varfreq_freq_logistic

This function calculates the observed variant prevalence after t time steps (e.g., days)
given a logistic growth rate and initial variant prevalence.

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_freq_logistic function

<dl><dt>t</dt>
<dd>time step number (e.g., days) at which to calculate prevalence</dd>
<dt>p0_v1</dt>
<dd>initial variant prevalence (# introductions / infected population size)</dd>
<dt>r_v1</dt>
<dd>logistic growth rate</dd>
<dt>c_ratio</dt>
<dd>coefficient of detection ratio, calculated as the ratio of the coefficients of variant 1 to variant 2; default = 1 (no bias)</dd></dl>

Arguments

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

Author

Calculate observed variant prevalence at time t given logistic growth — varfreq_freq_logistic

<dl>

<dt>t</dt>
<dd>time step number (e.g., days) at which to calculate prevalence</dd>


<dt>p0_v1</dt>
<dd>initial variant prevalence (# introductions / infected population size)</dd>


<dt>r_v1</dt>
<dd>logistic growth rate</dd>


<dt>c_ratio</dt>
<dd>coefficient of detection ratio, calculated as the ratio of the coefficients of variant 1 to variant 2; default = 1 (no bias)</dd>

</dl>

varfreq_freq_logistic: Calculate observed variant prevalence at time t given logistic growth

Description

Usage

Value

Arguments

Author

See Also

Examples