varfreq_obs_freq

This function calculates the observed variant prevalence from the coefficient of detection ratio
and the actual variant prevalence. This function assumes that variant 1 is the variant of concern.
This function is specific to the two-variant system.

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

varfreq_obs_freq function

<dl><dt>p_v1</dt>
<dd>actual variant prevalence (proportion)</dd>
<dt>c_ratio</dt>
<dd>coefficient of detection ratio, calculated as the ratio of the coefficients of variant 1 to variant 2</dd></dl>

Arguments

Shirlee Wohl, Elizabeth C. Lee, Bethany L. DiPrete, and Justin Lessler

Author

Calculate observed variant prevalence — varfreq_obs_freq

<dl>

<dt>p_v1</dt>
<dd>actual variant prevalence (proportion)</dd>


<dt>c_ratio</dt>
<dd>coefficient of detection ratio, calculated as the ratio of the coefficients of variant 1 to variant 2</dd>

</dl>

varfreq_obs_freq: Calculate observed variant prevalence

Description

Usage

Value

Arguments

Author

See Also

Examples