Fit Script

The fit script is probably the script you will use most often, as it performs the most common form of PK/PD analysis - finding parameter estimates for a PK/PD model given a set of observations.

See Fitting a Simple PopPK Model using PoPy or Fitting a Two Compartment PopPK Model for walk through examples.

Main Sections of a Fit Script

• METHOD_OPTIONS
• DESCRIPTION
• FILE_PATHS
• DATA_FIELDS
• PREPROCESS
• LEVEL_PARAMS
• MODEL_PARAMS
• STATES
• DERIVATIVES
• PREDICTIONS
• ODE_SOLVER
• FIT_METHODS
• COVARIANCE
• OUTPUT_SCRIPTS

Full Structure of a Fit Script

• METHOD_OPTIONS
  • py_module
  • rand_seed
  • float_format
• DESCRIPTION
  • name
  • title
  • author
  • abstract
  • keywords
• FILE_PATHS
  • input_data_file
  • output_folder
  • temp_folder
  • log_folder
  • output_file_ext
  • input_solution_file
  • output_iteration_results
• DATA_FIELDS
  • type_field
  • id_field
  • time_field
• PREPROCESS
• LEVEL_PARAMS
  • params
  • split_field
  • split_dict
• MODEL_PARAMS
• STATES
• DERIVATIVES
• PREDICTIONS
• ODE_SOLVER
  • NO_SOLVER
  • ANALYTIC
  • SCIPY_ODEINT
    • atol
    • rtol
    • max_nsteps
    • use_sens
• FIT_METHODS
  • JOE
    • max_n_main_iterations
    • CONVERGER
      • NONE
      • OBJ_INC
      • OBJ_SIM
    • recompute_jacobians_flag
    • use_chain
    • reset_re_flag
• COVARIANCE
  • NO_COVARIANCE
  • FINITE_DIFF
    • var_covariance_flag
    • inv_hessian_flag
• OUTPUT_SCRIPTS
  • GRPH
    • output_mode
    • share_axes
  • SIM
    • output_mode
    • sim_time_step
    • share_axes
  • MSIM
    • output_mode
  • FITSUM
    • output_mode