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.


Travis-CI Build Status

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")

Using 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.

A simple working example

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

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("growthcurver")

0.3.0 by Kathleen sprouffske, 7 months 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 minpack.lm, stats, graphics, grDevices

Suggests testthat, knitr, dplyr, ggplot2


See at CRAN