Summarise an omop table from a cdm object. You will obtain information related to the number of records, number of subjects, whether the records are in observation, number of present domains and number of present concepts.
Source:R/summariseClinicalRecords.R
summariseClinicalRecords.Rd
Summarise an omop table from a cdm object. You will obtain information related to the number of records, number of subjects, whether the records are in observation, number of present domains and number of present concepts.
Usage
summariseClinicalRecords(
cdm,
omopTableName,
recordsPerPerson = c("mean", "sd", "median", "q25", "q75", "min", "max"),
inObservation = TRUE,
standardConcept = TRUE,
sourceVocabulary = FALSE,
domainId = TRUE,
typeConcept = TRUE,
sex = FALSE,
ageGroup = NULL
)
Arguments
- cdm
A cdm_reference object.
- omopTableName
A character vector of the names of the tables to summarise in the cdm object.
- recordsPerPerson
Generates summary statistics for the number of records per person. Set to NULL if no summary statistics are required.
- inObservation
Boolean variable. Whether to include the percentage of records in observation.
- standardConcept
Boolean variable. Whether to summarise standard concept information.
- sourceVocabulary
Boolean variable. Whether to summarise source vocabulary information.
- domainId
Boolean variable. Whether to summarise domain id of standard concept id information.
- typeConcept
Boolean variable. Whether to summarise type concept id field information.
- sex
Boolean variable. Whether to stratify by sex (TRUE) or not (FALSE).
- ageGroup
A list of age groups to stratify results by.
Examples
# \donttest{
cdm <- mockOmopSketch()
summarisedResult <- summariseClinicalRecords(
cdm = cdm,
omopTableName = "condition_occurrence",
recordsPerPerson = c("mean", "sd"),
inObservation = TRUE,
standardConcept = TRUE,
sourceVocabulary = TRUE,
domainId = TRUE,
typeConcept = TRUE
)
#> ℹ Summarising table counts
#> ℹ The following estimates will be computed:
#> → Start summary of data, at 2024-09-26 11:48:34.408847
#> ✔ Summary finished, at 2024-09-26 11:48:34.542303
#> ℹ Summarising records per person
#> ℹ The following estimates will be computed:
#> • records_per_person: mean, sd
#> → Start summary of data, at 2024-09-26 11:48:35.317126
#> ✔ Summary finished, at 2024-09-26 11:48:35.551666
#> ℹ Summarising in_observation, standard, domain_id, source, and type information
summarisedResult
#> # A tibble: 15 × 13
#> result_id cdm_name group_name group_level strata_name strata_level
#> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 1 mockOmopSketch omop_table condition_occur… overall overall
#> 2 1 mockOmopSketch omop_table condition_occur… overall overall
#> 3 1 mockOmopSketch omop_table condition_occur… overall overall
#> 4 1 mockOmopSketch omop_table condition_occur… overall overall
#> 5 1 mockOmopSketch omop_table condition_occur… overall overall
#> 6 1 mockOmopSketch omop_table condition_occur… overall overall
#> 7 1 mockOmopSketch omop_table condition_occur… overall overall
#> 8 1 mockOmopSketch omop_table condition_occur… overall overall
#> 9 1 mockOmopSketch omop_table condition_occur… overall overall
#> 10 1 mockOmopSketch omop_table condition_occur… overall overall
#> 11 1 mockOmopSketch omop_table condition_occur… overall overall
#> 12 1 mockOmopSketch omop_table condition_occur… overall overall
#> 13 1 mockOmopSketch omop_table condition_occur… overall overall
#> 14 1 mockOmopSketch omop_table condition_occur… overall overall
#> 15 1 mockOmopSketch omop_table condition_occur… overall overall
#> # ℹ 7 more variables: variable_name <chr>, variable_level <chr>,
#> # estimate_name <chr>, estimate_type <chr>, estimate_value <chr>,
#> # additional_name <chr>, additional_level <chr>
PatientProfiles::mockDisconnect(cdm = cdm)
# }