outbreak_model: Run a single instance of the branching process model

In lgs85/covidsch: School-based network model for COVID-19

Description

Run a single instance of the branching process model

Usage

outbreak_model(
  net,
  df,
  num.initial.cases,
  prop.ascertain,
  cap_max_days,
  R,
  presymrate,
  delay_shape,
  delay_scale,
  asym.adult,
  asym.child,
  asym.adult.inf,
  sym.child.inf,
  asym.child.inf,
  quarantine,
  isolation,
  tracing,
  secondary,
  outside,
  sensitivity = "high",
  testing = "none",
  cap_max_tests = NULL,
  output = "weekly",
  s = NULL
)

Arguments

net	network from which to sample cases, in pairwise list format. Object haslemere is built into the package
num.initial.cases	integer number of initial cases
prop.ascertain	numeric proportion of infectious contacts ascertained by contact tracing (must be 0<=x<=1)
R	scaling factor for infection probability
presymrate	the proportion of cases with pre-onset transmission (must be 0<=x<=1)
delay_shape	numeric shape parameter of delay distribution
delay_scale	numeric scale parameter of delay distribution
quarantine	logical whether quarantine is in effect, if TRUE then traced contacts are isolated before symptom onset
isolation	logical whether isolation is in effect
tracing	logical whether tracing is in effect
secondary	logical whether secondary contact tracing is in effect
sensitivity	app sensitivity - "high" or "low"
testing	"realistic", "random" or "none"
cap_max_tests	integer - maximum number of tests
s	seed - optional for reproducing the same output. Useful for plot_network()
weekly	logical - return summarised weekly cases or the raw case data

Value

data.frame of cases by week, cumulative cases, and weekly isolations, quarantines and tests

Author(s)

Joel Hellewell

Lewis Spurgin

Examples

## Not run: 
outbreak_model(net = haslemere, num.initial.cases = 1, prop.ascertain = 0.8, cap_max_days = 69, R = 6.5, presymrate = 0.4,
delay_shape = 1,delay_scale = 1.4,prop.asym = 0.4, quarantine = TRUE, isolation = TRUE, tracing = TRUE, secondary = TRUE,
outside = 0.001, sensitivity = "high", testing = "none"
## End(Not run)

lgs85/covidsch documentation built on May 24, 2020, 4:31 a.m.