init release 0.0.1

2026-09-09 21:00:42 +02:00
commit 994fb4af60
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@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Interactive Medical Data App authors (University Medicine Greifswald)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
@@ -0,0 +1,171 @@
+# Interactive Medical Data App
+
+**Version**: 0.0.1
+
+---
+
+## Authors
+
+* Tom Gebhardt
+* Sarah Braun
+* Christian Draeger
+* Lea Michaelis
+* Sherry Freiesleben
+* Dagmar Waltemath
+* Matthias Löbe
+* Judith Wodke
+
+---
+
+## Abstract
+
+> This Shiny application provides an interactive platform for uploading, integrating, visualizing, and summarizing heterogeneous medical datasets (CSV, JSON, FHIR). Built on state-of-the-art R packages (e.g., **shiny**, **fhircrackr**, **ggplot2**, **leaflet**), it enables researchers and clinical IT teams to explore data quality, distributions, and shared categories across multiple sources with full reproducibility and modularity.
+
+---
+
+## Background
+
+* **Heterogeneous Data Sources**
+  Clinical and research data often exist in disparate formats: CSV exports, JSON-formatted histograms, and HL7 FHIR APIs.
+
+* **Need for Integration**
+  Comparative analyses require harmonization of these diverse formats into a unified view.
+
+* **Interactive Dashboards**
+  Shiny apps facilitate real-time exploration for non-technical users.
+
+---
+
+## Features
+
+| **Category**                       | **Description**                                                                                                                                             |
+|------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| **Data Import**                    | • Upload multiple CSV, JSON, or FHIR® bundle JSON files (e.g. pre-fetched from a HAPI Test Server)<br>• Live FHIR server connection code exists (`fhircrackr`/`httr`) but is currently not wired into the UI — no immediate use case was found, so it's unused for now    |
+| **Column Mapping**                 | • Dynamically map ‘Category’ and ‘Count’ columns when CSV headers differ                                                                                   |
+| **Visual Exploration**             | • Draggable mini-plots (Histogram, Pie Chart, Line Chart) with adjustable transparency<br>• “Stack All” and “Stack Selected” controls                       |
+| **Data Combination & Intersection**| • Stacked-bar combination of selected categories across datasets<br>• Identify and export category intersections as JSON                                     |
+| **Statistical Overview**           | • Auto-generated tables: dataset sizes, mean counts<br>• Color-coded summary of category prevalence (all/multiple/single sources)                         |
+| **Geospatial Visualization**       | • *Currently disabled*: code for an interactive map of German Data Integration Centers (**leaflet** + **geodata**) exists but is commented out and not part of the running app                                                                      |
+| **FHIR Bin Reports**               | • Bin FHIR attribute values (text, numeric, boolean) and export as a FHIR `MeasureReport` (separate or composite stratifier format)                        |
+
+---
+
+## System Architecture
+
+This application adopts a **modular Shiny framework** for clarity, testability, and maintainability:
+
+1. **UI Layer**
+   Defined via `fluidPage()` and `navbarPage()`, grouping functionality into:
+
+   * Data Upload
+   * Census Data
+   * FHIR in bins
+   * Visualization
+   * Combined Data
+   * Statistics
+
+2. **Server Layer**
+
+   * Reactivity: `reactive()`, `eventReactive()` ensure immediate UI updates
+   * Observers: `observe()`, `observeEvent()` handle user-driven events
+
+3. **Helper Modules**
+
+   * `loadJsonData()`, `loadCsvData()`, `make_safe_id()` encapsulate parsing, validation, sanitization
+
+4. **Plotting Components**
+
+   * `ggplot2` charts via separate render functions (`renderPlot()`); a **leaflet** map render function exists but is currently commented out (see Geospatial Visualization above)
+
+5. **Data Integration Pipeline**
+   Central reactive `allData` unifies datasets from uploads, powering both visualization and statistics without redundant computations.
