Overview
============


Model structure
----------------

The MEmilio library uses a modular organization of models where :doc:`compartmental or aggregated models<cpp/aggregated_models>` based on ODEs (ordinary differential equations) without and with Linear Chain Trick, IDEs (integro-differential equations), and SDEs (stochastic differential equations) share a maximum properties and interfaces (implemented in the *memilio* folder) to allow simple and straightforward model adaption with, e.g., demographic or spatial stratification (e.g. found in the *memilio/mobility* folder to create :doc:`metapopulation models<cpp/metapop>`) as shown in the following figure. :doc:`Agent-based models<cpp/individual_models>` are furthermore harmonized with most structures such as parameters, contact patterns, and non-pharmaceutical interventions (e.g. found in *memilio/epidemiology*).

.. image:: http://martinkuehn.eu/research/images/memilio_backend.png
   :alt: Overview on MEmilio's model backend
   :width: 100%

For a quick run through MEmilio's functionality see :doc:`installation`.

The MEmilio C++ project is organized as follows:

Main directory structure
---------------------------

The main directory structure in the ``cpp`` directory includes:

- **memilio/**: Contains the core framework for developing epidemiological models
  
  - **ad/**: Algorithmic differentiation framework
  - **compartments/**: Classes for compartment models and simulations
  - **data/**: Data analysis functions
  - **epidemiology/**: Base classes for epidemiological modeling
  - **geography/**: Geographic region data (e.g. school vacations) and functions
  - **io/**: Input/output utilities for various formats (JSON, HDF5...)
  - **math/**: Mathematical utilities such as integrators (Euler, RK)
  - **mobility/**: Different Metapopulation mobility approaches
  - **utils/**: General helper functions (logging, etc.)

- **models/**: Concrete implementation of epidemiological models

- **simulations/**: Applications for scientific publications

- **examples/**: Example applications demonstrating the use of the framework

- **tests/**: Unit tests for framework and models

- **thirdparty/**: Configuration of external dependencies

- **benchmarks/**: Analyzing runtime performance

Build system
-------------

The project uses CMake as a build system with various configuration options. 
For an explanation, refer to :doc:`installation`.