Increased competition flattens the dominance hierarchy

This repository contains the data and code for our project: Redefining dominance calculation: Increased competition flattens the dominance hierarchy in dairy cows.

Getting Started

To load this project, please follow the instructions below:

1. Set your working directory to the folder where this README.md file is located using setwd().

2. Run the following R code to install required R packages:

# List of packages to be installed
packages <- c("ProjectTemplate", "lubridate", "plyr", "here", "zoo", "ggplot2", "EloRating", "EloSteepness", "viridis", "dplyr", "lme4", "lmerTest", "rstudioapi")

# Function to check and install missing packages
install_if_missing <- function(pkg) {
  if (!require(pkg, character.only = TRUE)) {
    install.packages(pkg, dependencies = TRUE)
  }
}

# Apply the function to each package
sapply(packages, install_if_missing)

4. Run the following R code to load this R project:

library('ProjectTemplate')
load.project()

3. Repository Structure Here's a brief overview of the repository's structure:

• cache: Contains crucial intermediate data used in the final analysis.
• config: Holds the configuration settings for this R project.
• data: Contains both the raw data and the processed data resulting from our analysis.
• graphs: Stores all the visual plots and graphs generated during the analysis.
• lib: Houses helper functions crafted to assist in analysis and preprocessing.
• munge: Contains scripts that utilize functions to preprocess the data.
• renv: Provides details about the R environment set up during the project's inception.
• reports: Contains the manuscript detailing our findings and observations.
• src: Contains scripts used for the final statistical analysis.

Thank you for your interest in our project. We hope you find the data and code insightful!

Dataset Information

• Title of Dataset: Replication Data for: Redefining dominance calculation: Increased competition flattens the dominance hierarchy in dairy cows
• Paper DOI: https://doi.org/10.3168/jds.2023-24587
• Dataset DOI: https://doi.org/10.5683/SP3/HT9EHX
• Dataset Created: 2023-07-29
• Created by: Kehan (Sky) Sheng
• Contact Email: [email protected]

Contributors

• Principal Investigator: Marina von Keyserlingk

  • ORCID: 0000-0002-1427-3152
  • Affiliation: University of British Columbia
  • Email: [email protected]

• Co-Investigator: Daniel Weary

  • ORCID: 0000-0002-0917-3982
  • Affiliation: University of British Columbia
  • Email: [email protected]

• Contributor: Kehan Sheng

  • ORCID: 0000-0001-6442-5284
  • Affiliation: University of British Columbia
  • Email: [email protected]

• Contributor: Borbala Foris

  • ORCID: 0000-0002-0901-3057
  • Affiliation while working on this project: University of British Columbia
  • Current affiliation: University of Veterinary Medicine, Vienna
  • Email: [email protected]

• Contributor: Joseph Krahn

  • ORCID: 0000-0002-1559-1216
  • Affiliation: University of British Columbia
  • Email: [email protected]

Project Information

• Date of Data Collection: July 15, 2020 - May 19, 2021
• Location of Data Collection: UBC Dairy Education and Research Centre, 6947 No. 7 Highway, Agassiz, BC V0M 1A0, Canada
• Funding: This project was supported by the NSERC Industrial Research Chair.