.check_time_args

This function checks the time-related inputs, i.e., start time of each chain,
<code>t0</code>, the end time of the simulation, <code>tf</code>, and the generation time,
generation_time. It also checks that the generation_time argument is
specified if <code>tf</code> is specified as these go hand-in-hand.

internal

Provides methods to simulate and analyse the size and length
of branching processes with an arbitrary offspring distribution. These
can be used, for example, to analyse the distribution of chain sizes
or length of infectious disease outbreaks, as discussed in Farrington
et al. (2003) <doi:10.1093/biostatistics/4.2.279>.

James M. Azam

epichains

Simulating and Analysing Transmission Chain Statistics Using
Branching Process Models

Sebastian Funk

Flavio Finger

Zhian N. Kamvar

Hugo Gruson

Karim Mané

Pratik Gupte

Joshua W. Lambert

.check_time_args function

<dl><dt>tf_specified</dt>
<dd><code>&lt;logical&gt;</code>; Whether the <code>tf</code> argument is specified. Only
makes sense in the context where this function is called, i.e., in
<code>simulate_chains()</code>. If <code>tf</code> is specified, generation_time must be specified.</dd>
<dt>tf</dt>
<dd>A number for the cut-off for the infection times (if generation
time is given); Defaults to <code>Inf</code>.</dd>
<dt>generation_time</dt>
<dd>The generation time function; the name
of a user-defined named or anonymous function with only one argument <code>n</code>,
representing the number of generation times to sample.</dd>
<dt>t0</dt>
<dd>Start time (if generation time is given); either a single value
or a vector of same length as <code>n_chains</code> (number of initial cases) with
corresponding initial times. Defaults to 0, meaning all cases started at
time 0.</dd></dl>

Arguments

Check inputs that control time events — .check_time_args

<dl>

<dt>tf_specified</dt>
<dd><code>&lt;logical&gt;</code>; Whether the <code>tf</code> argument is specified. Only
makes sense in the context where this function is called, i.e., in
<code>simulate_chains()</code>. If <code>tf</code> is specified, generation_time must be specified.</dd>


<dt>tf</dt>
<dd>A number for the cut-off for the infection times (if generation
time is given); Defaults to <code>Inf</code>.</dd>


<dt>generation_time</dt>
<dd>The generation time function; the name
of a user-defined named or anonymous function with only one argument <code>n</code>,
representing the number of generation times to sample.</dd>


<dt>t0</dt>
<dd>Start time (if generation time is given); either a single value
or a vector of same length as <code>n_chains</code> (number of initial cases) with
corresponding initial times. Defaults to 0, meaning all cases started at
time 0.</dd>

</dl>

Check inputs that control time events

.check_time_args: Check inputs that control time events

Description

Usage

Value

Arguments