pyDarwin 2.0.0

About:

• Overview
• Algorithms
  • Exhaustive Search
  • Genetic Algorithm
  • Gaussian Process
  • Random Forest
  • Gradient Boosted Random Tree
  • Particle Swarm Optimization (PSO)
• Support
  • Development Support
  • Help
• Releases
  • pyDarwin-Certara 2.0
  • pyDarwin-Certara 1.1.1
  • pyDarwin-Certara 1.1
  • pyDarwin-Certara 1.0

User Guide:

• Installation
  • System Requirements
    • Windows
    • Linux
  • Hardware Requirements
    • Grid Computing Requirements
  • Software Requirements
  • Install pyDarwin
• Usage
  • Execution Overview
    • Running search on local machine
    • Stopping Execution
    • Execution on Linux Grids
      • Running Grid Search
    • Search Info
  • Required Files
    • Template File
      • Special notes on structure of $THETA/$OMEGA/$SIGMA:
    • Tokens File
    • Options File
  • Searching Omega Structure
    • Omega Block Search
    • Omega Band Search
    • Omega Submatrices Search
  • pyDarwin Outputs
    • Console output
    • File output
      • Messages.txt
      • models.json
      • results.csv
    • File Structure and Naming
      • Saving NONMEM outputs
      • Model/folder naming
• Examples
• Options List
  • Description
  • Aliases
    • Common aliases
    • Grid job aliases
      • Job submit aliases
      • Job delete/poll aliases
  • Environment variables
    • PYDARWIN_HOME
    • PYDARWIN_OPTIONS
  • Settings override
• API
  • High level functions
    • run_search
      • run_search()
    • run_search_in_folder
      • run_search_in_folder()
  • Algorithms
    • exhaustive
      • run_exhaustive()
      • get_search_space()
      • get_search_space_size()
    • GA
      • run_ga()
    • OPT
      • run_skopt()
    • downhill
      • run_downhill()
  • Model classes
    • darwin.Template
      • Template
        • Template.get_search_space_coordinates()
    • darwin.Model
      • Model
        • Model.genotype()
        • Model.to_dict()
        • Model.from_dict()
    • darwin.ModelCode
      • ModelCode
        • ModelCode.from_full_binary()
        • ModelCode.from_min_binary()
        • ModelCode.from_int()
    • darwin.ModelResults
      • ModelResults
        • ModelResults.get_message_text()
        • ModelResults.to_dict()
        • ModelResults.from_dict()
        • ModelResults.calc_fitness()
    • darwin.ModelRun
      • ModelRun
        • ModelRun.set_status()
        • ModelRun.init_stem()
        • ModelRun.is_duplicate()
        • ModelRun.started()
        • ModelRun.to_dict()
        • ModelRun.from_dict()
        • ModelRun.make_control_file()
        • ModelRun.check_files_present_impl()
        • ModelRun.run_command()
        • ModelRun.run_model()
        • ModelRun.finish()
        • ModelRun.keep()
        • ModelRun.cleanup()
        • ModelRun.output_results()
      • write_best_model_files()
      • run_to_json()
      • json_to_run()
      • log_run()
    • darwin.Population
      • Population
        • Population.__init__()
        • Population.from_codes()
        • Population.add_model_run()
        • Population.get_best_run()
        • Population.get_best_runs()
        • Population.run()
      • init_pop_nums()
      • get_remaining_model_num()
  • Caching model runs
    • darwin.ModelCache
      • ModelCache
        • ModelCache.store_model_run()
        • ModelCache.find_model_run()
        • ModelCache.load()
        • ModelCache.dump()
        • ModelCache.finalize()
      • set_model_cache()
      • get_model_cache()
      • register_model_cache()
      • create_model_cache()
    • darwin.MemoryModelCache
      • MemoryModelCache
        • MemoryModelCache.store_model_run()
        • MemoryModelCache.find_model_run()
        • MemoryModelCache.load()
        • MemoryModelCache.dump()
      • AsyncMemoryModelCache
        • AsyncMemoryModelCache.finalize()
        • AsyncMemoryModelCache.dump()
      • register()
• Glossary
• Troubleshooting
  • Installation
  • Error Messages

Indices and tables

• Index

• Module Index

• Search Page