The event date could be first contact, last contact or other.
.data |
A <data.frame> containing the infectious history from a
branching process simulation (.sim_network_bp() ).
|
first_contact_distribution , last_contact_distribution |
A function to
generate the time for the first or last contact between the infector
and infectee (exposure window). See create_config() .
|
outbreak_start_date |
A date for the start of the outbreak.
|
onset_to_hosp |
A function or an <epiparameter> object for the
onset-to-hospitalisation delay distribution. onset_to_hosp can also be
set to NULL to not simulate hospitalisation (admission) dates.
The function can be defined or anonymous. The function must return a vector
of numeric s for the length of the onset-to-hospitalisation delay. The
function must have a single argument.
An <epiparameter> can be provided. This will be converted into a random
number generator internally.
The default is an anonymous function with a lognormal distribution random
number generator (rlnorm() ) with meanlog = 1.5 and sdlog = 0.5 .
If onset_to_hosp is set to NULL then hosp_risk and hosp_death_risk
will be automatically set to NULL if not manually specified.
|
hosp_risk |
Either a single numeric for the hospitalisation risk of
everyone in the population, or a <data.frame> with age specific
hospitalisation risks. Default is 20% hospitalisation (0.2 ) for the entire
population. If the onset_to_hosp argument is set to NULL this argument
will automatically be set to NULL if not specified or can be manually
set to NULL . See details and examples for more information.
|
onset_to_death |
A function or an <epiparameter> object for the
onset-to-death delay distribution. onset_to_death can also be set to
NULL to not simulate dates for individuals that died.
The function can be defined or anonymous. The function must return a vector
of numeric s for the length of the onset-to-death delay. The function must
have a single argument.
An <epiparameter> can be provided. This will be converted into a random
number generator internally.
The default is an anonymous function with a lognormal distribution random
number generator (rlnorm() ) with meanlog = 2.5 and sdlog = 0.5 .
If onset_to_death is set to NULL then non_hosp_death_risk and
hosp_death_risk will be automatically set to NULL if not manually
specified.
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_death ) cannot be sampled that is
greater than a onset-to-hospitalisation time (from onset_to_hosp ) then
the function will error. Due to this conditional sampling, the
onset-to-death times in the line list may not resemble the distributional
form input into the function.
|
onset_to_recovery |
A function or an <epiparameter> object for the
onset-to-recovery delay distribution. onset_to_recovery can also be NULL
to not simulate dates for individuals that recovered.
The function can be defined or anonymous. The function must return a vector
of numeric s for the length of the onset-to-recovery delay. The function
must have a single argument.
An <epiparameter> can be provided. This will be converted into a random
number generator internally.
The default is NULL so by default cases that recover get an NA in the
$date_outcome line list column.
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 onset_to_recovery ) cannot be sampled
that is greater than a onset-to-hospitalisation time (from onset_to_hosp )
then the function will error. Due to this conditional sampling, the
onset-to-recovery times in the line list may not resemble the distributional
form input into the function.
|
hosp_death_risk |
Either a single numeric for the death risk for
hospitalised individuals across the population, or a <data.frame> with age
specific hospitalised death risks Default is 50% death risk in hospitals
(0.5 ) for the entire population. If the onset_to_death argument is set
to NULL this argument will automatically be set to NULL if not specified
or can be manually set to NULL . See details and examples for more
information. The hosp_death_risk can vary through time if specified in
the time_varying_death_risk element of config , see
vignette("time-varying-cfr", package = "simulist") for more information.
|
non_hosp_death_risk |
Either a single numeric for the death risk for
outside of hospitals across the population, or a <data.frame> with age
specific death risks outside of hospitals. Default is 5% death risk outside
of hospitals (0.05 ) for the entire population. If the onset_to_death
argument is set to NULL this argument will automatically be set to NULL
if not specified or can be manually set to NULL . See details and examples
for more information. The non_hosp_death_risk can vary through time if
specified in the time_varying_death_risk element of config , see
vignette("time-varying-cfr", package = "simulist") for more information.
|
config |
A list of settings to adjust the randomly sampled delays and
Ct values. See create_config() for more information.
|
anonymise |
A logical boolean for whether case names should be
anonymised. Default is FALSE .
|
reporting_delay |
A function for the reporting delay distribution or
NULL . The (random) number generating function creates delays between the
time of symptom onset ($date_onset ) and the case being reported
($date_reporting ).
The function can be defined or anonymous. The function must return a vector
of numeric s for the length of the reporting delay. The function must have
a single argument.
The default is NULL so by default there is no reporting delay, and the
$date_reporting line list column is identical to the $date_onset column.
|