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Project Status: Active The project has reached a stable, usable state and is being actively developed. minimal R version Maintenance Last-changedate

octopusNiche

Code and data to replicate the article "Climate change effect on Octopus maya (Voss and Solís-Ramírez, 1966) suitability and distribution in the Yucatan Peninsula, Gulf of Mexico: A correlative and mechanistic approach".

In order to replicate the results of this study, open the octopusNiche.Rproj and follow the order provided in the code folder:

    1. 0_auxiliar_functions.R (You do not need to run this code. It will be called from the following scripts).
    1. 1_niche_model_maxent.R
    1. 2_binary_maps.R
    1. 3_physiology_maps.R

All the scripts have comments for an easy understanding of the process.

Nevertheless, you must download maxent software from: https://biodiversityinformatics.amnh.org/open_source/maxent/. After that, you have to create a folder named maxent, inside this folder there will be: maxent.bat, maxent.jar, maxent.sh, readme.txt.

Also, you need to install kuenm package. Please follow the instructions provided in this link: https://github.com/marlonecobos/kuenm#installing-the-package

The file structure of this project is:

  • code

  • dataset

  • G_variables

  • M_variables

  • maxent

  • octopusNiche.Rproj

  • README.md

If you want to replicate the maps or other plots of the paper, contact to Luis Enrique Angeles-González (luis.angeles0612@gmail.com) or Josymar Torrejón-Magallanes (ejosymart@gmail.com).

For Mac users: Before install the kuenm package, follow these instructions to install Xcode on your Mac: https://clanfear.github.io/CSSS508/docs/compiling.html Xcode will replace RTools.

If you find any problem in the code, please add this at the Issues section of the github.

Reference

Ángeles-González, L. E., Martínez-Meyer, E., Yañez-Arenas, C., Velázquez-Abunader, I., López-Rocha, J. A., Torrejón-Magallanes, J., & Rosas, C. (2021). Climate change effect on Octopus maya (Voss and Solís-Ramírez, 1966) suitability and distribution in the Yucatan Peninsula, Gulf of Mexico: A correlative and mechanistic approach. Estuarine, Coastal and Shelf Science, 107502. https://doi.org/10.1016/j.ecss.2021.107502.