Abstract
This repository contains the code used for the study on the climate impacts on the Alpine salamander. You can access the publication here.
Project Structure
The project is organized into the following main directories:
data_processing/: Scripts for initial data preparation and cleaning.
explore/: Exploratory data analysis scripts.
figures/: Code to generate figures used in the manuscript.
functions/: Custom R functions used across various analysis scripts.
model/: Scripts pertaining to the fitting and projecting species distribution modeling (SDM).
niche_overlap/: Analysis pertaining to the niche overlap between subspecies.
main_setup.R: The main R script to set up the project environment, such as file and folder paths, and parameter settings.
Automated Workflow
The entire analysis workflow is controlled via a Makefile that is orchestrated via GNU Make to execute the scripts in a specified sequence. See the documentation on Make and Makefiles for more info.
Using the Makefile
To run the entire analysis pipeline or specific parts of it, you can use commands specified in the Makefile. For example:
make fit_model taxon=points_atra will run the model fitting for the specified taxon.
make project_future runtype=slurm will project the biomod models to future climate scenarios using a SLURM scheduler for parallel processing.
Data Availability
All original data sources are cited within the manuscript. More specifically, climate variables data you can retrieve from CHELSA climate website. Species occurrence data you can retrieve from digital supporting information.
Contact
For any additional questions or requests, please contact the corresponding author at m.cengic@science.ru.nl.
