calc_lag_fit_to_baranyi_with_lag

Runs nlsLM/nls algorithms with three different parameter setups to fit the best Logistic model parameters to our data and chooses the best model

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_lag_fit_to_baranyi_with_lag function

<dl><dt>gr_curve</dt>
<dd>data from one specific growth curve with these two columns: time and biomass</dd>
<dt>LOG10N0</dt>
<dd>the decimal logarithm of initial biomass</dd>
<dt>init_lag</dt>
<dd>initial value for the lag parameter</dd>
<dt>init_mumax</dt>
<dd>initial value for the mumax parameter</dd>
<dt>init_LOG10Nmax</dt>
<dd>initial value for the LOG10Nmax parameter</dd>
<dt>algorithm</dt>
<dd>defaults to "auto" which chooses between bounded and unbounded Levenberg-Marquardt method and the bounded port method</dd>
<dt>max_iter</dt>
<dd>max. number of itertaions; defaults to 100</dd>
<dt>lower_bound</dt>
<dd>lower.bound for the bounded nls optimisation; defaults to 0</dd></dl>

Arguments

calc_lag_fit_to_baranyi_with_lag — calc_lag_fit_to_baranyi_with_lag

<dl>

<dt>gr_curve</dt>
<dd>data from one specific growth curve with these two columns: time and biomass</dd>


<dt>LOG10N0</dt>
<dd>the decimal logarithm of initial biomass</dd>


<dt>init_lag</dt>
<dd>initial value for the lag parameter</dd>


<dt>init_mumax</dt>
<dd>initial value for the mumax parameter</dd>


<dt>init_LOG10Nmax</dt>
<dd>initial value for the LOG10Nmax parameter</dd>


<dt>algorithm</dt>
<dd>defaults to "auto" which chooses between bounded and unbounded Levenberg-Marquardt method and the bounded port method</dd>


<dt>max_iter</dt>
<dd>max. number of itertaions; defaults to 100</dd>


<dt>lower_bound</dt>
<dd>lower.bound for the bounded nls optimisation; defaults to 0</dd>

</dl>

calc_lag_fit_to_baranyi_with_lag: calc_lag_fit_to_baranyi_with_lag

Description

Usage

Value

Arguments