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, number of present concepts, missing data and inconsistencies in start date and end date

Usage

summariseClinicalRecords(
  cdm,
  omopTableName,
  recordsPerPerson = c("mean", "sd", "median", "q25", "q75", "min", "max"),
  conceptSummary = TRUE,
  missingData = TRUE,
  quality = TRUE,
  sex = FALSE,
  ageGroup = NULL,
  dateRange = NULL,
  inObservation = lifecycle::deprecated(),
  standardConcept = lifecycle::deprecated(),
  sourceVocabulary = lifecycle::deprecated(),
  domainId = lifecycle::deprecated(),
  typeConcept = lifecycle::deprecated()
)

Arguments

cdm

A cdm_reference object.

omopTableName

A character vector of the names of the tables to summarise in the cdm object. Run OmopSketch::clinicalTables() to check the available options.

recordsPerPerson

Generates summary statistics for the number of records per person. Set to NULL if no summary statistics are required.

conceptSummary

Logical. If TRUE, includes summaries of concept-level information, including:

Domain ID of standard concepts
Type concept ID
Standard vs non-standard concepts
Source vocabulary usage

missingData

Logical. If TRUE, includes a summary of missing data for relevant fields.

quality

Logical. If TRUE, performs basic data quality checks, including:

Percentage of records within the observation period
Number of records with end date before start date
Number of records with start date before the person's birth date

sex

Boolean variable. Whether to stratify by sex (TRUE) or not (FALSE).

ageGroup

A list of age groups to stratify results by.

dateRange

A vector of two dates defining the desired study period. Only the start_date column of the OMOP table is checked to ensure it falls within this range. If dateRange is NULL, no restriction is applied.

inObservation

Deprecated. Use quality = TRUE instead.

standardConcept

Deprecated. Use conceptSummary = TRUE instead.

sourceVocabulary

Deprecated. Use conceptSummary = TRUE instead.

domainId

Deprecated. Use conceptSummary = TRUE instead.

typeConcept

Deprecated. Use conceptSummary = TRUE instead.

Value

A summarised_result object.

Examples

# \donttest{
library(OmopSketch)

cdm <- mockOmopSketch()

summarisedResult <- summariseClinicalRecords(
  cdm = cdm,
  omopTableName = "condition_occurrence",
  recordsPerPerson = c("mean", "sd"),
  quality = TRUE,
  conceptSummary = TRUE,
  missingData = TRUE
)
#> ℹ Adding variables of interest to condition_occurrence.
#> ℹ Summarising records per person in condition_occurrence.
#> ℹ Summarising records in observation in condition_occurrence.
#> ℹ Summarising records with start before birth date in condition_occurrence.
#> ℹ Summarising records with end date before start date in condition_occurrence.
#> ℹ Summarising domains in condition_occurrence.
#> ℹ Summarising standard concepts in condition_occurrence.
#> ℹ Summarising source vocabularies in condition_occurrence.
#> ℹ Summarising concept types in condition_occurrence.
#> ℹ Summarising missing data in condition_occurrence.

summarisedResult
#> # A tibble: 69 × 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     
#> # ℹ 59 more rows
#> # 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)
# }