do_growth_analysis: Perform growth analysis on a varioscan data set

In MichielNoback/growthis: Loads, analyses and visualises Varioscan data

Perform growth analysis on a varioscan data set

Description

Perform growth analysis on a varioscan data set

Usage

do_growth_analysis(varioscan)

Arguments

varioscan

the varioscan data in long format

Details

Most data comes from the growthcurver package. Only yield is added here.

The population size at the beginning of the growth curve is given by N0. The maximum possible population size in a particular environment, or the carrying capacity, is given by K. The intrinsic growth rate of the population, r, is the growth rate that would occur if there were no restrictions imposed on total population size.

The most useful values are k, n0, and r, which are the values of the parameters for the logistic equation that best fit the data. The fitting algorithm provides a measure of uncertainty for each, which is available (for n) in the n_p and n_se values, for example. The values sigma and df are both determined during the nonlinear regression fit. Df is the degrees of freedom and sigma is a measure of the goodnesss of fit of the parameters of the logistic equation for the data; it is the residual standard error from the nonlinear regression model. Smaller sigma values indicate a better fit of the logistic curve to the data than larger values.

t_mid is the time at which the population density reaches 12K (which occurs at the inflection point), t_gen is the fastest possible generation time (also called the doubling time), auc_l is the area under the logistic curve obtained by taking the integral of the logistic equation, and auc_e is the empirical area under the curve which is obtained by summing up the area under the experimental curve from the measurements in the input data. If you decide to use auc_l or auc_e, make sure that you specify the parameter t_trim so that these metrics are comparable across samples or plates that were grown for different lengths of time.

The note value provides additional information about problems with fitting the logistic curve to your data. No common problems were identified if it is empty.

MichielNoback/growthis documentation built on Jan. 4, 2023, 10:30 a.m.