2026 Memilio paper

2026_Bicker_et_al_Memilio_paper/Fig4_d_and_e/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.13)
+
+project(memilio-simulations-2026_Bicker_et_al_Memilio_paper-Fig4_d_and_e VERSION 1.0.0)
+
+# Executables should be stored in the build/bin/ folder.
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin")
+
+# Download MEmilio with the git tag defined in git_tag.cmake.
+include(${CMAKE_SOURCE_DIR}/git_tag.cmake)
+# If git tag is not set, throw error.
+if(NOT DEFINED GIT_TAG_MEMILIO)
+  message(FATAL_ERROR "GIT_TAG_MEMILIO is not defined. Please make sure the git_tag.cmake file is correct.")
+endif()
+
+# FetchContent to fetch the MEmilio library in the correct version.
+include(FetchContent)
+
+FetchContent_Declare(
+  memilio
+  GIT_REPOSITORY https://github.com/SciCompMod/memilio.git
+  GIT_TAG ${GIT_TAG_MEMILIO}
+)
+
+FetchContent_MakeAvailable(memilio)
+
+add_custom_target(install_memilio_py ALL
+  COMMAND bash ../install.sh
+)

2026_Bicker_et_al_Memilio_paper/Fig4_d_and_e/README.md

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+# Figure 4: Fits of the ODE SECIR-type model for SARS-CoV-2 related ICU cases in Germany and Spain for national and district level
+
+## Requirements
+
+- **MEmilio**: See `git_tag.cmake` for the required version.
+- **Python**: Required for all simulations and plots. See the requirements.txt for the required python packages.
+- **Shapefiles**: The map plots of Germany and Spain require shapefiles. We use the geodata from the [Bundesamt für Kartographie und Geodäsie](https://gdz.bkg.bund.de/index.php/default/open-data/verwaltungsgebiete-1-2-500-000-stand-31-12-vg2500-12-31.html) (VG2500 31.12.) for Germany and [Instituto Geográfico Nacional](https://centrodedescargas.cnig.es/CentroDescargas/limites-municipales-provinciales-autonomicos#licencias) for Spain.
+
+## Files
+
+- **Data gathering**:
+    - `getSimulationDataSpain.py`: Get the data for the simulations of Spain.
+- **Python Simulations**:
+    - `graph_germany_nuts0.py`: Simulation, fitting and plots of the Germany model without spatial resolution (Fig. 4d, top).
+    - `graph_germany_nuts3.py`: Simulation, fitting and plots of the Germany model with spatial resolution on county level (Fig. 4d, bottom).
+    - `graph_spain_nuts0.py`: Simulation, fitting and plots of the Spain model without spatial resolution (Fig. 4e, top).
+    - `graph_spain_nuts3.py`: Simulation, fitting and plots of the Spain model with spatial resolution on provinces level (Fig. 4e, bottom).
+
+## How to Run
+
+1.  **Install the project**:
+    Configure the project using CMake. This already installs the necessary packages for the simulations.
+
+2. **Download the required data**:
+    Download the data for Germany by running 
+    ```bash
+    source build/venv/bin/activate
+    python build/_deps/memilio-src/pycode/memilio-epidata/memilio/epidata/getSimulationData.py -o "build/_deps/memilio-src/data"
+    ```
+    or 
+    ```bash
+    source build/venv/bin/activate
+    python getSimulationDataSpain.py
+    ```
+    for the simulations of Spain.
+
+    Then you can run the simulations by executing the corresponding python scripts:
+    ```bash
+    python graph_germany_nuts0.py
+    python graph_germany_nuts3.py
+    python graph_spain_nuts0.py
+    python graph_spain_nuts0.py
+    ```