fit_exp_lag_to_curve

Fits the lag to one growth curve based on the basic tangent 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

fit_exp_lag_to_curve function

<dl><dt>data</dt>
<dd>a data frame with two required columns names: "time" and "biomass",
This is data from one growth curve only, one (mean) observation per time</dd>
<dt>n0</dt>
<dd>the initial biomass (a tangent line crossing N0 line will determine the lag)</dd>
<dt>tangent_method</dt>
<dd>"local.regression" (if the tangent is fitted to a number of points around the maximal growth rate)
or "to.point" (if the tangent is fitted only to the point where the growth rate is maximal); defaults to "to.point"</dd>
<dt>curve_points</dt>
<dd>if tangent_method = "local.regression" then curve_points is the number of points the line is fitted to;
defaults to 3 i.e. the point with the maximal uptake rate one point before and one point after</dd></dl>

Arguments

fit_exp_lag_to_curve — fit_exp_lag_to_curve

<dl>

<dt>data</dt>
<dd>a data frame with two required columns names: "time" and "biomass",
This is data from one growth curve only, one (mean) observation per time</dd>


<dt>n0</dt>
<dd>the initial biomass (a tangent line crossing N0 line will determine the lag)</dd>


<dt>tangent_method</dt>
<dd>"local.regression" (if the tangent is fitted to a number of points around the maximal growth rate)
or "to.point" (if the tangent is fitted only to the point where the growth rate is maximal); defaults to "to.point"</dd>


<dt>curve_points</dt>
<dd>if tangent_method = "local.regression" then curve_points is the number of points the line is fitted to;
defaults to 3 i.e. the point with the maximal uptake rate one point before and one point after</dd>

</dl>

fit_exp_lag_to_curve: fit_exp_lag_to_curve

Description

Usage

Value

Arguments