Package index • OmopSketch

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.

Clinical Tables

Summarise and plot tables in the OMOP Common Data Model

summariseClinicalRecords(): 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

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.

Observation Periods

Summarise and plot the observation period table in the OMOP Common Data Model

summarisePerson(): Summarise the person table

tablePerson(): Visualise the results of summarisePerson() into a table

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.

Counts

Summarise concept code use in the OMOP Common Data Model

summariseConceptIdCounts(): Summarise concept use in patient-level data. Only concepts recorded during observation period are counted.

tableConceptIdCounts(): Create a visual table from a summariseConceptIdCounts() result.

tableTopConceptCounts(): Create a visual table of the most common concepts from summariseConceptIdCounts() output. This function takes a summarised_result object and generates a formatted table highlighting the most frequent concepts.

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().

Mock Database

Create a mock database to test the OmopSketch package

mockOmopSketch(): Creates a mock database to test OmopSketch package.

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() deprecated: Summarise concept counts in patient-level data. Only concepts recorded during observation period are counted.

summariseConceptSetCounts(): Summarise concept counts in patient-level data. Only concepts recorded during observation period are counted.

plotConceptSetCounts(): Plot the concept counts of a summariseConceptSetCounts output.

summariseRecordCount(): Summarise record counts of an omop_table using a specific time interval. Only records that fall within the observation period are considered.

plotRecordCount(): Create a ggplot of the records' count trend.

tableRecordCount(): Create a visual table from a summariseRecordCount() result.

summariseInObservation(): Summarise the number of people in observation during a specific interval of time.

plotInObservation(): Create a ggplot2 plot from the output of summariseInObservation().

tableInObservation(): Create a visual table from a summariseInObservation() result.