| indData {nbTransmission} | R Documentation |
Individual-level simulated outbreak dataset
Description
A dataset of an outbreak of 100 individuals starting from one case. It was simulated with using the package TransPhylo with parameters resembling TB:
average reproductive number = 1.2
generation interval = gamma(1.2, 2) years
outbreak duration = 14 years
mutation rate 0.5 snps/genome/year
Usage
indData
Format
A data frame with 100 rows and 8 variables:
- individualID
An individual-level id for each case.
- infector
The individualID of the true infector.
- infectionDate
The date and time of infection.
- sampleDate
The date and time of sampling.
- X1
Covariate with 2 values: a, b (e.g. sex).
- X2
Covariate with 4 values: a, b, c, d (e.g. nationality).
- X3
Covariate with 2 values: a, b (e.g. homelessness).
- X4
Covariate with 10 values: a-j (e.g. county of residence).
References
Didelot X, Fraser C, Gardy J, Colijn C. Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks. Mol Biol Evol. 2017;34(4):997-1007.