SysBio_EvolvingViews_CharacterEvolution

• Figures346

  • this directory contains the code for Fig. 3, Fig. 4 and Fig. 6 of the manuscript
    • /code
      • DiscreteModels_Fig3.Rmd - Rmarkdown file to generate Fig. 3
      • ContiouseModels_Fig4.Rmd - Rmarkdown file to generate Fig. 4
      • JointDiscreteContiouseModels_Fig6.Rmd - Rmarkdown file to generate Fig. 6
      • HelperFunctions.R - A set of functions for plotting and simulating. Note many of the function are limited to plotting/ simulated the data in this paper, in otherwords they are not generaliziable to other data types (e.g., tree of different sizes.
    • /simulated_data
      • All Rmakdown scripts simulate some data. The data used to generate plots in the figured have been saved and store in this directory
      • Below we briefly described what each data is used for
        • stochastic_map_tree.newick - 5 tip phylogeny used in Fig. 3.
        • threeTaxonTree.nwk - 3 tip phylogeny used in Fig. 3, Fig. 4, Fig. 5.
        • SYM_stochasticMap.rds - Rdata for Fig 3A
        • OrderedstochasticMap.rds - Rdata for Fig 3B
        • p94_stochasticMap.rds - Rdata for Fig 3C
        • Threshold_model_Simulation.csv - Simulated Brownion motion data used in Fig. 3D
        • BM_model_simulation.csv - Simulated Brownion motion data used in Fig. 4A
        • OU_model_simulation.csv - Simulated OU data used in Fig. 4B
        • RAT_model_simulation.csv - Siulated data for Fig. 6A

• SSE analyses for section State-dependent speciation and extinction models and the importance of cladogenetic change

  • this directory contains code and data for the SSE simulations we did to compare two-step and joint analysis.
  • the directory is structure as follows:
    • /data
      • tree.tre: the true tree simulated under the two-state Yule model
      • data.nex: binary data for the tips of the simulated tree
      • seq.nex: molecular data simulated on the simulated tree
      • mcc_tree.tre: the MCC tree estimated from the first step of the two-step analysis
      • mcc_tree_2type.tre: the MCC tree estimated under the joint model
      • mcc_tree_alt.tre and mcc_tree_2type_alt.tre: MCC trees estimated in the two-step and joint analyses with clock hyperparameter fixed to true values
    • data simulation:
      • scripts/simulated_tree.R: script to simulate the true tree under the two-state Yule model
      • scripts/sim_seq_data.Rev: script to simulate sequence data on the true tree
    • true-tree analysis
      • scripts/mcmc_true_tree_2type.Rev: script to estimate speciation rates under the two-state Yule model from the true tree
    • two-step analysis:
      • scripts/mcmc_div_times.Rev: script to estimate chronogram under a constant-rate Yule model (first step)
      • scripts/summarize_div_times.Rev: script to compute MCC tree from first step
      • scripts/mcmc_mcmc_est_tree_2type.Rev: script to estimate speciation rates under the two-state Yule model from the MCC tree (second step)
    • joint analysis:
      • scripts/mcmc_div_times_2type.Rev: script to estimate chronogram and speciation rates for two-state Yule model
      • scripts/summarize_div_times_2type.Rev: script to compute MCC tree from previous analysis
    • two-step analysis with fixed hyperparameters:
      • scripts/mcmc_div_times_alt.Rev: script to estimate chronogram under a constant-rate Yule model (first step)
      • scripts/summarize_div_times_alt.Rev: script to compute MCC tree from first step
      • scripts/mcmc_mcmc_est_tree_2type_alt.Rev: script to estimate speciation rates under the two-state Yule model from the MCC tree (second step)
    • joint analysis with fixed hyperparameters:
      • scripts/mcmc_div_times_2type_alt.Rev: script to estimate chronogram and speciation rates for two-state Yule model
      • scripts/summarize_div_times_2type_alt.Rev: script to compute MCC tree from previous analysis