Individual-level simulated outbreak dataset

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

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.