Run a single instance of the branching process model for post-exposure prophylaxis for high-risk contacts. See Details for a full description of branching process model.
Usage
outbreak_model(
prop_pep,
rel_risk,
hrc_mu,
hrc_disp,
lrc_mu,
lrc_disp,
p_hrc_case,
p_lrc_case,
n_initialcases,
cap_max_gen,
cap_max_cases
)Arguments
- prop_pep
Proportion of high-risk contacts that receive PEP
- rel_risk
Relative risk of a high-risk contact becoming a case after receiving PEP
- hrc_mu
Average number of high-risk contacts
- hrc_disp
Dispersion parameter for number of high-risk contacts
- lrc_mu
Average number of low-risk contacts
- lrc_disp
Dispersion parameter for number of low-risk contacts
- p_hrc_case
Probability that a high-risk contact becomes a case
- p_lrc_case
Probability that a low-risk contact becomes a case
- n_initialcases
Integer number of initial cases
- cap_max_gen
Stop the simulation when this many generations is reached
- cap_max_cases
Stop the simulation when this many cases is reached
Value
A data.frame of cases by generation, with columns:
generation
case_id
case_type: one of "PEP", "HRC" (no PEP), "LRC".
infector: case_id of infector (currently not used)
new_cases: total new cases
new_cases_hrc: new cases that were high-risk contacts
new_cases_pep: new cases that were high-risk contacts that received PEP
new_cases_lrc: new cases that were low-risk contacts
n_hrc: number of high-risk contacts that did not receive PEP
n_pep: number of high-risk contacts that received PEP
n_lrc: number of low-risk contacts
Details
The outbreak begins with a given number of initial cases. Each case has some number of high- and low-risk contacts, each defined by a negative binomial distribution.
A fixed proportion prop_pep of high-risk contacts receive PEP.
High-risk contacts who do not receive PEP become cases with probability p_hrc_case; high-risk contacts who receive PEP become cases with lower probability p_hrc_case*rel_risk.
Low-risk contacts do not receive PEP, and become cases with probability p_lrc_case.