Estimation of proportionality factors using the next generation method

Code and data related to the manuscript: "Inferring age-specific differences in susceptibility to and infectiousness after SARS-CoV-2 infection based on Belgian social contact data"

The folder prop_factor contains all necessary codes and data concerning the estimation of proportionality factors using the next generation method (Figures 1-4 of the manuscript).

The folder r_t contains all necessary codes and data concerning the estimation of the reproduction number R_t (figure 5 of the manuscript).

The subfolder prop_factor/socrates_rshiny-master contains a local copy of the socrates tool (v. 1.51) together with needed CoMix data and sufficient to run the core. The full updated code of the socrates tool is freely available at https://github.com/lwillem/socrates_rshiny. More information on the socrates tool and on CoMix data can be found at http://socialcontactdata.org.

The prop_factor/PCR_REAGGREGATE_DATA.rds file contains the minimal re-aggregate data concerning PCR tests needed to run the code. We are not the owner of the full unaggregate data which can be requested from Sciensano via the online form https://epistat.wiv-isp.be/datarequest.