Simple Metrics to Summarize Growth Curves

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

install.packages("growthcurver")

You can install the latest development version from github with

# install devtools first if you don't already have the package
install.packages("devtools")
 
# then install growthcurver
devtools::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

  • What your input data should look like
  • How to use growthcurver to get summary metrics on a single growth curve sample
  • How to use growthcurver to get summary metrics on an entire plate of growth curves
  • What those metrics mean and some best practices for quality control

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 package
d <- growthdata                          # load some sample, simulated data
gc_fit <- SummarizeGrowth(d$time, d$A1)  # do the analysis
plot(gc_fit)                             # plot your data and the best fit
gc_fit                                   # view some returned metrics

News

Reference manual

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install.packages("growthcurver")

0.2.1 by Kathleen sprouffske, 2 years ago


https://github.com/sprouffske/growthcurver


Report a bug at https://github.com/sprouffske/growthcurver/issues


Browse source code at https://github.com/cran/growthcurver


Authors: Kathleen sprouffske [aut, cre]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports caTools, minpack.lm, stats, graphics, grDevices

Suggests testthat, knitr, dplyr, ggplot2


See at CRAN