true_pairs

<a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated"><img src="figures/lifecycle-deprecated.svg?package=phylosamp&version=1.0.1" alt="[Deprecated]"></a>
This function calculates the expected number true transmission pairs in a sample of size <code>M</code>.
Assumptions about transmission and linkage (single or multiple) can be specified.

Implements novel tools for estimating sample sizes needed for phylogenetic studies, including
studies focused on estimating the probability of true pathogen transmission between two cases given phylogenetic linkage and studies focused on tracking pathogen variants at a population level. Methods described in Wohl, Giles, and Lessler (2021) and in Wohl, Lee, DiPrete, and Lessler (2023).

Justin Lessler

phylosamp

Sample Size Calculations for Molecular and Phylogenetic Studies

Shirlee Wohl

Elizabeth C Lee

Lucy D'Agostino McGowan

John R Giles

true_pairs function

<dl><dt>eta</dt>
<dd>scalar or vector giving the sensitivity of the linkage criteria</dd>
<dt>rho</dt>
<dd>scalar or vector giving the proportion of the final outbreak size that is sampled</dd>
<dt>M</dt>
<dd>scalar or vector giving the number of cases sampled</dd>
<dt>R</dt>
<dd>scalar or vector giving the effective reproductive number of the pathogen (default=NULL)</dd>
<dt>assumption</dt>
<dd>a character vector indicating which assumptions about transmission and linkage criteria. Default = <code>'mtml'</code>. Accepted arguments are:<ol>
<li><code>'stsl'</code> for the single-transmission single-linkage assumption (<code>prob_trans_stsl()</code>).</li>
<li><code>'mtsl'</code> for the multiple-transmission single-linkage assumption (<code>prob_trans_mtsl()</code>).</li>
<li><code>'mtml'</code> for the multiple-transmission multiple-linkage assumption (<code>prob_trans_mtml()</code>).</li>
</ol></dd></dl>

Arguments

John Giles, Shirlee Wohl, and Justin Lessler

Author

<a href='https://lifecycle.r-lib.org/articles/stages.html#deprecated'><img src='figures/lifecycle-deprecated.svg' alt='[Deprecated]' /></a>
This function calculates the expected number true transmission pairs in a sample of size <code>M</code>.
Assumptions about transmission and linkage (single or multiple) can be specified.

Calculate expected number of true transmission pairs — true_pairs

<dl>

<dt>eta</dt>
<dd>scalar or vector giving the sensitivity of the linkage criteria</dd>


<dt>rho</dt>
<dd>scalar or vector giving the proportion of the final outbreak size that is sampled</dd>


<dt>M</dt>
<dd>scalar or vector giving the number of cases sampled</dd>


<dt>R</dt>
<dd>scalar or vector giving the effective reproductive number of the pathogen (default=NULL)</dd>


<dt>assumption</dt>
<dd>a character vector indicating which assumptions about transmission and linkage criteria. Default = <code>'mtml'</code>. Accepted arguments are:<ol>
<li><code>'stsl'</code> for the single-transmission single-linkage assumption (<code>prob_trans_stsl()</code>).</li>
<li><code>'mtsl'</code> for the multiple-transmission single-linkage assumption (<code>prob_trans_mtsl()</code>).</li>
<li><code>'mtml'</code> for the multiple-transmission multiple-linkage assumption (<code>prob_trans_mtml()</code>).</li>
</ol></dd>

</dl>

true_pairs: Calculate expected number of true transmission pairs

Description

Usage

Value

Arguments

Author

See Also

Examples