MEmilio v1.2.0 - 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.

v1.2.0 Changes

Added features / functionality:

Stochastic differential equation based SIR and SEIR models Linear Chain Trick ODE-based model with initialization methods for real world data Automatic differentiation for ODE-based models and dynamic optimization examples Allow contact increase for simulation of larger events Allow flexible start day in IDE SECIR model Added seasonality for IDE SECIR model Alternative computation of compartments in IDE SECIR Implement initialization scheme for flows in IDE SECIR model Add Gamma distribution and other parameters to state age function for IDE models Python support for ODE SECIRVVS model Python support for 2021 metapopulation/Graph-ODE SECIRVVS simulation Age group resolution for ODE SIR and SEIR models Use ccache in CI for linux builds

General changes:

Use times for exposed and infected, no symptoms state in particular ODE models instead of SerialInterval and IncubationTime Updated CI actions Updated epidata readme Improve IDE SECIR model readme Handle pandas read excel engines Bundle the boost git repo instead of providing a targz archive Streamline ODE SECIR python code

Corrections:

Corrected handling of minimal step size in numerical integration Corrected functionality of IDE SECIR model example Prevent NaNs in newly added SDE models Resolve size_t underflow in dynamic NPIs Fix failing RKI urls Make python serialization working again Corrected IDE SECIR model simulation for certain conditions Corrected gcc compiler version in CI