Codes used for analyses in "Structured models of competition to understand the coexistence of species" manuscript

All codes have been written in R by Gaël Bardon.

The "analysis_article" folder contains codes to perform the analysis presented in the article.

• Invasion_analysis folder contains the scripts that allowed us to choose the parameter sets (section 2.2) and to perform the invasion analysis computations (section 3.1)
• Invasion_analysis_MB folder corresponds to the supplement A (invasion analysis with the M&B's model structure)
• sensitivity_analysis folder contains the functions to compute the sensitivity (section 2.4) and the associated results (section 3.2 ; Appendix B)
• community_simulations folder gathers the scripts and figures corresponding to the section 3.3 and appendix C
• community_simulations_MB folder gathers the scripts and figures corresponding to the supplement D
• dynamics_simulations folder gathers the scripts and figures correspondting to the Supplement B

The "analysis_report" folder corresponds to the codes used before september 2020. These codes were used to perform analysis described in "Rapport M2 Gael Bardon". The codes in this folder correspond to:

• computation_R0_combined_model.R : Computation of invasion criteria in the combined model (section 2.4)
• conics_intersection_plot.R : Representation of the intersection of the conic sections (section 2.5)
• multispecies_community_simulation.R : Simulation of population dynamics in communities with large number of species. (section 4.3)
• Prelim_Num_Study_ComModels.R : Preliminary numerical study on combined model (section 2.2)
• SensiAna_CombMod_3Sets.R :Sensitivity analysis and representation on the combined model (section 3.3)
• SensiAna_CompetIntensity.R : Sensitivity analysis on parameter sets with different competition intensities (section 3.4)
• SensiAna_RarityEffect.R : Sensitivity analysis on parameter sets with different level of rarity for 1 species (section 3.5)
• sensitivity_analysis_function.R : functions to perform simulations of population dynamics, computation of invasion criteria and sensitivity analysis
• Simul_CompetIntensity.R : Simulations to check the effect of competition intensity on the sensitivity (section 3.4)