+
+6. **Extensibility & Testing**
+
+   * Modular structure allows adding new data sources or plot types
+   * Supports unit testing of individual functions independent of UI
+
+---
+
+## Requirements
+
+* **R** ≥ 4.2
+* **OS**: Linux, macOS, Windows
+* **Packages** (installed automatically via `ensure_pkg()`):
+
+  ```r
+  install.packages(c(
+    "shiny", "shinythemes", "shinyjqui",
+    "jsonlite", "readr", "fhircrackr", "httr",
+    "dplyr", "tidyr", "ggplot2", "leaflet",
+    "DT"
+  ))
+  ```
+
+---
+
+## Installation
+
+1. **Clone repository**
+
+   ```bash
+   git clone https://git.uni-greifswald.de/MILA_public/DQ-App.git
+   cd DQ-App
+   ```
+
+2. **Install & Run**
+
+   ```r
+   source("app.R")  # ensure_pkg() installs missing dependencies
+   runApp("app.R")
+   ```
+
+> **Need a ready-made R environment?**
+> If you don't have a suitable R installation, use a container image from the
+> [Rocker Project](https://rocker-project.org/). The `rocker/shiny` or
+> `rocker/tidyverse` images provide R with Shiny preinstalled and give you a
+> reproducible environment for running the app.
+
+---
+
+## Usage
+
+1. Run the app (see Installation above) — Shiny will open it automatically in a browser window/tab.
+2. Navigate tabs:
+
+   * **Data Upload**: Upload CSV/JSON/FHIR bundle files
+   * **Census Data**: Visualize census population data and uploaded FHIR patient data
+   * **FHIR in bins**: Bin FHIR attribute values and export as a FHIR `MeasureReport`
+   * **Visualization**: Arrange & filter mini-plots
+   * **Combined Data**: Combine categories, download JSON
+   * **Statistics**: View summaries & category presence
+
+---
+
+## Quality Assurance & Reproducibility
+
+* **Version Control**: Git with feature branches & peer review
+* **Unit Testing**: Planned `testthat` coverage for core functions
+* **Documentation**: Inline comments + precise README ensure transparency
+
+---
+
+## Future Directions
+
+* **Extended FHIR Support**: Add Observations, Conditions
+* **Automated Testing**: Full `testthat` suite integration
+
+---
+
+## License & Citation
+
+* **License**: [MIT](LICENSE)
+* **Citation**:
+
+  > Gebhardt T., Braun S., Draeger C., Michaelis L., et al. (2025). *Interactive Medical Data App*. [https://git.uni-greifswald.de/MILA_public/DQ-App](https://git.uni-greifswald.de/MILA_public/DQ-App)
+
+---
+
+> **Note**: A live FHIR-server connection was implemented and works, but is currently not exposed in the UI — no immediate use case was found for it. FHIR data is currently provided via uploading pre-fetched bundle JSON files instead.
+
+
@@ -0,0 +1,40 @@
+{
+  "Histogram": [
+    {
+      "Category": {
+        "@value": "18-25"
+      },
+      "Count": {
+        "@value": 80,
+        "@type": "xsd:decimal"
+      }
+    },
+    {
+      "Category": {
+        "@value": "26-35"
+      },
+      "Count": {
+        "@value": 120,
+        "@type": "xsd:decimal"
+      }
+    },
+    {
