AntColonyPerformance compendium

A compendium of code, data, and author's manuscript draft for In Preparation work

This pre-release can be cited as the following:

Greg T. Chism. (2022). Gchism94/AntColonyPerformance: (Pre-release) Research Compendium for In preparation work (v0.1.0). Zenodo. https://doi.org/10.5281/zenodo.6872019

Overview

This repository is organized as a reproducible research compendium. Click the button above to explore in an interactive RStudio session. Binder uses rocker-project.org Docker images to ensure a consistent and reproducible computational environment. These Docker images can also be used locally.

This repository promotes the use of CyVerse, a cloud-based alternative to the RStudio IDE, and a more scalable option to RStudio Cloud.

To use CyVerse, subscribe at the top-right corner found in the link here. Next click the badge above to open the latest version of rocker-verse, which opens an RStudio container with the tidyverse meta-package installed.

Once loaded, run git clone https://github.com/Gchism94/Data7_EDA_In_R_Workshops.git to clone this repository and run everything as normal.

File Organization

analysis/
|
├── paper/
│   ├── paper.Rmd       # this is the main document to edit
│   └── paper.pdf       # this is an elsevier .pdf written from paper.Rmd
|
├── figures/            # location of the figures produced by the scripts in R
|
├── data/
│   ├── raw_data/       # data obtained from elsewhere
|   ├── derived_data    # data derived from the code in analysis/R
│   └── ref_data/       # data used to obtain final data and during the analysis
|   
├── supplementary-materials/
│   ├── Supplementary_Figures/     
|   |                   # supplementary figures for the main manuscript
│   └── Supplementary_Tables/      
|                       # supplementary tables for the main manuscript (currently empty)
|
└── R                   # Suggested run order is shown (also see associated README.md files)
    |                   
    ├── AggnPerformance.R        
    |                   # R script used to determine colony performance against an invader, including code for analyses and figures
    ├── ABCTracker_Movement.R 
    |                   # R script used to transform raw ABCTracker movement data to analyze colony activity
    ├── MovementBins_Density.R  
    |                   # R script used to bin data from ABCTracker_Movement.R to calculate worker traffic jams in relation to worker density
    ├── ABCTracker_AdjacencyMatrix.R  
    |                   # R script used to create adjacency matrices from raw ABCTracker movement data
    └── ABCTracker_Networks.R  
                        # R script used to create and analyze worker interaction networks from adjacency matrices per ABCTracker_AdjacencyMatrix.R

An Rmd notebook and associated pdf for the manuscript can be found in analysis/paper. This notebook produces a .pdf document in elsevier format.

README.md files are included in all subdirectories with explanations or contents related to the paper. It should also provide a useful starting point for extending and exploring these materials for other projects.

Or to explore the code locally, clone or download this repository into RStudio or your preferred environment and install the compendium by running devtools::install(). To install additional dependencies used only in formatting the figures, use devtools::install(dep=TRUE).