samplesize

<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 sample size needed to obtain at least a defined false discovery rate given
a final outbreak size \(N\).

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

samplesize function

<dl><dt>eta</dt>
<dd>scalar or vector giving the sensitivity of the linkage criteria</dd>
<dt>chi</dt>
<dd>scalar or vector giving the specificity of the linkage criteria</dd>
<dt>N</dt>
<dd>scalar or vector giving the final outbreak size</dd>
<dt>R</dt>
<dd>scalar or vector giving the effective reproductive number of the pathogen</dd>
<dt>phi</dt>
<dd>scalar or vector giving the desired true discovery rate (1-false discovery rate)</dd>
<dt>min_pairs</dt>
<dd>minimum number of linked pairs observed in the sample, defaults to 1 pair (2 samples); this is to ensure reasonable results are obtained</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 sample size needed to obtain at least a defined false discovery rate given
a final outbreak size \(N\).

Calculate sample size — samplesize

<dl>

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


<dt>chi</dt>
<dd>scalar or vector giving the specificity of the linkage criteria</dd>


<dt>N</dt>
<dd>scalar or vector giving the final outbreak size</dd>


<dt>R</dt>
<dd>scalar or vector giving the effective reproductive number of the pathogen</dd>


<dt>phi</dt>
<dd>scalar or vector giving the desired true discovery rate (1-false discovery rate)</dd>


<dt>min_pairs</dt>
<dd>minimum number of linked pairs observed in the sample, defaults to 1 pair (2 samples); this is to ensure reasonable results are obtained</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>

samplesize: Calculate sample size

Description

Usage

Value

Arguments

Author

Examples