Code for analyses used on A Diffusion-Based Approach for Simulating Forward-in-Time State-Dependent Speciation and Extinction Dynamics paper.
This folder consists of code used to compute time to stationary state frequencies in a two-region GeoSSE model (Section 2.8 of the manuscript).
- find_stationary_time.R: R code to compute the time to stationary give the model's rate parameters.
- DATA: A compilation of sets of model parameters used on the manuscript.
- Dataset_1: model parameters used for Figure 7 (left panel).
- Dataset_2: model parameters used for Figure 7 (right panel).
- Dataset_3: model parameters used for Figure 8 (left panel).
- Dataset_4: model parameters used for Figure 8 (right panel)
This folder is used for analyses involving a two-region GeoSSE model and it consists of the following code
- compute_params_2reg.R : generate values for model parameters according to sets of rules from a given set of state frequencies (Section 3.3 of the manuscript).
- compute_1repli_2reg.R : simulate one replicate of state dynamics given the model parameters.
- compute_1repli_2reg.sh : a shell script for compute_1repli_2reg.R to generate multiple simulation replicates.
- wrapper_2reg.R : a wrapper script to combine all the replicates.
- plot_diff_2reg.R : plot the dynamics (Figures 7 and 8 of the manuscript).
This folder is used for analyses involving a three-region GeoSSE model and it consists of the following sub-folders
- wrbet folder : consists of codes used for analyses using a GeoSSE model with only within-region and between-region speciation events included.
- wr_bet.R : generate one simulation replicate of state dynamics under a 3-region GeoSSE model with only within-region and between-region speciation events included.
- wr_bet.sh : a shell script to generate multiple replicates from wr_bet.R.
- wrapper_combined_wrbet.R : a wrapper script to combine all the replicates from wr_bet.sh.
- do_comparison_wrbet.R : plot the output (Figure 3) and do the statistical tests (Example 1, Table 1).
- wrdi folder : consists of codes used for analyses using a GeoSSE model with only within-region speciation and dispersal events included.
- wr_di_v2.R : generate one simulation replicate of state dynamics under a 3-region GeoSSE model with only within-region speciation and dispersal events included.
- wr_di_v2.sh : a shell script to generate multiple replicates from wr_di_v2.R.
- wrapper_combined_wrdi.R : a wrapper script to combine all the replicates from wr_di_v2.sh.
- do_comparison_wrdi.R : plot the output (Figure 4) and do the statistical tests (Example 2, Table 1).
- wrext folder : consists of codes used for analyses using a GeoSSE model with only within-region speciation and extinction events included.
- wr_ext.R : generate one simulation replicate of state dynamics under a 3-region GeoSSE model with only within-region speciation and extinction events included.
- wr_ext.sh : a shell script to generate multiple replicates from wr_ext.R.
- wrapper_combined_wrext.R : a wrapper script to combine all the replicates from wr_ext.sh.
- do_comparison_wrext.R : plot the output (Figure 4) and do the statistical tests (Example 3, Table 1).
- geosse_all folder : consists of codes used for analyses using a GeoSSE model with all the events included.
- geosse_all.R : generate one simulation replicate of state dynamics under a full 3-region GeoSSE model.
- geosse_all.sh : a shell script to generate multiple replicates from geosse_all.R.
- wrapper_combined_geosseall.R : a wrapper script to combine all the replicates from geosse_all.sh.
- do_comparison_geosseall.R : plot the output (Figure 6) and do the statistical tests (Example 4, Table 1).
Note: In each of these folders above, MASTER Data folder is used to store outputs from MASTER Scripts folder.
Note: Inside MASTER Scripts folder, geosse.xml is used to generate one replicate of state dynamics using tree-based approach, and run_beast.sh is a shell script to simulate multiple replicates of geosse.xml output.