Package: OmopSketch 0.1.2

Marta Alcalde-Herraiz

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], Edward Burn [aut], Martí Català [aut]

OmopSketch_0.1.2.tar.gz
OmopSketch_0.1.2.tar.gz(r-4.5-noble)OmopSketch_0.1.2.tar.gz(r-4.4-noble)
OmopSketch_0.1.2.tgz(r-4.4-emscripten)OmopSketch_0.1.2.tgz(r-4.3-emscripten)
OmopSketch.pdf |OmopSketch.html✨
OmopSketch/json (API)

# Install 'OmopSketch' in R:

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

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

3.48 score 7 scripts 286 downloads 21 exports 114 dependencies

Last updated 9 days agofrom:1864fe2ff8. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 13 2024
R-4.5-linux	OK	Nov 13 2024

Exports:bind exportSummarisedResult importSummarisedResult mockOmopSketch plotConceptCounts plotInObservation plotObservationPeriod plotRecordCount settings summariseClinicalRecords summariseConceptCounts summariseInObservation summariseObservationPeriod summariseOmopSnapshot summarisePopulationCharacteristics summariseRecordCount suppress tableClinicalRecords tableObservationPeriod tableOmopSnapshot tablePopulationCharacteristics

Dependencies:askpass backports base64enc bigD bit bit64 bitops blob bslib cachem CDMConnector checkmate cli clipr clock CohortCharacteristics CohortConstructor colorspace commonmark cpp11 crayon curl data.table DBI dbplyr diffobj digest dplyr duckdb evaluate fansi farver fastmap flextable fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics ggplot2 glue gt gtable highr hms htmltools htmlwidgets isoband jquerylib jsonlite juicyjuice knitr labeling lattice lifecycle lubridate magrittr markdown MASS Matrix memoise mgcv mime munsell nlme officer omock omopgenerics openssl PatientProfiles pillar pkgconfig prettyunits progress purrr R6 ragg rappdirs RColorBrewer Rcpp reactable reactR readr rlang rmarkdown sass scales snakecase stringi stringr sys systemfonts textshaping tibble tidyr tidyselect timechange tinytex tzdb utf8 uuid V8 vctrs viridisLite visOmopResults vroom waldo withr xfun xml2 yaml zip

Summarise clinical tables records

Rendered fromA-summarise_clinical_tables_records.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-09-26
Started: 2024-09-26

Summarise concept counts

Rendered fromB-summarise_concept_counts.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-11-12
Started: 2024-09-26

Citation

Readme and manuals

Help Manual

Help page	Topics
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 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 code use in patient-level data	summariseConceptCounts
Summarise the number of people in observation during a specific interval of time.	summariseInObservation
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 the characteristics of the base population of a cdm_reference object.	summarisePopulationCharacteristics
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 summariseClinicalRecord() output.	tableClinicalRecords
Create a visual table from a summariseObservationPeriod() result.	tableObservationPeriod
Create a visual table from a summarise_omop_snapshot result.	tableOmopSnapshot
Create a visual table from a summarise_population_characteristics result.	tablePopulationCharacteristics