Short title: Code-sharing policies matter

Title: Code-sharing policies are associated with increased reproducibility potential of ecological findings

Contributors: Alfredo Sánchez-Tójar, Aya Bezine, Marija Purgar, Antica Culina

Date created: November 2024

Identifer: DOI (10.5281/zenodo.14357339)

Category: Project

Code License: MIT

Data License: CC BY 4.0

Description: This repository contains the data, code and other materials used in the following study:

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Alfredo Sánchez-Tójar, Aya Bezine, Marija Purgar, Antica Culina. 2024. Code-sharing policies are associated with increased reproducibility potential of ecological findings. EcoEvoRxiv. Preprint available at: DOI

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The repository consists of an Rproject with 3 scripts and 3 folders containing the data either needed to run these scripts or created by these scripts, including the figures. For a detailed description of all the files, please see below. To run this repository, first download and unzipped the entire repository and open the Rproject file: analyses.Rproj. The scripts are named in the order that they should be run, from 001 to 003. For any further information about this repository, please contact: Alfredo Sánchez-Tójar, email: alfredo.tojar@gmail.com.

Information about folders and files within:

Folders:

• code: contains all three scripts used to process, clean, standardize data, and generate figures for the project.

• • 001_data_cleaning_and_standardization_without_policies.R: used to clean and standardize the dataset for studies without a code-sharing policys. This script imports raw data, processes inconsistencies, and prepares the data for analysis.
• • 002_data_cleaning_and_standardization_with_policies.R: used to clean and standardize the dataset for studies with a code-sharing policy. Similar to the first script (i.e., "001_") but tailored to datasets that incorporate policy information.
• • 003_plotting.R: used to import the final cleaned databases (generated by the first two scripts) and generate the figures included in the main text.

• data: contains all raw and clean data files necessary for or generated by our three scripts.

• figures: contains all figures generated by 003_plotting.R and included in the main text of this study.

Codebooks and metadata:

We provide a codebook and a metadata file for each of the two clean databases corresponding to journals with and without a code-sharing policy, separately. These files are in the folder codebooks_and_metadata. The codebooks were generated using the Web application of the codebook R package, available at: https://codebook.formr.org/. The metadata files were obtained, adjusted, and completed from the codebooks, and saved as separate .csv files.

Software and {Packages} used

R version 4.3.1 (2023-06-16 ucrt)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 10 x64 (build 19044)

• {ggpattern} v.1.1.1
• {patchwork} v.1.3.0
• {ggplot2} v.3.5.1
• {readxl} v.1.4.3
• {dplyr} v.1.1.4
• {stringr} v.1.5.1