lag_biomass_incr

Fits the lag to multiple growth curves based on the biomass increase method

Microbial growth is often measured by growth curves i.e. a table of population sizes and times of measurements.
This package allows to use such growth curve data to determine the duration of "microbial lag phase" i.e. the time needed for microbes to restart divisions.
It implements the most commonly used methods to calculate the lag duration, these methods are discussed and described in Opalek et.al. 2022.
Citation: Smug, B. J., Opalek, M., Necki, M., & Wloch-Salamon, D. (2024). Microbial lag calculator: A shiny-based application and an R package for calculating the duration of microbial lag phase. Methods in Ecology and Evolution, 15, 301–307 <doi:10.1111/2041-210X.14269>.

Bogna Smug 

miLAG

Calculates Microbial Lag Duration (on the Population Level) from
Provided Growth Curve Data

Bogna Smug

lag_biomass_incr function

<dl><dt>data</dt>
<dd>a data frame with two required columns names: "time" and "biomass",and one optional column: "curve_id"
This is data from may come from multiple growth curves</dd>
<dt>threshold</dt>
<dd>A value of the biomass increase that we can surely associate with the end of the lag phase rather than random variation during the lag</dd>
<dt>n0</dt>
<dd>the initial biomass (lag will be defined as the time point where the difference between biomass and N0 reaches a predefined threshold)</dd></dl>

Arguments

lag_biomass_incr — lag_biomass_incr

<dl>

<dt>data</dt>
<dd>a data frame with two required columns names: "time" and "biomass",and one optional column: "curve_id"
This is data from may come from multiple growth curves</dd>


<dt>threshold</dt>
<dd>A value of the biomass increase that we can surely associate with the end of the lag phase rather than random variation during the lag</dd>


<dt>n0</dt>
<dd>the initial biomass (lag will be defined as the time point where the difference between biomass and N0 reaches a predefined threshold)</dd>

</dl>

lag_biomass_incr: lag_biomass_incr

Description

Usage

Value

Arguments