.sample_outcome_time

The outcome of a case, either died or recovered, can have a time of event,
but this must be after the hospitalisation time, if a case has been admitted
to hospital. This function samples either the onset-to-death or
onset-to-recovery time conditional on it being greater than a
onset-to-hospitalisation time for a given case, if the case was admitted
to hospital. It does this by resampling onset-to-outcome (death or recovery)
times if they are less than the onset-to-hospitalisation time (from
<code>.add_hospitalisation()</code>).

internal

Tools to simulate realistic raw case data for an epidemic in
the form of line lists and contacts using a branching process.
Simulated outbreaks are parameterised with epidemiological parameters
and can have age-structured populations, age-stratified
hospitalisation and death risk and time-varying case fatality risk.

Joshua W. Lambert

simulist

Simulate Disease Outbreak Line List and Contacts Data

Carmen Tamayo

Hugo Gruson

Pratik R. Gupte

Adam Kucharski

Chris Hartgerink

Sebastian Funk

London School of Hygiene and Tropical Medicine, LSHTM 

.sample_outcome_time function

<dl><dt>.data</dt>
<dd>A <code>&lt;data.frame&gt;</code> containing the infectious history from a
branching process simulation (<code>.sim_network_bp()</code>).</dd>
<dt>onset_to_outcome</dt>
<dd>A <code>function</code> for either the onset-to-death or
onset-to-recovery delay distribution. <code>onset_to_outcome</code> can also be set to
<code>NULL</code> to not simulate dates for individuals that died or recovered. See
<code>sim_linelist()</code> documentation for more information.</dd>
<dt>idx</dt>
<dd>Either the <code>infected_lgl_idx</code> or <code>died_lgl_idx</code> from
<code>.add_outcomes()</code> to define who to sample recovery or death times for,
respectively.</dd></dl>

Arguments

Sample the onset-to-outcome time conditional that the outcome is after
a hospitalisation event — .sample_outcome_time

<dl>

<dt>.data</dt>
<dd>A <code>&lt;data.frame&gt;</code> containing the infectious history from a
branching process simulation (<code>.sim_network_bp()</code>).</dd>


<dt>onset_to_outcome</dt>
<dd>A <code>function</code> for either the onset-to-death or
onset-to-recovery delay distribution. <code>onset_to_outcome</code> can also be set to
<code>NULL</code> to not simulate dates for individuals that died or recovered. See
<code>sim_linelist()</code> documentation for more information.</dd>


<dt>idx</dt>
<dd>Either the <code>infected_lgl_idx</code> or <code>died_lgl_idx</code> from
<code>.add_outcomes()</code> to define who to sample recovery or death times for,
respectively.</dd>

</dl>

Sample the onset-to-outcome time conditional that the outcome is after
a hospitalisation event

.sample_outcome_time: Sample the onset-to-outcome time conditional that the outcome is after a hospitalisation event

Description

Usage

Value

Arguments