nestarchorg
Research Compendium for the preprint DOI: https://doi.org/10.1101/2022.06.30.498314
Science Score: 59.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 6 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
2 of 4 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.2%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Research Compendium for the preprint DOI: https://doi.org/10.1101/2022.06.30.498314
Basic Info
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 1
- Releases: 3
Topics
Metadata Files
README.md
NestArchOrg compendium
A compendium of code, data, and author's manuscript accompanying the preprint:
Greg Chism, 
. William Nichols, Anna Dornhaus, Cavity geometry shapes overall ant colony organization through spatial limits but workers maintain fidelity zones. Preprint on bioRxiv, 30 Oct 2023 https://doi.org/10.1101/2022.06.30.498314
This compendium includes data found on the Zenodo repository:
To cite this repository use the following:
Chism, G., Nichols, W., & Dornhaus, A. (2022). NestArchOrg (Version 1.0.0) [Computer software]. https://doi.org/10.5281/zenodo.6828919
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.
File Organization
analysis/
|
paper/
paper.Rmd # this is the main document to edit
paper.pdf # this is an elsevier .pdf written from paper.Rmd
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figures/ # location of the figures produced by the scripts in R
tables/ # location of the tables produced by the scripts in R
data/
rawData/ # data obtained from elsewhere
| processed/ # processed output data from R scripts
refData/ # data used to obtain final data and during the analysis
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supplementaryMaterials/
supplementaryFigures/
| | # supplementary figures for the main manuscript
supplementaryTables/
| # supplementary tables for the main manuscript
|
R # Run in the following order (also see associated README.md)
Stat_boxplot_custom.R
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binsWorking.R # R script used to bin raw x, y coordinates into nest sections
distanceFunctions.R
| # R script used to calculate distances in the nest from binned x, y coordinates
fidelityZonesFunctions.R # R script used to calculate site fidelity for binned marked worker x, y coordinates
nestArchFunctsAnalyses.R
# R script used to produce all statistical analyses and figures
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).
Owner
- Name: Greg T. Chism
- Login: Gchism94
- Kind: user
- Location: Tucson, AZ
- Company: University of Arizona
- Website: https://gregtchism.com/
- Repositories: 14
- Profile: https://github.com/Gchism94
Data Scientist | PhD, University of Arizona | R/RStudio Evangelist
GitHub Events
Total
Last Year
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Greg T. Chism | g****m@e****u | 128 |
| dependabot[bot] | 4****] | 8 |
| Gchism94 | g****m@a****u | 4 |
| Gchism94 | G****4@g****m | 3 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 2 years ago
All Time
- Total issues: 0
- Total pull requests: 15
- Average time to close issues: N/A
- Average time to close pull requests: 2 months
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.53
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 15
Past Year
- Issues: 0
- Pull requests: 11
- Average time to close issues: N/A
- Average time to close pull requests: 25 days
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.45
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 11
Top Authors
Issue Authors
Pull Request Authors
- dependabot[bot] (19)
Top Labels
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Dependencies
- bookdown * imports
- here * imports
- devtools * suggests
- git2r * suggests
- testthat >= 3.0.0 suggests
- actions/checkout v2 composite
- docker/build-push-action v2 composite
- docker/login-action v1 composite
- actions/checkout master composite
- rocker/binder latest build
- rocker/verse latest build
- rocker/verse latest build