Type: Package
Title: Visualise OMOP Results using 'shiny' Applications
Version: 0.4.0
Maintainer: Martí Català <marti.catalasabate@ndorms.ox.ac.uk>
Description: Visualise results obtained from analysing data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model using 'shiny' applications.
License: Apache License (≥ 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
URL: https://ohdsi.github.io/OmopViewer/
Depends: R (≥ 4.1)
Imports: bslib, cli, dplyr, DT, glue, gt, lifecycle, markdown, omopgenerics (≥ 0.4.0), purrr, rlang, shiny, snakecase, stringr, styler, tidyr, usethis, visOmopResults (≥ 0.5.0), yaml
Suggests: CDMConnector, CodelistGenerator (≥ 3.2.0), CohortCharacteristics (≥ 1.0.0), CohortConstructor, cpp11, devtools, DiagrammeR, DiagrammeRsvg, DrugUtilisation (≥ 0.7.1), duckdb, ggplot2, here, htmlwidgets, IncidencePrevalence (≥ 0.8.0), knitr, omock (≥ 0.3.0), OmopSketch, PatientProfiles, plotly, progress, reactable, renv, rmarkdown, RPostgres, rsconnect, rsvg, shiny.fluent, shinycssloaders, shinyTree, shinyWidgets (≥ 0.9.0), sortable, testthat (≥ 3.1.5), utils, webshot2, zip
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/testthat/parallel: true
NeedsCompilation: no
Packaged: 2025-07-09 00:37:24 UTC; martics
Author: Martí Català ORCID iD [aut, cre], Yuchen Guo ORCID iD [aut], Edward Burn ORCID iD [ctb], Nuria Mercade-Besora ORCID iD [ctb], Elin Rowlands ORCID iD [ctb], Cecilia Campanile ORCID iD [ctb]
Repository: CRAN
Date/Publication: 2025-07-09 02:10:02 UTC

OmopViewer: Visualise OMOP Results using 'shiny' Applications

Description

Visualise results obtained from analysing data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model using 'shiny' applications.

Author(s)

Maintainer: Martí Català marti.catalasabate@ndorms.ox.ac.uk (ORCID)

Authors:

Other contributors:

See Also

Useful links:

Default panels defined in the package.

Description

Default panels defined in the package.

Usage

defaultPanels()

Value

Names of the default panels defined in the package.

Examples


defaultPanels()

Export and launch a static shiny specific to the provided results.

Description

Export and launch a static shiny specific to the provided results.

Usage

exportStaticApp(
  result,
  directory,
  logo = "ohdsi",
  title = "",
  background = TRUE,
  summary = TRUE,
  panelDetails = panelDetailsFromResult(result),
  panelStructure = NULL,
  theme = NULL,
  updateButtons = TRUE,
  open = rlang::is_interactive()
)

Arguments

result

A summarised_result object.

directory

Directory to create the shiny.

Name of a logo or path to a logo. If NULL no logo is included. Only svg format allowed for the moment.

title

title of the shiny

background

Whether to include a background panel. Background panel content will be controlled from the generated background.md file.

summary

Whether to include a panel with a summary of content in the result.

panelDetails

A named list to provide details for each one of the panels, such as: result_id, result_type, title, icon, filters and content. By default it is created using the panelDetailsFromResult() function.

panelStructure

A named list of panel identifiers to organise them in drop-down menus. Identifiers names are the ones used in panelDetails. By default one panel per each panelDetails element is created.

theme

Specify the theme for the Shiny application. You can either select a predefined theme provided by the package (e.g., "theme1"), or define a custom theme using bslib::bs_theme(). If using a custom theme, it must be provided as a character string (e.g., "bslib::bs_theme(bg = 'white', fg = 'black')").

updateButtons

Whether to include update buttons for visualisations.

open

Whether to open the shiny app project.

Value

The shiny app will be created in directory.

Examples

exportStaticApp(
  result = omopgenerics::emptySummarisedResult(),
  directory = tempdir()
)

Get one of the default pre-built panels.

Description

Get one of the default pre-built panels.

Usage

getPanel(panelId)

Arguments

panelId

Name of the one of the default panels. Use defaultPanels() to see the available default panels.

Value

A panel definition.

Examples


getPanel("incidence")

Launch a dynamic shiny app where you can upload results.

Description

[Experimental]

Usage

launchDynamicApp()

Value

Launches the shiny app.

Panels defined in the package.

Description

The panels are generated using the following file: https://github.com/OHDSI/OmopViewer/blob/main/data-raw/panels.R.

Usage

omopViewerPanels

Format

omopViewerPanels

A list of 26 omopviewer_panel obejcts:

Mock results obtained from GiBleed dataset.

Description

The results are generated using the following file: https://github.com/OHDSI/OmopViewer/blob/main/data-raw/results.R.

Usage

omopViewerResults

Format

omopViewerResults

A summarised_result object with 12,017 rows:

Obtain default panel details from a ⁠<summarised_result>⁠ object.

Description

Obtain default panel details from a ⁠<summarised_result>⁠ object.

Usage

panelDetailsFromResult(result)

Arguments

result

A summarised_result object.

Value

A list of omop_viewer_panel objects.

Examples


panelDetailsFromResult(omopViewerResults)