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

Three Zenodo repositories are linked to the preprint Space-time Species Distribution Modeling for Opportunistic Presence-Only Data: A Case Study of Passerines in a Protected Area  (Lasgorceux et al., unpublished, https://hal.science/hal-04616332):

Data, scripts, and code (Lasgorceux et al., Zenodo, https://doi.org/10.5281/zenodo.12545052)

Outputs from fitted models across the cross-validation scenarios (Lasgorceux et al., Zenodo, https://doi.org/10.5281/zenodo.12544212)

Supplementary information at (Lasgorceux et al., Zenodo, https://doi.org/10.5281/zenodo.12541412)

This repository contains data, scripts, and code. It is organized into two main directories: Materials and Methods, and Results.

Materials and Methods

The raw data can be accessed in the Materials_and_Methods/Data directory. The processed data used for modeling is available in Materials_and_Methods/Data_for_modeling/Data_for_modeling.RData. All scripts for data processing are located in Materials_and_Methods/Processing_scripts. The Plots_and_Figures directory 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 Main_script.R.

Results

The Results directory contains three subdirectories and the script Models_Outputs.R. The Results/Fitted_models directory includes all .RData files with fitted models for each species. The script Models_Outputs.R 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, https://doi.org/10.5281/zenodo.12544212. The plots are stored in the Results/Plots folder, while Results/RData contains intermediate .RData files created by Models_Outputs.R to manage computational costs.