Plot and tables in OmopViewer
supported_result_type.RmdThe OmopViewer package will display by default the
‘tidy’ tab that will allow the user to explore the data. With the tidy
tab there will be displayed different output tabs. By default a table
created with OmopViewer::omopViewerTable() will be
displayed, but some packages have some extra output tabs configured. In
the following table you can see the result_type that are
configured and which are the visualisations.
#> Registered S3 method overwritten by 'visOmopResults':
#> method from
#> tidy.summarised_result omopgenerics| Result type | Function | Output type |
|---|---|---|
| CohortCharacteristics | ||
| summarise_cohort_overlap | tableCohortOverlap | gt |
| plotCohortOverlap | ggplot2 | |
| summarise_cohort_attrition | tableCohortAttrition | gt |
| plotCohortAttrition | grViz | |
| summarise_cohort_timing | tableCohortTiming | gt |
| plotCohortTiming | ggplot2 | |
| summarise_characteristics | tableCharacteristics | gt |
| plotCharacteristics | ggplot2 | |
| summarise_cohort_count | tableCohortCount | gt |
| plotCohortCount | ggplot2 | |
| CodelistGenerator | ||
| orphan_code_use | tableOrphanCodes | gt |
| cohort_code_use | tableCohortCodeUse | gt |
| code_use | tableCodeUse | gt |
| achilles_code_use | tableAchillesCodeUse | gt |
| OmopSketch | ||
| summarise_observation_period | tableObservationPeriod | gt |
| plotObservationPeriod | ggplot2 | |
| summarise_omop_snapshot | tableOmopSnapshot | gt |
| IncidencePrevalence | ||
| incidence | tableIncidence | gt |
| plotIncidence | ggplot2 | |
| incidence_attrition | tableIncidenceAttrition | gt |
| prevalence | tablePrevalence | gt |
| plotPrevalence | ggplot2 | |
| prevalence_attrition | tablePrevalenceAttrition | gt |
| DrugUtilisation | ||
| summarise_dose_coverage | tableDoseCoverage | gt |
| summarise_drug_restart | tableDrugRestart | gt |
| plotDrugRestart | ggplot2 | |
| summarise_drug_utilisation | tableDrugUtilisation | gt |
| summarise_indication | tableIndication | gt |
| plotIndication | ggplot2 | |
| summarise_proportion_of_patients_covered | tableProportionOfPatientsCovered | gt |
| plotProportionOfPatientsCovered | ggplot2 | |
| summarise_treatment | tableTreatment | gt |
| plotTreatment | ggplot2 | |
Note for developers
If you wish to configure a new result_type this can be
done editing the internal data: omopViewerTabs,
omopViewerOutput and omopViewerOutputArguments in file
internalData.R.
Please feel free to submit your PR.