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+        "@value": "36-45"
+      },
+      "Count": {
+        "@value": 60,
+        "@type": "xsd:decimal"
+      }
+    },
+    {
+      "Category": {
+        "@value": "46+"
+      },
+      "Count": {
+        "@value": 40,
+        "@type": "xsd:decimal"
+      }
+    }
+  ]
+}
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@@ -0,0 +1,101 @@
+Index,User Id,First Name,Last Name,Sex,Email,Phone,Date of birth,Job Title
+1,88F7B33d2bcf9f5,Shelby,Terrell,Male,elijah57@example.net,001-084-906-7849x73518,1945-10-26,Games developer
+2,f90cD3E76f1A9b9,Phillip,Summers,Female,bethany14@example.com,214.112.6044x4913,1910-03-24,Phytotherapist
+3,DbeAb8CcdfeFC2c,Kristine,Travis,Male,bthompson@example.com,277.609.7938,1992-07-02,Homeopath
+4,A31Bee3c201ef58,Yesenia,Martinez,Male,kaitlinkaiser@example.com,584.094.6111,2017-08-03,Market researcher
+5,1bA7A3dc874da3c,Lori,Todd,Male,buchananmanuel@example.net,689-207-3558x7233,1938-12-01,Veterinary surgeon
+6,bfDD7CDEF5D865B,Erin,Day,Male,tconner@example.org,001-171-649-9856x5553,2015-10-28,Waste management officer
+7,bE9EEf34cB72AF7,Katherine,Buck,Female,conniecowan@example.com,+1-773-151-6685x49162,1989-01-22,Intelligence analyst
+8,2EFC6A4e77FaEaC,Ricardo,Hinton,Male,wyattbishop@example.com,001-447-699-7998x88612,1924-03-26,Hydrogeologist
+9,baDcC4DeefD8dEB,Dave,Farrell,Male,nmccann@example.net,603-428-2429x27392,2018-10-06,Lawyer
+10,8e4FB470FE19bF0,Isaiah,Downs,Male,virginiaterrell@example.org,+1-511-372-1544x8206,1964-09-20,"Engineer, site"
+11,BF0BbA03C29Bb3b,Sheila,Ross,Female,huangcathy@example.com,895.881.4746,2008-03-20,Advertising account executive
+12,F738c69fB34E62E,Stacy,Newton,Male,rayleroy@example.org,710.673.3213x80335,1980-10-20,Warden/ranger
+13,C03fDADdAadAdCe,Mandy,Blake,Male,jefferynoble@example.org,(992)466-1305x4947,2007-12-08,"Scientist, clinical (histocompatibility and immunogenetics)"
+14,b759b74BD1dE80d,Bridget,Nash,Female,mercedes44@example.com,(216)627-8359,2004-06-28,Social worker
+15,1F0B7D65A00DAF9,Crystal,Farmer,Male,pmiranda@example.org,+1-024-377-5391,1992-03-09,Agricultural consultant
+16,50Bb061cB30B461,Thomas,Knight,Female,braunpriscilla@example.net,+1-360-880-0766,2006-02-18,Sport and exercise psychologist
+17,D6dbA5308fEC4BC,Maurice,Rangel,Male,sheenabanks@example.com,(246)187-4969,2004-08-20,Secretary/administrator
+18,311D775990f066d,Frank,Meadows,Male,gbrewer@example.org,429.965.3902x4447,2008-09-16,Audiological scientist
+19,7F7E1BAcb0C9AFf,Alvin,Paul,Male,gilbertdonaldson@example.com,219.436.0887x07551,1949-05-12,"Teacher, adult education"
+20,88473e15D5c3cD0,Jared,Mitchell,Female,jcortez@example.com,+1-958-849-6781,1921-01-18,Paediatric nurse
+21,b31D271F8c200AB,Jacqueline,Norton,Female,carias@example.net,819.309.7679x59173,1952-10-09,"Scientist, marine"
+22,42F4BdA841aBadC,Colleen,Hatfield,Female,fknox@example.org,638.584.1090,1949-10-14,Commercial horticulturist
