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omopviewer

https://github.com/ohdsi/omopviewer

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (19.3%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

Basic Info
Statistics
  • Stars: 2
  • Watchers: 4
  • Forks: 0
  • Open Issues: 8
  • Releases: 3
Created over 1 year ago · Last pushed 8 months ago
Metadata Files
Readme License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# OmopViewer


[![R-CMD-check](https://github.com/OHDSI/OmopViewer/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/OHDSI/OmopViewer/actions/workflows/R-CMD-check.yaml)
[![CRAN status](https://www.r-pkg.org/badges/version/OmopViewer)](https://CRAN.R-project.org/package=OmopViewer)
[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![Codecov test coverage](https://codecov.io/gh/OHDSI/OmopViewer/branch/main/graph/badge.svg)](https://app.codecov.io/gh/OHDSI/OmopViewer?branch=main)


The goal of OmopViewer is to allow the user to easily create Shiny Apps to visualise study results in `` format.

## Installation

Install it from cran:

```{r, eval = FALSE}
install.packages("OmopViewer")
```

Or you can install the development version of OmopViewer from [GitHub](https://github.com/OHDSI/OmopViewer) with:

``` {r, eval = FALSE}
install.packages("pak")
pak::pkg_install("OHDSI/OmopViewer")
```

## Main functionalities

```{r}
library(OmopViewer)
```

The package has two functionalities:

- Static app
- Dynamic app

## Static shiny app

The static shiny app functionality creates a static shiny from a list of `summarised_result` objects. This shiny is specific to the set of results and can be modified later locally.

```{r, message=TRUE}
# lets generate some results
library(CohortCharacteristics)
cdm <- mockCohortCharacteristics()
result <- summariseCharacteristics(cdm$cohort1) |>
  bind(summariseCohortAttrition(cdm$cohort1))

exportStaticApp(result = result, directory = tempdir())
```

This function allow some customisation of the shiny with the arguments:

- `theme` (to choose a pre-built theme or a bslib one).
- `logo` (you can point to one of the pre-builr logos or to a local image).
- `title`
- `background` whether to allow for an .md file for customisation of a background panel.
- `summary` whether to include or not a summary panel.
- `panelStructure` allows you to structure the different panels in dropdown menus.
- `panelDetails` allows you to create panels at result_id level and assign which are the outputs that we want to include in each panel.

The shiny generated will have the following structure:

- `global.R` loads the data.
- `ui.R` with all the ui code. You can edit there the buttons and its default values.
- `server.R` server logic, you can edit that file to change some of the displays.
- `functions.R` some utility functions that are used in the shiny app.
- `data/result.csv` the original summarised_result provided.
- `data/ShinyData.RData` the .RData file that contains the data used in the shiny.
- `data/preprocess.R` the file to generate ShinyData.RData from results.csv

## Dynamic shiny app

The dynamic shiny app can be easily launched with `launchDynamicApp()` function. This function creates a shinyApp where you can upload multiple results sets and visualise them.

```{r, eval = FALSE}
launchDynamicApp()
```

By default the shiny generated will have no data, you have to upload data from a csv or zip file that you have it locally. The summarised_results will be processed and you will be allowed to choose which results to visualise.

## Example shiny

An example shiny can be found in: . This `shinyApp` is automatically build from `main` using the latest versions of `omopViewerResults` dataset and `omopViewerPanels` panels definitions.

Owner

  • Name: Observational Health Data Sciences and Informatics
  • Login: OHDSI
  • Kind: organization

GitHub Events

Total
  • Create event: 46
  • Release event: 2
  • Issues event: 144
  • Watch event: 2
  • Delete event: 56
  • Member event: 1
  • Issue comment event: 44
  • Push event: 293
  • Pull request review event: 4
  • Pull request event: 98
Last Year
  • Create event: 46
  • Release event: 2
  • Issues event: 144
  • Watch event: 2
  • Delete event: 56
  • Member event: 1
  • Issue comment event: 44
  • Push event: 293
  • Pull request review event: 4
  • Pull request event: 98

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 98
  • Total pull requests: 165
  • Average time to close issues: 22 days
  • Average time to close pull requests: 3 days
  • Total issue authors: 13
  • Total pull request authors: 6
  • Average comments per issue: 0.38
  • Average comments per pull request: 0.08
  • Merged pull requests: 152
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 97
  • Pull requests: 154
  • Average time to close issues: 22 days
  • Average time to close pull requests: 3 days
  • Issue authors: 13
  • Pull request authors: 6
  • Average comments per issue: 0.37
  • Average comments per pull request: 0.07
  • Merged pull requests: 142
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • catalamarti (41)
  • edward-burn (29)
  • cecicampanile (5)
  • wanningwang (5)
  • MimiYuchenGuo (5)
  • martapineda (3)
  • annasaura (2)
  • ilovemane (2)
  • martaalcalde (2)
  • nmercadeb (1)
  • xihang-chen (1)
  • daniellenewby (1)
  • elinrow (1)
Pull Request Authors
  • catalamarti (119)
  • MimiYuchenGuo (20)
  • nmercadeb (8)
  • edward-burn (8)
  • cecicampanile (5)
  • elinrow (5)
Top Labels
Issue Labels
needs discussion (3) enhancement (3) help wanted (2) duplicate (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 487 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
cran.r-project.org: OmopViewer

Visualise OMOP Results using 'shiny' Applications

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 487 Last month
Rankings
Dependent packages count: 28.0%
Dependent repos count: 34.5%
Average: 49.8%
Downloads: 86.8%
Maintainers (1)
marti.catalasabate@ndorms.ox.ac.uk
Last synced: 7 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.5.0 composite
  • actions/checkout v4 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • CohortCharacteristics * suggests
  • duckdb * suggests
  • omopgenerics * suggests
  • testthat * suggests