#################### Description of code and simulations ####################

Two .rar archives are included. 'code' contains the R code required to replicate the simulations, analyse the realisations,
and create the figures as represented in the main text. 'sims' contains the simulation model output generated by the different models.

### NOTE: The 'sims'archive is not required to re-create the figures as represented in the main text as analysis output is provided in the 'code'archive ###

---sims
├───IS	(Invader-superiority realisations)
│   ├───A_peripatry	(realisations resulting from the peripatric speciation model)
│   ├───B_vicariance	(realisations resulting from the vicariant speciation model)
│   ├───C_unbounded	(realisations resulting from the peripatric speciation model w/ unbounded niche space)
│   ├───D_global_dispersal	(realisations resulting from the peripatric speciation model w/ global dispersal)
│   ├───E_invasion	(realisations resulting from the post hoc invasion experiment)
│   ├───F_large_start_range	(realisations resulting from the peripatric speciation model w/ a large ancestral start range)
│   └───G_vary_competition_intensity	(realisations resulting from the peripatric speciation model where respectively the psi and sigma parameter are varried)
│       ├───vary_psi
│       └───vary_sigma
├───RS	(Resident-superiority realisations)
│   ├───A_peripatry
│   ├───B_vicariance
│   ├───C_unbounded
│   ├───D_global_dispersal
│   ├───E_invasion
│   ├───F_large_start_range
│   └───G_vary_competition_intensity
│       ├───vary_psi
│       └───vary_sigma
└───SC	(Symmetric competition realisations)
    ├───A_peripatry
    ├───B_vicariance
    ├───C_unbounded
    ├───D_global_dispersal
    ├───E_invasion
    ├───F_large_start_range
    └───G_vary_competition_intensity
        ├───vary_psi
        └───vary_sigma


--- code
│   0_stepup_script.R (script with the required packages)
│   1_analyse_realisations.R (script for analysis to create Figure 2 and Figure S4)
│   2_analyse_realisation_fig_4_5.R (script for analysis to create Figure 4, 5 and S5)
│   3_analyse_realisations_Jac_Pairwise_S4_S6.R (computes the temporal turnover in community composition; script for analysis required for Figure S4 and S6)
│   Figure_2.R (plot Figure 2)
│   Figure_3.R
│   Figure_4.R
│   Figure_5.R
│   Figure_6.R
│   Figure_S1.R
│   Figure_S2.R
│   Figure_S3.R
│   Figure_S4.R
│   Figure_S5.R
│   Figure_S6.R
│   
├───1_results	(1_analyse_realisations.R results)
│       rates_bounded.csv
│       rates_bounded.RData
│       
├───2_results	(2_analyse_realisation_fig_4_5.R results)
│       primary_mu_0_0.csv
│       primary_mu_0_0005.csv
│       primary_mu_0_00125.csv
│       primary_mu_0_0025.csv
│       primary_mu_0_005.csv
│       primary_mu_0_0075.csv
│       primary_mu_0_0125.csv
│       T360_vicariance_mu_0_0.005.csv
│       T360_vicariance_mu_0_0.0125.csv
│       T360_vicariance_mu_0_0.025.csv
│       T360_vicariance_mu_0_0.05.csv
│       T360_vicariance_mu_0_0.075.csv
│       T360_vicariance_mu_0_0.125.csv
│       T360_vicariance_mu_0_0.csv
│       
├───3_input (input for Figure_3.R)
│       IS_simulation401_series_A_lambda_0.5_gamma_0.25_psi_0.25_alpha_1_sigma_0.25_mu_0_0_mu_max_5.RData
│       RS_simulation401_series_A_lambda_0.5_gamma_0.25_psi_0.25_alpha_1_sigma_0.25_mu_0_0_mu_max_5.RData
│       
├───6_input (output of the invasion-experiment used for creating Figure 6)
│   ├───IS
│   ├───RS
│   └───SC
│               
├───figures (Figures created by the R-scripts)
│       Figure2.pdf
│       Figure_3.pdf
│       Figure_4.pdf
│       Figure_5.pdf
│       Figure_6.pdf
│       Figure_6_legend_extract.pdf
│       Figure_S1.pdf
│       Figure_S2.pdf
│       Figure_S3.pdf
│       Figure_S4.pdf
│       Figure_S5.pdf
│       Figure_S6.pdf
│       
├───run_invasion_model	(scripts required to replicate the invasion-experiment)
│   │   1_call_script_invaders.R
│   │   invasibility_functions.R	(functions for the IS and RS model)
│   │   invasibility_functions_symmetric.R	(functions for the SC model)
│   │   
│   └───sims (input realisations used for the invasion-experiment)
│       ├───IS
│       ├───RS
│       └───SC
│               
├───run_model (scripts required to run the main model)
│       1_call_script.R
│       functions_incumbency_sample_rates.R	(functions for the IS and RS model)
│       functions_incumbency_sample_rates_global_dispersal.R	(functions for the IS and RS model w/ global dispersal)
│       functions_incumbency_sample_rates_symmetric.R	(functions for the SC model)
│       functions_incumbency_sample_rates_symmetric_global_dispersal.R	(functions for the SC model w/ global dispersal)
│       functions_incumbency_vicariance_sample_rates.R	(functions for the IS and RS model w/ vicariant speciation)
│       functions_incumbency_vicariance_sample_rates_symmetric.R	(functions for the SC model w/ vicariant speciation)
│       IS_functions.cpp	(supporting Rcpp functions for the IS model, and can also be used for SC)
│       RS_functions.cpp	(supporting Rcpp functions for the RS model, and can also be used for SC)
│       
├───S1_results
│       GLOB_rich_bal.csv
│       LS_rich_bal.csv
│       PRIM_rich_bal.csv
│       UNB_rich_bal.csv
│       VIC_rich_bal.csv
│       
├───S2_results
│       summary_T360_psi_025_var_sigma.csv
│       T360_psi_025_var_sigma.csv
│       
├───S3_results
│       T360_sigma_025_var_psi.csv
│       
├───S4_results
│       jac_pairwise_bounded.csv
│       
├───S6_results
│       Jaccard_metric_unbounded.csv
│       rates_unbounded.csv
│       
└───support_functions	(supporting functions required for the analysis or plotting)
        functions_code_paleophylo.R