Package index

Snapshots

Create snapshots of OMOP databases

summariseOmopSnapshot()

Summarise a cdm_reference object creating a snapshot with the metadata of the cdm_reference object

tableOmopSnapshot()

Create a visual table from a summarise_omop_snapshot result

Person and Observation Periods

Summarise and plot the person and observation period table

summarisePerson()

Summarise person table

tablePerson()

Visualise the results of summarisePerson() into a table

plotPerson()

Visualise the output of summarisePerson()

summariseObservationPeriod()

Summarise the observation period table getting some overall statistics in a summarised_result object

plotObservationPeriod()

Create a plot from the output of summariseObservationPeriod()

tableObservationPeriod()

Create a visual table from a summariseObservationPeriod() result

Clinical Tables

Summarise and plot tables in the OMOP Common Data Model

summariseClinicalRecords()

Summarise an omop table from a cdm object

tableClinicalRecords()

Create a visual table from a summariseClinicalRecord() output

summariseMissingData()

Summarise missing data in omop tables

tableMissingData()

Create a visual table from a summariseMissingData() result

Counts

Summarise concept code use in the OMOP Common Data Model

summariseConceptIdCounts()

Summarise concept use in patient-level data

tableConceptIdCounts()

Create a visual table from a summariseConceptIdCounts() result

tableTopConceptCounts()

Create a visual table of the most common concepts from summariseConceptIdCounts() output

Temporal Trends

Summarise and plot temporal trends in tables in the OMOP Common Data Model

summariseTrend()

Summarise temporal trends in OMOP tables

tableTrend()

Create a visual table from a summariseTrend() result

plotTrend()

Create a ggplot2 plot from the output of summariseTrend()

Characterisation

Characterise the database

databaseCharacteristics()

Summarise Database Characteristics for OMOP CDM

shinyCharacteristics()

Generate an interactive Shiny application that visualises the results obtained from the databaseCharacteristics() function

Helper functions

Functions to help populate and summariseClinicalRecords()

clinicalTables()

Tables in the cdm_reference that contain clinical information

Deprecated functions

These functions have been deprecated

summariseConceptCounts()

Summarise concept counts in patient-level data

summariseConceptSetCounts()

Summarise concept counts in patient-level data

plotConceptSetCounts() deprecated

Plot the concept counts of a summariseConceptSetCounts output

summariseRecordCount()

Summarise record counts of an omop_table using a specific time interval

plotRecordCount() deprecated

Create a ggplot of the records' count trend

tableRecordCount() deprecated

Create a visual table from a summariseRecordCount() result

summariseInObservation() deprecated

Summarise the number of people in observation during a specific interval of time

plotInObservation() deprecated

Create a ggplot2 plot from the output of summariseInObservation()

tableInObservation() deprecated

Create a visual table from a summariseInObservation() result

mockOmopSketch() deprecated

Creates a mock database to test OmopSketch package