EstimNetReprodNumber

This repository contains code supporting the text "Estimation of the Epidemic Branching Factor in Noisy Contact Networks"

https://arxiv.org/abs/2002.05763

R

• Algorithm 1 : MME_BF.R
• Create random networks  : createNetwork_random.R
• Create hospital networks : createNetwork_hospital.R
• Create school networks  : createNetwork_school.R

Results

• Figure 1 : NoisyBF.R
• Figure 2 : BF_MME_simulation.R
• Figures 3, 4 and Table 1 : BF_MME_application.R
• Figure 5 : BF_MME_HeterogeneousNoise.R
• Figure 6 : BF_MME_DependentNoise.R
• Figure 1 in the supplement : NoisyBF_supp.R
• Figure 2 in the supplement : BF_MME_HeterogeneousNoise_supp.R
• Figure 3 in the supplement : BF_MME_DependentNoise_supp.R

Data

French Hospital

Vanhems, Philippe, et al. "Estimating potential infection transmission routes in hospital wards using wearable proximity sensors." PloS one 8.9 (2013): e73970.

British secondary schools

Kucharski, Adam J., et al. "Structure and consistency of self-reported social contact networks in British secondary schools." PloS one 13.7 (2018): e0200090.