Data, scripts and code for 'Space-time species distribution modeling with opportunistic presence-only data: a case study of passerines in a protected area'

<p>Three Zenodo repositories are linked to the preprint <em>Space-time Species Distribution Modeling for Opportunistic Presence-Only Data: A Case Study of Passerines in a Protected Area&nbsp; </em>(Lasgorceux et al., unpublished, <a href="https://hal.science/hal-04616332">https://hal.science/hal-04616332</a>):</p> <ul> <li>Data, scripts, and code (Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12545052">https://doi.org/10.5281/zenodo.12545052</a>)</li> <li>Outputs from fitted models across the cross-validation scenarios (Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12544212">https://doi.org/10.5281/zenodo.12544212</a>)</li> <li>Supplementary information at (Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12541412">https://doi.org/10.5281/zenodo.12541412</a>)</li> </ul> <p>This repository contains data, scripts, and code. It is organized into two main directories: <em>Materials and Methods,</em> and <em>Results</em>.</p> <h2>Materials and Methods</h2> <p>The raw data can be accessed in the <em>Materials_and_Methods/Data directory</em>. The processed data used for modeling is available in&nbsp;<em>Materials_and_Methods/Data_for_modeling/Data_for_modeling.RData</em>. All scripts for data processing are located in <em>Materials_and_Methods/Processing_scripts</em>. The&nbsp;<em>Plots_and_Figures </em>directory<em>&nbsp;</em>includes illustrations of the data used for modeling, such as PCA correlation plots presented in Supplementary information. The main script for running the model for each species is <em>Main_script.R</em>.</p> <h2>Results</h2> <p>The <em>Results</em> directory contains three subdirectories and the script <em>Models_Outputs.R</em>. The&nbsp;<em>Results/Fitted_models</em> directory includes all .RData files with fitted models for each species. The script <em>Models_Outputs.R </em>generates all outputs (Figures, Tables, Numbers) included in the paper and additional results in the Supplementary Information, except for Figure 1 and AUC values. For these, refer to Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12544212">https://doi.org/10.5281/zenodo.12544212</a>. The plots are stored in the <em>Results/Plots </em>folder, while <em>Results/RData</em> contains intermediate .RData files created by <em>Models_Outputs.R</em> to manage computational costs.</p>