+23,cBbBcA0FCA3C4Bc,Randy,Barnes,Male,huangbill@example.org,001-960-629-7164x67214,1947-12-30,Outdoor activities/education manager
+24,f1f89173353aD90,Janice,Rhodes,Female,juarezdominique@example.net,001-249-314-9742x6996,1999-11-01,Drilling engineer
+25,c5B09fb33e8bA0A,Alfred,Mcneil,Female,cassandramorris@example.com,(468)276-9509x53058,1993-05-28,Systems analyst
+26,c9F2282C40BEC1E,Sean,Levine,Male,sallymiller@example.net,4915828504,2010-10-09,"Conservation officer, nature"
+27,9c1bc7EC53Fb7cE,Louis,Payne,Male,bsullivan@example.net,6232695307,1916-01-29,Counsellor
+28,ddEc50e2A2e3a2B,Brittney,Vega,Female,ayalajose@example.net,945-739-8686,1932-10-31,Recycling officer
+29,66F096D36Ebae11,Judy,Buckley,Male,irosales@example.net,001-654-208-1241x52830,1963-07-28,Art gallery manager
+30,F0fE2faAd78F8b5,Norman,Weber,Male,mconrad@example.com,223.002.0429,1957-05-21,Gaffer
+31,5d2feAfbdCAA6B5,Isaiah,Camacho,Female,jimblake@example.org,001-536-544-3367,1966-04-07,Food technologist
+32,cDa5F303fCd6dEa,Jacqueline,Gallagher,Male,nsampson@example.net,(247)762-8934,1999-02-25,Building services engineer
+33,8Ef7DBfcaB02b6B,Bonnie,Andrews,Female,caitlin24@example.net,+1-253-987-2776x9161,1953-12-21,Seismic interpreter
+34,6Dec5b5542F8ed8,Brandon,Schmidt,Female,mconley@example.net,+1-386-673-1465x006,1931-05-12,"Engineer, biomedical"
+35,3Fb8a7f68e12784,Jackson,Sparks,Female,reynoldsdarryl@example.net,(137)908-3129x65035,1980-11-18,Set designer
+36,035eff50B9A0F24,Melody,Cook,Male,jeannovak@example.org,(826)792-7381,1963-06-25,Research scientist (life sciences)
+37,aa614aAE4B7Cf0C,Leonard,Hurst,Male,clinton78@example.org,941-038-0427x38800,1938-03-13,"Accountant, chartered management"
+38,ACcde95AAe3e6cC,Gene,Rich,Female,luisdeleon@example.org,+1-356-818-6604x89537,1946-08-22,"Surveyor, quantity"
+39,b6a35de5CB6fc25,Cynthia,Wiggins,Female,rosariodave@example.org,(110)858-2437x70190,1984-01-27,Outdoor activities/education manager
+40,e92A191E345fA3A,Tanya,Mckinney,Female,vickihouston@example.com,(830)774-9002x086,2003-03-12,Information systems manager
+41,7D0AcBF6CCac3fd,Matthew,Stone,Female,evelyn31@example.org,952-381-6360,2017-08-23,"Scientist, clinical (histocompatibility and immunogenetics)"
+42,CEFA7BBCef013AE,Kirk,Walsh,Female,stephenfuller@example.org,001-826-496-5529x8661,2009-04-08,Accounting technician
+43,9edBC94aE7cA22a,Willie,Vang,Female,haleymathews@example.net,741.168.6854x067,1978-02-02,Management consultant
+44,fFe7BAA737aDbe2,Miguel,Hill,Female,tyrone56@example.org,5247842945,1930-08-26,Make
+45,5F2f3fAca8B0946,Darren,Andrews,Male,lhernandez@example.com,(975)799-4261,1997-10-04,Retail banker
+46,6bFcfc3cc1BC6B4,Haley,Pugh,Female,molly03@example.org,(746)182-6137x2453,1980-09-16,Commissioning editor
+47,f3BD2cBF7eEb6df,Danielle,Estrada,Female,jvang@example.org,(890)374-9518x772,1930-07-09,"Accountant, chartered management"
+48,Ee4eB129dC7913A,Becky,Brady,Male,erikmueller@example.org,(390)002-0863,1957-06-27,Seismic interpreter
