Simulate an outbreak — simulateOutbreak • TransPhylo

Simulate an outbreak

simulateOutbreak(
  off.r = 1,
  off.p = 0.5,
  neg = 0.25,
  nSampled = NA,
  pi = 0.5,
  w.shape = 2,
  w.scale = 1,
  ws.shape = NA,
  ws.scale = NA,
  w.mean = NA,
  w.std = NA,
  ws.mean = NA,
  ws.std = NA,
  dateStartOutbreak = 2000,
  dateT = Inf
)

Arguments

off.r: First parameter of the negative binomial distribution for offspring number
off.p: Second parameter of the negative binomial distribution for offspring number
neg: the within-host effective population size (Ne) timesgeneration duration (g)
nSampled: number of sampled infected individuals, or NA for any
pi: probability of sampling an infected individual
w.shape: Shape parameter of the Gamma probability density function representing the generation time
w.scale: Scale parameter of the Gamma probability density function representing the generation time
ws.shape: Shape parameter of the Gamma probability density function representing the sampling time
ws.scale: Scale parameter of the Gamma probability density function representing the sampling time
w.mean: Mean of the Gamma distribution representing the generation time
w.std: Std of the Gamma distribution representing the generation time
ws.mean: Mean of the Gamma distribution representing the sampling time
ws.std: Std of the Gamma distribution representing the sampling time
dateStartOutbreak: Date when index case becomes infected
dateT: Date when process stops (this can be Inf for fully simulated outbreaks)

Value

Combined phylogenetic and transmission tree

Examples

simulateOutbreak()
#> Colored phylogenetic tree
#> Number of sampled individuals=3
#> Total number of hosts=5
simulateOutbreak(off.r=2,dateStartOutbreak=2010,dateT=2015)
#> Note that rejection sampling was used 1 times
#> Colored phylogenetic tree
#> Number of sampled individuals=12
#> Total number of hosts=16