Fossil Simulations

The folder “fossil_simulations” contains the R and Python scripts used for the fossils simulation study.
The folder “1.simulators” contains the R scripts adapted from (Hagen and Stadler 2014) used to simulate the initial complete phylogenies. “SimulatorScenarioIandII_ConstantOverTime.R” was used for simulating scenarios I and II, “SimulatorScenarioIII_2TimeBin.R” was used for simulating scenario III and “SimulatorScenarioIV_2TimeBin_BIGDROP.R” was used for simulating scenario IV. Please note that these files require the parameters given at “parametersage.csv” and generated by the scripts “Parametersage_Generator.R” found respectively inside each scenario folder. Please change the working directories before running the scripts.
To generate fossil data from the phylogenies the script “2.FossilSamplerRunOverFolder.py” was run, evoking “fossil_sampler.py” for all fossils inside the respective scenario. The script “3.GetPyRateEstimatesRunOverFolders.py” automates a PyRate estimation while “4.PlottingScenarios.R” is used for visualizing the result. “SummarySimulations.RData” summarizes the results and analysis conducted. Each scenario folder also contains a “summary_ScenarioX.csv” file recording the number of: sampled species, singletons, simulated extinct species, simulated extant species, fossil occurrences and several other returned values from PyRate.
References
- Hagen O., Hartmann K., Steel M., Stadler T. 2015. Age-Dependent Speciation Can Explain the Shape of Empirical Phylogenies. Syst Biol. 64 (3): 432-440. doi: 10.1093/sysbio/syv001.
- Hagen O., Stadler T. 2017. Treesimgm: Simulating phylogenetic trees under general bellman harris models with lineage-specific shifts of speciation and extinction in r. Methods Ecol. Evol. in press.