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Initializes the controller. fdist_dir is the directory where fdist2 is. ext is the extension of binaries (.exe on windows, none on Unix) |
Generates an INTFILE. Parameter: data_dir - data directory |
Returns the path to an fdist application. Includes Path where fdist can be found plus executable extension. |
Gets a temporary file name. Returns a temporary file name, if executing inside jython tries to replace unexisting tempfile.mkstemp(). |
Executes cplot. ci - Confidence interval. data_dir - Where the data is found. |
Executes datacal. data_dir - Where the data is found. |
Executes (d)fdist. Parameters: npops - Number of populations nsamples - Number of populations sampled fst - expected Fst sample_size - Sample size per population For dfdist: if zero a sample size file has to be provided mut - 1=Stepwise, 0=Infinite allele num_sims - number of simulations data_dir - Where the data is found is_dominant - If true executes dfdist theta - Theta (=2Nmu) beta - Parameters for the beta prior max_freq - Maximum allowed frequency of the commonest allele Returns: fst - Average Fst Important Note: This can take quite a while to run! |
Executes fdist trying to force Fst. Parameters: try_runs - Number of simulations on the part trying to get Fst correct limit - Interval limit Other parameters can be seen on run_fdist. |
Executes pv. out_file - Name of output file. data_dir - Where the data is found. |
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