+49,dBCEf340C3657Eb,Caitlyn,Frey,Male,rivasdominique@example.org,805-021-3965x46344,1968-01-26,Jewellery designer
+50,E47FB71DD9ACCd9,Joshua,Sweeney,Male,daisymcgee@example.net,875.994.2100x535,1954-07-28,"Education officer, museum"
+51,eA3fDd79BE9f0E7,Heidi,Escobar,Female,staffordtravis@example.net,601-155-3065x1131,1931-09-25,Estate manager/land agent
+52,aF0eE4547Bc025c,Brian,Oconnell,Female,saralong@example.net,952-283-1423x733,1911-10-23,Physiotherapist
+53,9F5DeD7aD228F5a,Beverly,Esparza,Female,iphelps@example.net,+1-327-578-8754x6771,1930-12-09,Passenger transport manager
+54,D3Fa0220dDE4d36,Nathaniel,Rivas,Female,roberto29@example.com,(655)887-2040x37888,1908-11-17,Call centre manager
+55,60FdBFd5e7BE8fF,Debra,Payne,Female,yolanda07@example.org,001-731-525-8400x52593,1927-08-20,Special educational needs teacher
+56,D8bF5Ab2b98caff,Mackenzie,Rocha,Female,abbottyvette@example.net,4225525458,1980-10-21,Museum/gallery exhibitions officer
+57,CD8d33aA25bc8BB,Courtney,Watkins,Female,ochang@example.org,210.683.2761x5883,2003-12-07,Pension scheme manager
+58,Fac3BfFf0A3d03c,Fred,Olsen,Female,amyanderson@example.com,497-774-3053,1910-04-10,Archaeologist
+59,e552D7ddafe1FFb,Ryan,Nelson,Female,qnorman@example.org,956.330.2951,1924-05-02,Historic buildings inspector/conservation officer
+60,0f8deedb629A5f6,Grace,Phelps,Male,clarkeangela@example.net,(034)867-8827x6777,1909-10-15,Petroleum engineer
+61,bB9e49E506F65ed,Shari,Daugherty,Male,kalvarado@example.org,001-951-655-4798x6124,1944-11-24,Curator
+62,Ed724605A403D91,Kelli,Garner,Male,jodyvincent@example.org,995.000.4213x0982,2010-01-17,Retail banker
+63,0aBE5ACb18E0c10,Jackie,Bennett,Male,hutchinsonkirk@example.com,001-740-937-0846x0087,1915-11-11,Neurosurgeon
+64,5D2cb63CaAF53f6,Leslie,Conway,Female,floreschristina@example.org,795.782.4384x555,1983-11-06,Chiropractor
+65,Ee6974f90eeCe18,Harold,Barnett,Female,nathan65@example.org,+1-026-265-6392,1943-03-15,"Biochemist, clinical"
+66,cEf02C076afa07f,Larry,Harper,Male,maria32@example.org,+1-244-630-3792x4121,2021-05-05,"Scientist, water quality"
+67,9Df5Ba591bF3EFf,Mike,Ward,Female,imccullough@example.com,116-729-5046,1967-11-09,Hydrologist
+68,3faB1CBfEFBDdD4,Brittney,Rubio,Female,corey92@example.com,593.976.2528,1959-12-24,"Biochemist, clinical"
+69,Ebcefdf75eCb0a9,Frank,Pineda,Male,daltoncalvin@example.net,(035)961-5060x9182,1926-03-10,Hospital pharmacist
+70,e75e5DBfcb68887,Sandra,Wu,Male,ubanks@example.com,+1-096-606-6454x067,1925-04-28,Warehouse manager
+71,6a53a8D41dDF6de,Ryan,Benton,Male,lopezdebbie@example.org,+1-695-557-9948x485,2020-10-06,Physiological scientist
+72,F0d3bD1aaf9E3Bc,Tamara,Hull,Male,meagan39@example.net,017.665.3744x7944,1933-01-31,English as a second language teacher
+73,5bC87340799FBD0,Jean,Ritter,Female,kristina76@example.com,(954)060-1066,1985-08-06,Financial trader
+74,dBfA17Aaf16b4ab,Veronica,Briggs,Female,weissbridget@example.com,+1-521-589-2387x48490,1974-06-08,Structural engineer
