MEmilio v1.2.1 - A high performance Modular EpideMIcs simuLatIOn software

Kurzfassung

MEmilio implements various models for infectious disease dynamics, from simple compartmental (ODE) models through Integro-Differential equation-based (IDE) models (sometimes also denoted "age of infection models") to agent- or individual-based models (ABMs). Its modular design allows the combination of different models with different mobility patterns. Through efficient implementation and parallelization, MEmilio brings cutting edge and compute intensive epidemiological models to a large scale, enabling a precise and high-resolution spatiotemporal infectious disease dynamics.

v1.2.1 Changes

Added features / functionality:

Implementation of stochastic two variant SEIR models Added delay in testing and planned mobility in ABM ScoreP performance profile of ABM gperftools profiler New initialization method from flows for LCT model Stub generation for python bindings

General changes:

Refactored ABM code: Rename EPI to MIO, migration to mobility, and World to Model Replaced pointers in ABM by new structure Make the LCT secir model a derived class of CompartmentalModel New parameters that describe the multiplicative factor used for the TestAndTraceCapacity Extended test for equilibrium of IDE model Change return type of check_constraints function in the populations class to bool Adapt parameters_io of IDE SECIR model Small refacturing of epidata package Remove necessity for credentials of population data download Download boost libs with URL instead of git repo Upgrade manylinux image used for python in CI Workaround for github action checkout@v3

Corrections:

Add warning for end_date later than 2024-07-21 in intensive care data OdeIntegrator could run indefinitely Removed bug in getting test parameters in specific test derived from generic test