https://github.com/ceefluz/radar
An interactive tool for rapid analysis of diagnostic and antimicrobial pattern in R using Shiny
https://github.com/ceefluz/radar
antimicrobial data-visualization electronic-medical-records shiny tool
Last synced: 4 months ago
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An interactive tool for rapid analysis of diagnostic and antimicrobial pattern in R using Shiny
- Host: GitHub
- URL: https://github.com/ceefluz/radar
- Owner: ceefluz
- License: gpl-2.0
- Created: 2017-12-07T10:02:19.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2020-06-30T15:03:19.000Z (almost 5 years ago)
- Last Synced: 2024-10-19T15:19:56.690Z (6 months ago)
- Topics: antimicrobial, data-visualization, electronic-medical-records, shiny, tool
- Language: R
- Homepage: https://ceefluz.shinyapps.io/radar/
- Size: 7.41 MB
- Stars: 105
- Watchers: 4
- Forks: 103
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# `RadaR` 
RadaR is an application for intuitive, rapid and reproducible quality of care pattern analysis of infectious patients.
Preprint about RadaR available: https://doi.org/10.1101/347534
See a running example [here](https://ceefluz.shinyapps.io/radar/).
## Prerequisites for using RadaR
RadaR was built in [R](https://www.r-project.org) , an open source programming language using the [Shiny package](https://shiny.rstudio.com), a web application framework for R. Users will need to download [R](https://cran.uni-muenster.de/) in order to use RadaR and we suggest the use of [RStudio](https://www.rstudio.com). R is completely free to use. All required code can be found in this github repositroy.
## Input type for RadaR's calculation
RadaR works with standard csv-files (.csv). The variables needed for RadaR are as follows:
### Input variables for **RadaR**
#### Admission data
| Variable | Detail |
|---------------------- |---------------------------------------------------------------------------------- |
| id | Patient ID or study ID |
| adm_id | Admission ID |
| gender | Gender |
| adm_start_date | Admission date (YYYY-MM-DD) |
| adm_end_date | Discharge date (YYYY-MM-DD) |
| death_during_adm | Death during admission (TRUE/FALSE) |
| adm_route | Origin at admission |
| sub_specialty | Sub-specialty |
| specialty | General specialty (internal medicine, surgery, other) |
| birth_date | Birth date (YYYY-MM-DD) |
#### Antimicrobial consumption data
| Variable | Detail |
|---------------------- |---------------------------------------------------------------------------------- |
| id| Patient ID or study ID |
| ab_start_date| Start of antimicrobial treatment (YYYY-MM-DD) |
| ab_stop_date| Stop of antimicrobial treatment (YYYY-MM-DD) |
| ab_route | Administration route (e.g. IV, oral, ...) |
| atc_code| ATC code according WHO ATC classification system |
| ddd_per_day| Defined daily dose of antimicrobial according to WHO ATC classification system per day|
#### Microbiological data
| Variable | Detail |
|---------------------- |---------------------------------------------------------------------------------- |
| id | Patient ID or study ID |
| specialty | Ordering specialty |
| antimicrobial susceptibility testing | Several columns of tested antimicrobial agents (e.g. amox, cipr etc.) with resistance results (R / I / S) |
| mo | Microbial ID (if test is positive) following the nomenclature of the Integrated Taxonomic Information System
| material | Test material (currently supported: blood and urine) |
| test_date | Test date (YYYY-MM-DD) |
| test_number | Test number |
These data will be loaded, merged, and transformed for analysis upon start of RadaR
## Privacy and storage
RadaR works with sensitive hospital data and is based on single observations on the patient level. All data for the running [example](https://ceefluz.shinyapps.io/radar/) is simulated and don't represent any real patients.
RadaR can be run locally on protected servers within institutions (for example: [Shiny server](https://www.rstudio.com/products/shiny/shiny-server/)) or on personal machines (mac, windows, linus).
## Author
RadaR was created at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl/) and the Medical Microbiology & Infection Prevention department of the University Medical Center Groningen (UMCG) by [Christian Luz](https://www.rug.nl/staff/c.f.luz/), PhD Student.
## Copyright
[](https://github.com/ceefluz/radar/blob/master/LICENSE)
RadaR is licensed under the [GNU General Public License (GPL) v2.0](https://github.com/ceefluz/radar/blob/master/LICENSE). In a nutshell, this means that this package:
- May be used for commercial purposes
- May be used for private purposes
- May be modified, although:
- Modifications **must** be released under the same license when distributing the package
- Changes made to the code **must** be documented
- May be distributed, although:
- Source code **must** be made available when the package is distributed
- A copy of the license and copyright notice **must** be included.
- Comes with a LIMITATION of liability
- Comes with NO warranty