base_MQ

This function does the actual calculations for <code>summarize_stats_CSV</code>.
It calculates mean and quantiles, writing output to the appropriate folder.

A simulation modeling framework which significantly extends capabilities from the
'MGDrivE' simulation package via a new mathematical and computational framework based on stochastic Petri nets.
For more information about 'MGDrivE', see our publication: Sánchez et al. (2019) <doi:10.1111/2041-210X.13318>
Some of the notable capabilities of 'MGDrivE2' include: incorporation of human populations,
epidemiological dynamics, time-varying parameters, and a continuous-time simulation
framework with various sampling algorithms for both deterministic and stochastic interpretations.
'MGDrivE2' relies on the genetic inheritance structures provided in package 'MGDrivE', so we
suggest installing that package initially.

Agastya Mondal

MGDrivE2

Mosquito Gene Drive Explorer 2

Sean L. Wu

Jared B. Bennett

Héctor Manuel Sánchez Castellanos

Tomás M. León

Andrew J. Dolgert

John M. Marshall

base_MQ function

<dl><dt>fList</dt>
<dd>File list, all files for this stage, organized by repetition</dd>
<dt>oDir</dt>
<dd>Output directory</dd>
<dt>sName</dt>
<dd>Stage signifier</dd>
<dt>nodeNames</dt>
<dd>Properly formatted vector of node names for printing</dd>
<dt>nNodes</dt>
<dd>Number of nodes in the simulation</dd>
<dt>genos</dt>
<dd>Vector of genotypes for the header</dd>
<dt>nGenos</dt>
<dd>Number of genotypes</dd>
<dt>times</dt>
<dd>Vector of sampling times</dd>
<dt>nTimes</dt>
<dd>Number of sampled times</dd>
<dt>num_repss</dt>
<dd>Number of repetitions from the simulation</dd>
<dt>mean</dt>
<dd>Boolean, calculate mean or not</dd>
<dt>quantiles</dt>
<dd>Vector of quantiles to calculate, or NULL</dd>
<dt>oDepth</dt>
<dd>Max(1, number of quantiles)</dd></dl>

Arguments

Base Summary Function — base_MQ

<dl>

<dt>fList</dt>
<dd>File list, all files for this stage, organized by repetition</dd>


<dt>oDir</dt>
<dd>Output directory</dd>


<dt>sName</dt>
<dd>Stage signifier</dd>


<dt>nodeNames</dt>
<dd>Properly formatted vector of node names for printing</dd>


<dt>nNodes</dt>
<dd>Number of nodes in the simulation</dd>


<dt>genos</dt>
<dd>Vector of genotypes for the header</dd>


<dt>nGenos</dt>
<dd>Number of genotypes</dd>


<dt>times</dt>
<dd>Vector of sampling times</dd>


<dt>nTimes</dt>
<dd>Number of sampled times</dd>


<dt>num_repss</dt>
<dd>Number of repetitions from the simulation</dd>


<dt>mean</dt>
<dd>Boolean, calculate mean or not</dd>


<dt>quantiles</dt>
<dd>Vector of quantiles to calculate, or NULL</dd>


<dt>oDepth</dt>
<dd>Max(1, number of quantiles)</dd>

</dl>

base_MQ: Base Summary Function

Description

Usage

Value

Arguments