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User Guide
This app accompanies the article: Bradbury NV, Hart WS, Lovell-Read FA, Polonsky JA and Thompson RN. 2023. Exact calculation of end-of-outbreak probabilities using contact tracing data. J.R. Soc. Interface.20:20230374. https://doi.org/10.1098/rsif.2023.0374
A csv file containing outbreak data can be uploaded to the app. The file must consist of three columns with the headings named exactly: ID, Onset_day, Infector_ID. All columns must contain only numeric, integer data.
- Column 1: ID must be numbered in integer order i.e. 1,2,3.
- Column 2: Onset_day contains the outbreak day when the case began i.e. the number of days after the first reported case.
- Infector_ID: Refers to the ID of the individual who infected this case. If this is unknown, it should be set to zero.
A discrete serial interval can also be uploaded. This must contain two columns of data with the headings: Serial_interval, Probability.
- Column 1: Serial_interval should list possible integer values of the serial interval (in days), starting from 0 and in increments of 1 up to a maximum possible value, i.e. 0,1,2,3,….
- Column 2: Probability should list the corresponding probabilities and must sum to 1. Columns with a sum greater than 1, less than 0.99 or containing negative values will show an error message.
This app is hosted at shinyapps.io. All data uploaded by the user are the user’s responsibility. The user should ensure that the data are accurate and are anonymised such that individuals are not identifiable. If you do not wish to upload your data, we recommend downloading the app files from the GitHub repository and running it locally on your own machine using R Studio.