# 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
- PARALLEL
- DESCRIPTION
- FILE_PATHS
- DATA_FIELDS
- PREPROCESS
- EFFECTS
- 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
- PARALLEL
  - SINGLE
  - MPI_WORKERS
    - n_workers
- 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
- EFFECTS
- 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
      - OBJ_LIN
    - recompute_jacobians_flag
    - use_chain
    - reset_re_flag
- COVARIANCE
  - NO_COVARIANCE
  - SANDWICH
    - 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