
doseUnit

Only descendants codes with the specified dose unit will be returned. If NULL, descendant codes will be returned regardless of dose unit
routeCategory

Only descendants codes with the specified route will be returned. If NULL, descendant codes will be returned regardless of dose form.
type

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

Value

Concepts with their format based on the type argument.

Examples

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

Generate candidate codelist for the OMOP CDM

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

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.
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.
includeAncestor

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

Value

tibble

Examples

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

getConceptClassId

Description

getConceptClassId

Usage

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

Arguments

cdm

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

Vocabulary domain

Value

The concept class used for a given set of domains

Examples

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

getDescendants

Description

getDescendants

Usage

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

Arguments

cdm

cdm_reference via CDMConnector
conceptId

concpet_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 descendants codes with the specified drug dose form will be returned. If NULL, descendant codes will be returned regardless of dose form.

Value

The descendants of a given concept id

Examples

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

getDomains

Description

getDomains

Usage

getDomains(cdm, standardConcept = "Standard")

Arguments

cdm

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

The domains of the cdm

Examples

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

getDoseForm

Description

getDoseForm

Usage

getDoseForm(cdm)

Arguments

cdm

cdm_reference via CDMConnector

Value

The dose forms available for drug concepts

Examples

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

Get available routes in a cdm reference.

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.

Value

A character vector with available routes

Get descendant codes for drug ingredients

Description

Get descendant codes for 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

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.
nameStyle

Name style to apply to returned list. Can be one of "{concept_code}_{concept_name}", "{concept_code}", or "{concept_name}".
doseForm

Only descendants codes with the specified dose form will be returned. If NULL, descendant codes will be returned regardless of dose form.
doseUnit

Only descendants codes with the specified dose unit will be returned. If NULL, descendant codes will be returned regardless of dose unit
routeCategory

Only descendants codes with the specified route will be returned. If NULL, descendant codes will be returned regardless of route category.
ingredientRange

Used to restrict descendant codes to those associated with a specific number of 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.
type

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

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 ICD-10 chapters and sub-chapters

Description

Get corresponding standard codes for ICD-10 chapters and sub-chapters

Usage

getICD10StandardCodes(
  cdm,
  level = c("ICD10 Chapter", "ICD10 SubChapter"),
  name = NULL,
  includeDescendants = TRUE,
  type = "codelist"
)

Arguments

cdm

cdm_reference via CDMConnector
level

Can be either "ICD10 Chapter" or "ICD10 SubChapter"
name

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

If FALSE only direct mappings from ICD-10 codes to standard codes will be returned. If TRUE descendants of standard concepts will also be included.
type

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

Value

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

Examples

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

cdm_reference via CDMConnector::cdm_from_con()
nonStandardVocabularies

Character vector

Value

tibble

Examples

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

Get relationship ID values from the concept relationship table

Description

Get relationship ID values from the concept relationship table

Usage

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

Arguments

cdm

A cdm reference
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 values

Examples

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

Get available routes in a cdm reference.

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.

Value

A character vector with available routes

getVocabularies

Description

getVocabularies

Usage

getVocabularies(cdm)

Arguments

cdm

cdm_reference via CDMConnector

Value

Names of available vocabularies

Examples

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

getVocabVersion

Description

getVocabVersion

Usage

getVocabVersion(cdm)

Arguments

cdm

cdm_reference via CDMConnector

Value

the vocabulary version being used

Examples

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

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

cdm <- mockVocabRef()
cdm

Use achilles counts to get source codes used in the database

Description

Use achilles counts to get source codes used in the database

Usage

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

Arguments

cdm

cdm_reference via CDMConnector
table

cdm table

Value

A list of source codes used in the database.

Examples

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

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

Value

A codelist

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
keepOriginal

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

Value

A codelist

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
keepOriginal

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

Value

A codelist

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)

Arguments

x

Codelist
cdm

A cdm reference
domain

Domains. Use getDomains() to find the available domains in a cdm

Value

The codelist with only those concepts associated with the domain

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)

Arguments

x

Codelist
cdm

A cdm reference
doseUnit

Dose unit. Use getDoseUnit() to find the available dose units in a cdm

Value

The codelist with only those concepts associated with the dose unit

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)

Arguments

x

Codelist
cdm

A cdm reference
routeCategory

Route category. Use getRoutes() to find the available route categories for a cdm

Value

The codelist with only those concepts associated with the specified route categories

Use achilles counts to filter a codelist to keep only the codes used in the database

Description

Use achilles counts to filter a codelist to keep only the codes used in the database

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

cdm_reference via CDMConnector
minimumCount

Any codes with a frequency under this will be removed.
table

cdm table

Value

Use achilles counts to filter codelist to 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

Codelist
cdm

cdm_reference via CDMConnector::cdm_from_con()
countBy

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

Value

A tibble with results

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
)

Arguments

x

List of concept IDs
cdm

cdm_reference via CDMConnector::cdm_from_con()
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: 
con <- DBI::dbConnect(duckdb::duckdb(),
                      dbdir = CDMConnector::eunomia_dir())
cdm <- CDMConnector::cdm_from_con(con,
                                  cdm_schem = "main",
                                  write_schema = "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

Vector of concept IDs
cdm

cdm_reference via CDMConnector::cdm_from_con()
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
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: 
con <- DBI::dbConnect(duckdb::duckdb(),
                      dbdir = CDMConnector::eunomia_dir())
cdm <- CDMConnector::cdm_from_con(con,
                                  cdm_schem = "main",
                                  write_schema = "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")

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 for which to find related codes used in the database
cdm

cdm_reference via CDMConnector
domain

The domains to restrict results too. Only concepts from these domains will be returned.

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)

Findunmapped concepts related to codelist

Description

Findunmapped 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
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

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"),
  groupColumns = 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

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.
groupColumns

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.
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.
.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"),
  groupColumns = 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.
groupColumns

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.
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.
.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::eunomia_dir())
cdm <- CDMConnector::cdm_from_con(con,
                                  cdm_schem = "main",
                                  write_schema = "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"),
  groupColumns = NULL,
  timing = FALSE,
  hide = character(),
  .options = list()
)

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.
groupColumns

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.
timing

If TRUE the timing setting will be displayed.
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.
.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

## Not run: 
con <- DBI::dbConnect(duckdb::duckdb(),
                      dbdir = CDMConnector::eunomia_dir())
cdm <- CDMConnector::cdm_from_con(con,
                                  cdm_schem = "main",
                                  write_schema = "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)

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"),
  groupColumns = 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

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.
groupColumns

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.
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.
.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"),
  groupColumns = 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

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.
groupColumns

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.
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.
.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.