calc_sample_sizes

This function takes a compiled data.frame following the format shown in the <code>template_WES_data</code> object
and calculates basic sample sizes and detection rates for all gene targets.

Provides reproducible functions for collating and analyzing
data from environmental sampling studies. Environmental Sampling (ES)
of infectious diseases involves collecting samples from various sources
(such as sewage, water, air, soil, or surfaces) to monitor the presence
of pathogens in the environment. Analysis of ES data often requires the
calculation of Real-Time Quantitative PCR (qPCR) variables, normalizing
ES observations, and analyzing sampling site characteristics. To help
reduce the complexity of these analyses we have implemented tools that
assist with establishing standardized ES data formats, absolute and
relative quantification of qPCR data, estimation of qPCR amplification
efficiency, and collating open-source spatial data for sampling sites.

John R Giles

Tools for Analyzing Wastewater and Environmental Sampling Data

calc_sample_sizes function

<dl><dt>df</dt>
<dd>A data.frame produced by the <code>compile_tac_data</code> function containing 'target_name' and 'ct_value' columns.</dd>
<dt>cutoff</dt>
<dd>Numeric scalar giving the cutoff Ct value over which a gene target is deemed absent from a sample. Default is 40.</dd></dl>

Arguments

Calculate sample sizes — calc_sample_sizes

<dl>

<dt>df</dt>
<dd>A data.frame produced by the <code>compile_tac_data</code> function containing 'target_name' and 'ct_value' columns.</dd>


<dt>cutoff</dt>
<dd>Numeric scalar giving the cutoff Ct value over which a gene target is deemed absent from a sample. Default is 40.</dd>

</dl>

calc_sample_sizes: Calculate sample sizes

Description

Usage

Value

Arguments

Examples