https://github.com/barricklab/fitnessr
R package for calculating relative fitness from co-culture competition assays
https://github.com/barricklab/fitnessr
Last synced: 4 months ago
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R package for calculating relative fitness from co-culture competition assays
- Host: GitHub
- URL: https://github.com/barricklab/fitnessr
- Owner: barricklab
- License: gpl-3.0
- Created: 2022-12-09T03:26:54.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2023-04-21T21:10:10.000Z (over 3 years ago)
- Last Synced: 2025-09-09T13:54:11.470Z (11 months ago)
- Language: HTML
- Homepage:
- Size: 1.27 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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:
```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:
```R
install.packages("devtools")
devtools::install()
```
## Quick Start
Download [competition_template.csv](https://raw.githubusercontent.com/barricklab/fitnessR/main/data-raw/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:
```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](https://htmlpreview.github.io/?https://github.com/barricklab/fitnessR/blob/main/vignettes/introduction.html) for more detailed examples that include calculating confidence intervals on relative fitness estimates and plotting competition data.