fitnessR

An R package for calculating relative fitness from co-culture competition assay data.

Installation

From GitHub

To install the current version of this package directly from GitHub, run this command in R:

install.packages("devtools")
devtools::install_github("barricklab/fitnessR")

From a Source Package

To install a version of this package from a source release downloaded from GitHub, run this command in R with your current working directory as the main directory of the uncompressed source release:

install.packages("devtools")
devtools::install()

Quick Start

Download competition_template.csv. (Right click this link and choose "Save Link As...")

Open the CSV file in a spreadsheet or text editor. Fill it in as directed by the comments in the file.

Calculate relative fitness by running these commands in R:

library(fitnessR)
competition_data = read.csv("competition_template.csv")
processed_competition_data = calculate_fitness(competition_data)
write.csv(processed_competition_data, "competition_template.csv")

More Information

See the Introduction to fitnessR Vignette for more detailed examples that include calculating confidence intervals on relative fitness estimates and plotting competition data.