calc_baranyi_fit_lag

Calculates lag based on fitting baranyi model to data

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

calc_baranyi_fit_lag 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>n0</dt>
<dd>a data frame describing initial biomass for each of the curves, i.e. it has two obligatory columns: "curve_id", "N0"</dd>
<dt>init_lag</dt>
<dd>initial value for the lag parameter, defaults to NULL in which case it will be approximated based on the data</dd>
<dt>init_gr_rate</dt>
<dd>initial value for the growth rate, defaults to NULL in which case it will be approximated based on the data</dd>
<dt>algorithm</dt>
<dd>eg. "auto", "Levenberg-Marquardt", "port", defaults to "auto"</dd>
<dt>max_iter</dt>
<dd>Maximum number of iterations, defaults to 100</dd></dl>

Arguments

calc_baranyi_fit_lag — calc_baranyi_fit_lag

<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>n0</dt>
<dd>a data frame describing initial biomass for each of the curves, i.e. it has two obligatory columns: "curve_id", "N0"</dd>


<dt>init_lag</dt>
<dd>initial value for the lag parameter, defaults to NULL in which case it will be approximated based on the data</dd>


<dt>init_gr_rate</dt>
<dd>initial value for the growth rate, defaults to NULL in which case it will be approximated based on the data</dd>


<dt>algorithm</dt>
<dd>eg. "auto", "Levenberg-Marquardt", "port", defaults to "auto"</dd>


<dt>max_iter</dt>
<dd>Maximum number of iterations, defaults to 100</dd>

</dl>

calc_baranyi_fit_lag: calc_baranyi_fit_lag

Description

Usage

Value

Arguments