o2geosocial1.1.3 package

Reconstruction of Transmission Chains from Surveillance Data

pre_clustering

Pre cluster cases in groups according using the genotypes and the arbi...

outbreaker

outbreaker: main function for reconstructing disease outbreaks

outbreaker_chains

Basic methods for processing outbreaker results

outbreaker_data

Process input data for outbreaker

create_config

Set and check parameter settings

create_param

Initializes outputs for outbreaker

custom_likelihoods

Customise likelihood functions for o2geosocial

custom_moves

Customise samplers for outbreaker

custom_priors

Customise priors for outbreaker

Download source packageRead PDF manual

Bayesian reconstruction of who infected whom during past outbreaks using routinely-collected surveillance data. Inference of transmission trees using genotype, age specific social contacts, distance between cases and onset dates of the reported cases. (Robert A, Kucharski AJ, Gastanaduy PA, Paul P, Funk S. (2020) <doi:10.1098/rsif.2020.0084>).

  • Maintainer: Alexis Robert
  • License: MIT + file LICENSE
  • Last published: 2024-06-21

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