Power_Analyses_4_BayesTraitsScripts&Results

There are two python scripts used to execute BayesTraits on the subdirectories in the previous bundle, "BayesTraits_wrapper_ML.py" and "BayesTraits_wrapper_Bayesian.py". Each will automatically generate the independent and dependent model files required to run BayesTraits, and automatically access the tree file and BayesTraits executable in the subdirectory. It will run serial analyses across all the input files in a subdirectory, using the maximum likelihood version or Bayesian version with stepping stone sampling. Instructions and details are annotated at the top of those scripts. The results can be summarized using the relevant python script, bayesian ("Summary_bf_testing.py") or ml ("Summary_lr_testing.py") version. These will open the output files from each of the 500 analyses in a subdirectory and perform either likelihood ratio tests or bayes factors to compare the independent and dependent models for each input file. The output of these scripts for our set of analyses is provided in the directory "4_Results".