+75,c935b7Eb6FA0B0F,Kim,Andrews,Female,wpetersen@example.org,7677125383,1990-11-15,"Biochemist, clinical"
+76,b3e15e65Ca2CcBf,Tina,Cunningham,Male,wongmary@example.org,079-907-5051,1956-11-29,Race relations officer
+77,dade3452F0c32FD,Jonathon,Atkinson,Male,gailfrench@example.net,874-037-2032x932,2011-07-19,"Psychologist, forensic"
+78,AdEd6cfD85DeC46,Jermaine,Reid,Female,vpaul@example.com,(742)214-8691,1974-08-18,Newspaper journalist
+79,DAf111987098ae4,Regina,Stevens,Male,xpoole@example.net,891-359-2684,2011-11-28,Public house manager
+80,6e6a5b885F6496d,Terrence,Huff,Male,cassandra80@example.org,221.800.6408x5416,1944-02-27,Careers information officer
+81,12DCb4ED8E01D5C,Tyler,Foley,Female,johnathan72@example.org,001-386-469-3075x8030,1908-09-19,Economist
+82,E1cB5cA8CA7CC0a,Andrew,Waters,Male,nhall@example.net,+1-376-865-2765x3351,1948-05-14,Jewellery designer
+83,AedDfaE8Cf49F07,Reginald,Stephenson,Male,erikaball@example.net,+1-832-500-6044x475,2010-02-08,Contracting civil engineer
+84,bff9853aFAeF772,Douglas,Reese,Female,nixonvanessa@example.net,001-834-660-8312x9864,1961-11-11,Higher education lecturer
+85,E883773cA5219Be,Helen,Williamson,Female,melvin08@example.net,001-377-726-4229,1911-08-11,"Lecturer, further education"
+86,CB19EafEbBfF9eC,Mario,Vaughn,Male,oblake@example.com,160-144-5039x12276,1990-07-08,Research scientist (life sciences)
+87,5834700fbEd2771,Chelsea,Dickson,Male,johnnyhendricks@example.net,001-698-651-0138x18588,1958-05-13,"Teacher, early years/pre"
+88,2b0Ab1Dc9E01D7E,Dustin,Bailey,Male,pbarron@example.net,+1-965-621-1157x345,1908-08-22,Travel agency manager
+89,3f3a3D89ad042Dd,Harry,Medina,Female,olsenmalik@example.net,+1-451-099-5805,1947-08-24,Technical sales engineer
+90,9425E2F38C408ef,Kathy,Haney,Female,teresa37@example.com,(164)105-8456,1955-09-02,Charity fundraiser
+91,F0aeC9c2759F3C6,Alison,Nixon,Female,zmiles@example.net,3506680871,1941-07-10,Patent attorney
+92,d6EA619A7C4aA95,Jamie,Hardy,Female,sheenadouglas@example.com,(900)803-9295x11533,1994-07-17,"Conservator, furniture"
+93,2A33E7Cad1bb0F5,Melody,Cox,Female,evan90@example.org,(626)520-5080x3511,1974-07-30,Dance movement psychotherapist
+94,d181FFB7d3E68bb,Xavier,Cole,Male,nicolas90@example.org,8164259975,1938-11-29,Financial planner
+95,feaBf8dAE0C0d6F,Dillon,Guzman,Female,angelanavarro@example.net,971-992-4521,1942-04-01,Air broker
+96,5eFda7caAeB260E,Dennis,Barnes,Female,bmartin@example.org,001-095-524-2112x257,1954-07-30,Software engineer
+97,CCbFce93d3720bE,Steve,Patterson,Female,latasha46@example.net,001-865-478-5157,1932-04-29,Barrister
+98,2fEc528aFAF0b69,Wesley,Bray,Male,regina11@example.org,995-542-3004x76800,1994-12-28,Police officer
+99,Adc7ad9B6e4A1Fe,Summer,Oconnell,Female,alexiscantrell@example.org,001-273-685-6932x092,2012-04-12,Broadcast journalist
+100,b8D0aD3490FC7e1,Mariah,Bernard,Male,pcopeland@example.org,(341)594-6554x44657,2016-11-15,IT sales professional