This is a simple package that fits the logistic equation to microbial growth curve data (e.g., repeated absorbance measurements taken from a plate reader over time). From this fit, a variety of metrics are provided, including the maximum growth rate, the doubling time, the carrying capacity, the area under the logistic curve, and the time to the inflection point.
Growthcurver is an R package that fits growth curve data to a standard form of the logistic equation common in ecology and evolution whose parameters (the growth rate, the initial population size, and the carrying capacity) provide meaningful population-level information with straight-forward biological interpretation.
You can install the latest released version from CRAN from within R with
You can install the latest development version from github with
# install devtools first if you don't already have the packageinstall.packages("devtools")# then install growthcurverdevtools::install_github("sprouffske/growthcurver")
The easiest way to get started with growthcurver is to work through the examples in the vignette. In the vignette, you can find information on
You can find the vignette at bit.ly/1p7w6dJ.
This code loads the
growthcurver package and some sample data. Then, it calls
SummarizeGrowth to do the analysis.
library(growthcurver) # load the packaged <- growthdata # load some sample, simulated datagc_fit <- SummarizeGrowth(d$time, d$A1) # do the analysisplot(gc_fit) # plot your data and the best fitgc_fit # view some returned metrics