Robert, A. 2020. geosocial-outbreaker: Integrating geographical and social contact data to reconstruct transmission chains. [Online]. Github. Available from: https://github.com/alxsrobert/o2geosocial
Robert, A. geosocial-outbreaker: Integrating geographical and social contact data to reconstruct transmission chains [Internet]. Github; 2020. Available from: https://github.com/alxsrobert/o2geosocial
Robert, A (2020). geosocial-outbreaker: Integrating geographical and social contact data to reconstruct transmission chains. [Data Collection]. Github. https://github.com/alxsrobert/o2geosocial
Description
o2geosocial infer probabilistic transmission trees from routinely-collected epidemiological data. It combines the age group, location, onset date and genotype of cases to infer their import status, and their likely infector. o2geosocial is adapted from the R package "outbreaker2" (https://github.com/reconhub/outbreaker2), it is designed to study datasets that do not include genetic sequences but genotype of the cases. o2geosocial will cluster cases from different genotypes in different trees, without computing the genetic distance between cases.
o2geosocial was originally designed to study measles outbreaks, as the evolution rate of the measles virus is slow and the genetic diversity minimal. It can be also applied to other viruses.
Keywords
Data capture method | Simulation |
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Date (Date published in a 3rd party system) | 13 February 2020 |
Language(s) of written materials | English |
Data Creators | Robert, A |
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LSHTM Faculty/Department | Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology |
Research Centre | Centre for the Mathematical Modelling of Infectious Diseases |
Participating Institutions | London School of Hygiene & Tropical Medicine, London, United Kingdom |
Funders |
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Date Deposited | 17 Feb 2020 14:23 |
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Last Modified | 08 Jul 2021 12:50 |
Publisher | Github |