plot_network: Run an outbreak model and generate network plot with...

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

Description

Run an outbreak model and generate network plot with contagion

Usage

plot_network(
  am,
  am.layout = NULL,
  day,
  num.initial.cases = NULL,
  prop.ascertain = NULL,
  R = NULL,
  presymrate = NULL,
  delay_shape = NULL,
  delay_scale = NULL,
  prop.asym = NULL,
  quarantine = NULL,
  isolation = NULL,
  tracing = NULL,
  secondary = NULL,
  outside = NULL,
  sensitivity = NULL,
  testing = NULL,
  cap_max_tests = NULL,
  s = NULL
)

Arguments

am	association matrix
am.layout	(if wanting to specify a layout e.g. to keep the layout the same across comparisons)
day	the day to do the contagion for
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()

Author(s)

Josh Firth

Lewis Spurgin

Examples

## Not run: 

load("data-raw/am_list.RData")
m <- am_list[[1]] #This is the association matrix for haslemere
plot_network(
am = m,
day = 20,
num.initial.cases = 1,
prop.asym = 0.4,
delay_shape =  1,
delay_scale = 1.4,
prop.ascertain = 0.8,
presymrate = 0.4,
R = 6.5,
outside = 0.001,
sensitivity = "high",
testing = "none",
isolation = FALSE,
secondary = FALSE,
tracing = FALSE,
quarantine = FALSE)

## End(Not run)

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