SoN_2023_Birds

This repository contains the essential scripts and data needed to recreate the analyses and figures for the bird group in the State of Nature Report 2023 by Hamaarag.

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License

This project is licensed under the MIT License – see the LICENSE file for details.

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Contents

This repository is organized into the following main directories and files:

• R/ – Contains R scripts for data preparation, analysis, and visualization. Key components include:

  • Data Preparation: Scripts for preprocessing bird data before analysis.
  • Analyses by Region: RMarkdown files conducting analyses for different ecological regions.
  • Plotting Functions: Scripts for generating figures used in the report.

• data/ – Includes input datasets required for the analyses.

  • Processed Data: Pre-prepared observation dataset used for analysis.
  • Raw Data: Taxonomic tables and species trait tables.

• output/ – Stores the output of the analyses.

  • Currently, this folder contains results from the species composition models run within the RMarkdown scripts, stored as .rds files. Using the saved .rds files will recreate the same results (p-values) and figures as published in SoN 2023. Alternatively, model summary and ANOVA can be re-run by uncommenting the relevant lines in the species composition section of the .Rmd script.
  • Future outputs (after executing markdown scripts) may include tables and figures.

• Project Configuration:

  • SoN_2023_Birds.Rproj – RStudio project file.
  • renv/ & renv.lock – Dependency management files for reproducibility.
  • .gitignore & .Rprofile – Configuration and environment settings.

• Documentation:

  • README.md – This documentation file.
  • LICENSE – License details.

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How to Use

To reproduce the analyses and figures, follow these steps:

1. Clone the repository

Run the following command in a Bash terminal (e.g., Git Bash, macOS/Linux terminal, or Windows Command Prompt with Git installed):

git clone https://github.com/Hamaarag/SoN_2023_Birds.git
cd SoN_2023_Birds

2. Open the project in RStudio

• Open RStudio and use the menu:
  File → Open Project... → Select SoN_2023_Birds.Rproj

Alternatively, you can open the project directly from the command line (Mac/Linux):

open SoN_2023_Birds.Rproj

or on Windows (if RStudio is in the PATH):

start SoN_2023_Birds.Rproj

3. Install required R packages

Inside RStudio, install the necessary dependencies using renv:

install.packages("renv")  # Install renv if not already installed. If running into problems, install version 1.0.7 using: `install.packages("renv", version = "1.0.7")`
renv::restore()           # Restore package environment

4. Run analyses

To execute the analyses and generate figures, run the RMarkdown scripts in the R/ directory.

Option 1: Run interactively in RStudio

Open any .Rmd file (e.g., R/Birds_National_with_Z_filter.Rmd) and click "Knit" to execute the script and generate outputs.

Option 2: Run from the command line

To render a specific RMarkdown file programmatically:

rmarkdown::render("R/Birds_National_with_Z_filter.Rmd")

5. View the results

• Figures and tables (if generated) will also be saved in output/, under a designated folder (the folder will be created automatically).
• The knitted reports (.html) will appear in the same directory as the executed .Rmd file.

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Additonal notes regarding environment

• R version:4.2.3
• RStudio version: 2024.12.1+563
• OS: Windows 10 x64
• The Rmd files are set to use the "Almoni ML v5 AAA" font. If you do not have this font installed, you may need to change the font in the Rmd files.

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Citation

If you use this repository or its contents, please cite both the main report and this repository.

State of Nature Report 2023 – Biodiversity

Grossbard S, Renan I (Eds). 2024. State of Nature Report 2023 – Biodiversity.
Hamaarag – Israel’s National Ecosystem Assessment Program, Steinhardt Museum of Natural History, Tel Aviv University.

SoN_2023_Birds Repository

Hamaarag. State of Nature Report 2023 - Birds. Public Repository, 2024.
Available at: https://github.com/Hamaarag/SoN_2023_Birds.

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Contact

For questions or feedback, contact Hamaarag at info@hamaarag.org.il.

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