This simulated outbreak of Ebola Virus Disease matches some key properties of the West African Ebola outbreak of 2014-2015. Specifically, care was taken to use realistic delays (incubation period, serial interval, time to hospitalisation, etc.) and reproduction number (see references).
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An object of class
list of length 2.
This dataset is used for teaching purposes during Imperial College's short course on infectious disease modelling. The exercise aims to simulate the response to an Ebola outbreak taking place in a single large city, and evaluate the impact of an intervention (increased bed capacity).
Note that to ensure realism, some errors have been introduced in this dataset. These can be
identified as negative incubation periods (delay from infection to onset of symptoms). See
example for a simple way to identify these cases. The dataset
ebola_sim_clean is the same
dataset, only dates of infection and onset have been set to 'NA'.
WHO Ebola Response Team. 2014. Ebola virus disease in West Africa–the first 9 months of the epidemic and forward projections. The New England journal of medicine 371:1481<e2><80><93>1495.
WHO Ebola Response Team, J. Agua-Agum, A. Ariyarajah, B. Aylward, I. M. Blake, R. Brennan, A. Cori, C. A. Donnelly, I. Dorigatti, C. Dye, T. Eckmanns, N. M. Ferguson, P. Formenty, C. Fraser, E. Garcia, T. Garske, W. Hinsley, D. Holmes, S. Hugonnet, S. Iyengar, T. Jombart, R. Krishnan, S. Meijers, H. L. Mills, Y. Mohamed, G. Nedjati-Gilani, E. Newton, P. Nouvellet, L. Pelletier, D. Perkins, S. Riley, M. Sagrado, J. Schnitzler, D. Schumacher, A. Shah, M. D. Van Kerkhove, O. Varsaneux, and N. Wijekoon Kannangarage. 2015. West African Ebola epidemic after one year–slowing but not yet under control. The New England journal of medicine 372:584<e2><80><93>587.
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## identify mistakes in data entry (negative incubation period) mistakes <- which(ebola_sim$linelist$date_of_onset <= ebola_sim$linelist$date_of_infection) mistakes ebola_sim$linelist[mistakes, ] ## check that ebola_sim_clean is identical after removing mistakes identical(ebola_sim_clean$linelist, ebola_sim$linelist[-mistakes, ])
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