bdext 0.1.96

Estimation of BDEISS-CT parameters from phylogenetic trees.

bdext

The bdext package provides scripts to train and assess Deep-Learning-enables estimators of BD(EI)(SS)(CT) model parameters from phylogenetic trees

BDEISS-CT model

The Birth-Death (BD) Exposed-Infectious (EI) with SuperSpreading (SS) and Contact-Tracing (CT) model (BDEISS-CT) can be described with the following 8 parameters:

• average reproduction number R;
• average total infection duration d;
• sampling probability ρ;
• incubation period d_inc or incubation fraction f_E = d_inc/d;
• fraction of superspreaders f_S < 0.5;
• super-spreading transmission increase X_S > 1;
• contact tracing probability υ;
• contact-traced removal speed up X_C > 1.

Setting d_inc=0 (equivalent to f_E=0) removes incubation (EI), setting f_S=0 or X_S=1 removes superspreading (SS), while setting υ=0 or X_C=1 removes contact-tracing (CT).

For identifiability, we require the sampling probability ρ to be given by the user. The other parameters are estimated from a time-scaled phylogenetic tree.