k-decomposition and analysis of mutualistic networks

Authors: Javier Garcia-Algarra/ Juan Manuel Pastor (UPM, Spain)

Description

This repository contains code for the kcore decomposition, analysis and visualization of mutualistic networks.

Prerequisites

R 3.2 or newer Python 3.0 or newer git bash installed

Intall kcorebip package with devtools package:

install_github("jgalgarra/kcorebip")

Reproducibility

• Clone the repository with git clone https://github.com/jgalgarra/kcore_robustness.git

• Move to kcore_robustness directory and set it as R working directory (RStudio use is recommended)

• The data directory contains the 89 network interaction matrices downloaded from the web of life site

• Run testing-all.R. The output file results/datos_analisis.RData stores the k-magnitudes in .csv format

• Run kdegree_calc_store_results.R to get the results/datos_analisis_condegs.RData (results + network degrees and correlation degree kdegree)

• Run network_k_parameters.R to create individual k-magnitude files in analysis_indiv_extended directory

• destruction_first_algorithm.R. Algorithm to find the number of primary extinctions of any guild to destroy half the giant component according to different indexes. Read the R file documentation header for detailed instructions

• Go to the python directory and run extictions_compare_new.py . This task may be slow, do not stop it

Go back to RStudio

• Run best_1stalg.R and best_2ndalg to have a fast count of comparative performances.
• Run paint_destructions_1stalg_network.R . The directory graphs/FIRST contains the plots of individual network performance
• Run paint_destructions_2ndalg_network.R . The directory graphs/pyhton contains the plots of individual network performance for the two outcomes ofthe second extinction algorithm
• Run paint_extinctions_1stalg_results.R and paint_extinctions_2ndtalg_results.R to create the four comparative figures in the directory graphs
• Run paint_degree_distribution_steps.R to create the comparative figure of degree vs. kdegree of network M_PL_001
• Run paint_2ndalg_areas.R to build the destruction AUC for the second algorithm under graphs/AREAS.
• Run create_007_destroy_2nd_alg to create the stages of destruction of network M_PL_007
• Run bipartite_graphs_007.R to create the bipartite plots of destruction of networkl M_PL_007