Package: OmopSketch 1.1.0

Cecilia Campanile

OmopSketch: Characterise Tables of an OMOP Common Data Model Instance

Summarises key information in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. Assess suitability to perform specific epidemiological studies and explore the different domains to obtain feasibility counts and trends.

Authors:Marta Alcalde-Herraiz [aut], Kim Lopez-Guell [aut], Elin Rowlands [aut], Cecilia Campanile [aut, cre], Edward Burn [aut], Martí Català [aut]

OmopSketch_1.1.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
OmopSketch/json (API)

# Install 'OmopSketch' in R:

install.packages('OmopSketch', repos = c('https://ohdsi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ohdsi/omopsketch/issues

Pkgdown/docs site:https://ohdsi.github.io

On CRAN:

8.18 score 4 stars 1 packages 140 scripts 916 downloads 36 exports 31 dependencies

Last updated from:f9249fb826. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	310
source / vignettes	OK	313
linux-release-x86_64	OK	310
macos-release-arm64	OK	181
macos-oldrel-arm64	OK	155
windows-devel	OK	313
windows-release	OK	237
windows-oldrel	OK	276
wasm-release	OK	155

Exports:bind clinicalTables databaseCharacteristics exportSummarisedResult importSummarisedResult mockOmopSketch plotConceptSetCounts plotInObservation plotObservationPeriod plotPerson plotRecordCount plotTrend settings shinyCharacteristics summariseClinicalRecords summariseConceptCounts summariseConceptIdCounts summariseConceptSetCounts summariseInObservation summariseMissingData summariseObservationPeriod summariseOmopSnapshot summarisePerson summariseRecordCount summariseTrend suppress tableClinicalRecords tableConceptIdCounts tableInObservation tableMissingData tableObservationPeriod tableOmopSnapshot tablePerson tableRecordCount tableTopConceptCounts tableTrend

Dependencies:blob cli clock CodelistGenerator CohortConstructor cpp11 DBI dbplyr dplyr generics glue jsonlite lifecycle magrittr omopgenerics PatientProfiles pillar pkgconfig purrr R6 rlang snakecase stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs withr

Summarise database characteristics

Rendered fromdatabase_characteristics.Rmdusingknitr::rmarkdown

Last update: 2025-11-11
Started: 2025-06-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Tables in the cdm_reference that contain clinical information	clinicalTables
Summarise Database Characteristics for OMOP CDM	databaseCharacteristics
Creates a mock database to test OmopSketch package	mockOmopSketch
Plot the concept counts of a summariseConceptSetCounts output	plotConceptSetCounts
Create a ggplot2 plot from the output of summariseInObservation()	plotInObservation
Create a plot from the output of summariseObservationPeriod()	plotObservationPeriod
Visualise the output of 'summarisePerson()'	plotPerson
Create a ggplot of the records' count trend	plotRecordCount
Create a ggplot2 plot from the output of summariseTrend()	plotTrend
Generate an interactive Shiny application that visualises the results obtained from the 'databaseCharacteristics()' function	shinyCharacteristics
Summarise an omop table from a cdm object	summariseClinicalRecords
Summarise concept counts in patient-level data	summariseConceptCounts
Summarise concept use in patient-level data	summariseConceptIdCounts
Summarise concept counts in patient-level data	summariseConceptSetCounts
Summarise the number of people in observation during a specific interval of time	summariseInObservation
Summarise missing data in omop tables	summariseMissingData
Summarise the observation period table getting some overall statistics in a summarised_result object	summariseObservationPeriod
Summarise a cdm_reference object creating a snapshot with the metadata of the cdm_reference object	summariseOmopSnapshot
Summarise person table	summarisePerson
Summarise record counts of an omop_table using a specific time interval	summariseRecordCount
Summarise temporal trends in OMOP tables	summariseTrend
Create a visual table from a summariseClinicalRecord() output	tableClinicalRecords
Create a visual table from a summariseConceptIdCounts() result	tableConceptIdCounts
Create a visual table from a summariseInObservation() result	tableInObservation
Create a visual table from a summariseMissingData() result	tableMissingData
Create a visual table from a summariseObservationPeriod() result	tableObservationPeriod
Create a visual table from a summarise_omop_snapshot result	tableOmopSnapshot
Visualise the results of 'summarisePerson()' into a table	tablePerson
Create a visual table from a summariseRecordCount() result	tableRecordCount
Create a visual table of the most common concepts from 'summariseConceptIdCounts()' output	tableTopConceptCounts
Create a visual table from a summariseTrend() result	tableTrend