Package: OmopSketch 0.1.1

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, cre], Kim Lopez-Guell [aut], Elin Rowlands [aut], Cecilia Campanile [aut], Edward Burn [aut], Martí Català [aut]

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OmopSketch.pdf |OmopSketch.html✨
OmopSketch/json (API)

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

Peer review:

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

On CRAN:

6.02 score 1 stars 9 scripts 321 downloads 23 exports 47 dependencies

Last updated 2 hours agofrom:a294069a61. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-winOKNov 21 2024
R-4.5-linuxOKNov 21 2024
R-4.4-winOKNov 21 2024
R-4.4-macOKNov 21 2024
R-4.3-winOKNov 21 2024
R-4.3-macOKNov 21 2024

Exports:bindexportSummarisedResultimportSummarisedResultmockOmopSketchplotConceptCountsplotInObservationplotObservationPeriodplotRecordCountsettingssummariseAllConceptCountssummariseClinicalRecordssummariseConceptCountssummariseInObservationsummariseMissingDatasummariseObservationPeriodsummariseOmopSnapshotsummariseRecordCountsuppresstableAllConceptCountstableClinicalRecordstableMissingDatatableObservationPeriodtableOmopSnapshot

Dependencies:backportsbitbit64blobCDMConnectorcheckmateclicliprclockCohortConstructorcpp11crayonDBIdbplyrdiffobjdplyrfansifsgenericsgluehmsjsonlitelifecyclemagrittromopgenericsPatientProfilespillarpkgconfigprettyunitsprogresspurrrR6readrrlangsnakecasestringistringrtibbletidyrtidyselecttzdbutf8vctrsvisOmopResultsvroomwaldowithr

Summarise clinical tables records

Rendered fromA-summarise_clinical_tables_records.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-11-13
Started: 2024-08-08

Summarise concept counts

Rendered fromB-summarise_concept_counts.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-11-13
Started: 2024-09-23

Readme and manuals

Help Manual

Help pageTopics
Creates a mock database to test OmopSketch package.mockOmopSketch
Plot the concept counts of a summariseConceptCounts output.plotConceptCounts
Create a ggplot2 plot from the output of summariseInObservation().plotInObservation
Create a plot from the output of summariseObservationPeriod().plotObservationPeriod
Create a ggplot of the records' count trend.plotRecordCount
Summarise concept use in patient-level datasummariseAllConceptCounts
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 and number of present concepts.summariseClinicalRecords
Summarise concept counts in patient-level data. Only concepts recorded during observation period are counted.summariseConceptCounts
Summarise the number of people in observation during a specific interval of time.summariseInObservation
Summarise missing data in omop tablessummariseMissingData
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 record counts of an omop_table using a specific time interval. Only records that fall within the observation period are considered.summariseRecordCount
Create a visual table from a summariseAllConceptCounts() result.tableAllConceptCounts
Create a visual table from a summariseClinicalRecord() output.tableClinicalRecords
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