zika_def_parms: Default Zika parameters for sims

In sjfox/rtZIKVrisk: Accompanies: "Real-time risk assessment for Zika in the United States"

Description

A function that gives a list of parameters for running a zika simulation. Defaults to parameters for Zika with no introductions.

Usage

zika_def_parms(r_not = 1.1, infBoxes = 3, incBoxes = 6,
  recov_p = 0.3040571/(3/infBoxes), incub_rate = 0.583917, prop_p = r_not
  * recov_p/infBoxes, e_thresh = 100, prob_symp = 1, dis_prob_symp = 0.01,
  dis_prob_asymp = 0, intro_rate = 0.01)

Arguments

r_not	value specifying outbreak R0, which automatically modulates transmission rate
infBoxes	Integer specifying number of infectious class boxes
incBoxes	Integer specifying number of incubation class boxes
recov_p	Daily probability of recovery for each infectious box
incub_rate	Daily probability of transitioning for each incubation box
prop_p	Daily Poisson rate of transmission for each infectious individual
e_thresh	Maximum number of cumulative infections before sim ends
prob_symp	Probability that cases are symptomatic (haven't tested anything <1)
dis_prob_symp	Probability of discovery for symptomatic individuals
dis_prob_asymp	Probability of discovery for asymptomatic individuals
intro_rate	Daily rate of new introductions according to poisson distribution

Value

A list of length num_reps, where each component is a single call to run_zika_sim.

Examples

zika_def_parms()
zika_def_parms(r_not=1.6, intro_rate=0.1)

sjfox/rtZIKVrisk documentation built on May 30, 2019, 12:04 a.m.