tracts.driver

The main entry point for tracts: run_tracts() loads a driver YAML file, runs the (optionally two-step) optimization via tracts.core, and writes the output files and plots via output_simulation_data_sex_biased(). The rest of the module implements the individual steps of that pipeline (running/re-running the optimization, sex-bias fixing and boundary re-optimizations, etc.), which run_tracts() orchestrates.

Functions

run_boundary_reoptimization(driver_spec, ...)	Repeatedly re-optimizes while one or more sex-bias parameters have an optimal value at a +-1 boundary.
run_model(genetic_model, population, ...[, ...])	Runs the optimization for any demographic model, including sex-biased models.
run_model_multi_init(genetic_model, ...[, ...])	Runs the model multiple times with different initial parameters.
run_optimization(physical_start_params, ...)	Runs the optimization (single-step, or two-step with the step 1 / step 2 / step-2-skipped branches) given a list of starting parameters in physical units, returning the optimal parameters and the corresponding likelihood.
run_sex_bias_fixing_reoptimizations(...)	Repeats driver_spec.optim.n_reoptimizations times: fixing the sex-bias parameters at their most recently optimized values and re-running the optimization starting from the current optimal parameters (using a copy of driver_spec with repetitions=1 and starting parameters set to the current optimum, see _get_driver_for_reoptimization; this also means, per core.py, that sex-bias parameters end up fixed only during step 1, remaining free to be optimized again in step 2).
run_tracts(driver_filename, script_dir)	Main function to run tracts with a specified driver file.