Create a visual table from a summariseClinicalRecord() output.
Source:R/tableClinicalRecords.R
tableClinicalRecords.RdCreate a visual table from a summariseClinicalRecord() output.
Arguments
- result
Output from summariseClinicalRecords().
- type
Type of formatting output table. See
visOmopResults::tableType()for allowed options.- style
Named list that specifies how to style the different parts of the gt or flextable table generated. Accepted style entries are: title, subtitle, header, header_name, header_level, column_name, group_label, and body. Alternatively, use "default" to get visOmopResults style, or NULL for gt/flextable style. Keep in mind that styling code is different for gt and flextable. Additionally, "datatable" and "reactable" have their own style functions. To see style options for each table type use
visOmopResults::tableStyle()
Examples
# \donttest{
library(OmopSketch)
cdm <- mockOmopSketch()
summarisedResult <- summariseClinicalRecords(
cdm = cdm,
omopTableName = c("condition_occurrence", "drug_exposure"),
recordsPerPerson = c("mean", "sd"),
inObservation = TRUE,
standardConcept = TRUE,
sourceVocabulary = TRUE,
domainId = TRUE,
typeConcept = TRUE
)
#> Warning: The `inObservation` argument of `summariseClinicalRecords()` is deprecated as
#> of OmopSketch 1.0.0.
#> ℹ Please use the `quality` argument instead.
#> Warning: The `standardConcept` argument of `summariseClinicalRecords()` is deprecated as
#> of OmopSketch 1.0.0.
#> ℹ Please use the `conceptSummary` argument instead.
#> Warning: The `sourceVocabulary` argument of `summariseClinicalRecords()` is deprecated
#> as of OmopSketch 1.0.0.
#> ℹ Please use the `conceptSummary` argument instead.
#> Warning: The `domainId` argument of `summariseClinicalRecords()` is deprecated as of
#> OmopSketch 1.0.0.
#> ℹ Please use the `conceptSummary` argument instead.
#> Warning: The `typeConcept` argument of `summariseClinicalRecords()` is deprecated as of
#> OmopSketch 1.0.0.
#> ℹ Please use the `conceptSummary` argument instead.
#> 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.
#> ℹ Adding variables of interest to drug_exposure.
#> ℹ Summarising records per person in drug_exposure.
#> ℹ Summarising records in observation in drug_exposure.
#> ℹ Summarising records with start before birth date in drug_exposure.
#> ℹ Summarising records with end date before start date in drug_exposure.
#> ℹ Summarising domains in drug_exposure.
#> ℹ Summarising standard concepts in drug_exposure.
#> ℹ Summarising source vocabularies in drug_exposure.
#> ℹ Summarising concept types in drug_exposure.
#> ℹ Summarising missing data in drug_exposure.
summarisedResult |>
suppress(minCellCount = 5) |>
tableClinicalRecords()
condition_occurrence
drug_exposure
PatientProfiles::mockDisconnect(cdm)
# }