Pair-level simulated outbreak dataset

A dataset of all pairs (unordered) of the outbreak of 100 individuals described in indData with SNP distance between each pair. Genomes were simulated using the package phangorn from the phylogentic tree created during the outbreak simulation.

pairData

Format

A data frame with 9900 rows and 17 variables:

pairID

A pair-level ID variable (the individual IDs separated by an '_').

individualID.1

The ID of the potential "infector".

individualID.2

The ID of the potential "infectee".

transmission

Did individual.1 infect individual.2.

snpDist

What is the number of SNPs between the individuals.

infectionDate.1

The date and time of infection of individualID.1.

infectionDate.2

The date and time of infection of individualID.2.

sampleDate.1

The date and time of sampling of individualID.1.

sampleDate.2

The date and time of sampling of individualID.2.

sampleDiff

The number of days between sampleDate.1 and sampleDate.2.

infectionDiff

The number of days between infectionDate.1 and infectionDate.2.

infectionDiffY

The number of years between infectionDate.1 and infectionDate.2.

timeCat

A categorical representation of infectionDiff: <1y, 1-2y, 2-3y, 3-4y, 4-5y, >5y.

Z1

Pair-level covariate derived from X1: 1 if match, 0 if not match.

Z2

Pair-level covariate derived from X2: 1 if match, 0 if not match.

Z3

Pair-level covariate derived from X3: 1 if a-a, 2 if b-b, 3 if a-b, 4 if b-a.

Z4

Pair-level covariate derived from X4: 1 if match, 2 if adjacent, 2 otherwise.

References

Schliep KP. phangorn: Phylogenetic analysis in R. Bioinformatics. 2011;27(4):592-3.