.sim_internal | R Documentation |
This internal function simulates a line list, and
when sim_type
is "contacts"
or "outbreak"
a contacts table as well.
.sim_internal(
sim_type = c("linelist", "contacts", "outbreak"),
contact_distribution,
infectious_period,
prob_infection,
onset_to_hosp = NULL,
onset_to_death = NULL,
onset_to_recovery = NULL,
reporting_delay = NULL,
hosp_risk = NULL,
hosp_death_risk = NULL,
non_hosp_death_risk = NULL,
outbreak_start_date,
anonymise = NULL,
outbreak_size,
population_age,
case_type_probs = NULL,
contact_tracing_status_probs = NULL,
config
)
sim_type |
A |
contact_distribution |
A The function can be defined or anonymous. The function must have a single
argument in the form of an An The default is an anonymous function with a Poisson probability mass function
( |
infectious_period |
A The function can be defined or anonymous. The function must return a vector of randomly generated real numbers representing sampled infectious periods. The function must have a single argument, the number of random infectious periods to generate. An The default is an anonymous function with a lognormal distribution random
number generator ( |
prob_infection |
A single |
onset_to_hosp |
A The function can be defined or anonymous. The function must return a vector
of An The default is an anonymous function with a lognormal distribution random
number generator ( If |
onset_to_death |
A The function can be defined or anonymous. The function must return a vector
of An The default is an anonymous function with a lognormal distribution random
number generator ( If For hospitalised cases, the function ensures the onset-to-death time is
greater than the onset-to-hospitalisation time. After many (1000) attempts,
if an onset-to-death time (from |
onset_to_recovery |
A The function can be defined or anonymous. The function must return a vector
of An The default is For hospitalised cases, the function ensures the onset-to-recovery time is
greater than the onset-to-hospitalisation time. After many (1000) attempts,
if an onset-to-recovery time (from |
reporting_delay |
A The function can be defined or anonymous. The function must return a vector
of The default is |
hosp_risk |
Either a single |
hosp_death_risk |
Either a single |
non_hosp_death_risk |
Either a single |
outbreak_start_date |
A |
anonymise |
A |
outbreak_size |
A |
population_age |
Either a |
case_type_probs |
A named |
contact_tracing_status_probs |
A named |
config |
A list of settings to adjust the randomly sampled delays and
Ct values. See |
A <data.frame>
if sim_type
is "linelist"
or "contacts"
, or a
list of two <data.frame>
s if sim_type
is "outbreak"
.
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