Transmission network

Transmission edges, including seeded infections (source = -1).

Usage

get_transmissions(x)

Arguments

x

An object of class epiworld_sir, epiworld_seir, etc. (any model).

Value

• The function get_transmissions returns a data.frame with the following columns: date, source, target, virus_id, virus, and source_exposure_date.

Details

The function get_transmissions includes the seeded infections, with the source column coded as -1.

Examples

# SEIR Connected model
seirconn <- ModelSEIRCONN(
  name              = "Disease",
  n                 = 10000,
  prevalence        = 0.1,
  contact_rate      = 2.0,
  transmission_rate = 0.8,
  incubation_days   = 7.0,
  recovery_rate     = 0.3
)

set.seed(937)
run(seirconn, 50)
#> _________________________________________________________________________
#> |Running the model...
#> |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
#> |

# Get transmission data
head(get_transmissions(seirconn))
#>   date source target virus_id   virus source_exposure_date
#> 1    0     -1   6653        0 Disease                    0
#> 2    0     -1   9871        0 Disease                    0
#> 3    0     -1   6580        0 Disease                    0
#> 4    0     -1   7067        0 Disease                    0
#> 5    0     -1   1113        0 Disease                    0
#> 6    0     -1   1991        0 Disease                    0