# METHOD_OPTIONS

Type: dict_record

method options for comp_script

Example:-

    METHOD_OPTIONS:
        py_module: comp
        rand_seed: 12345
        float_format: default

## py_module

Type: one_of(comp)

Python module required to process this script file

Example:-

    py_module: comp

## rand_seed

Type: int / auto

Option to set seed to make run result reproducible -e.g. when debugging.

Example:-

    rand_seed: 12345

## float_format

Type: str

Format string for numerical output

Example:-

    float_format: default

# PARALLEL

Type: one_of_record

one of many possible servers

Example:-

    PARALLEL:
        SINGLE: {progress_bar_length: 0}

## SINGLE

Type: dict_record

single process server spec.

Example:-

    SINGLE:
        progress_bar_length: 0

### progress_bar_length

Type: int

Length of progress bar on screen (default=0, off)

Example:-

    progress_bar_length: 0

## MPI_WORKERS

Type: dict_record

MPI local server spec.

Example:-

    MPI_WORKERS:
        n_workers: auto
        cpu_load: 1.0
        progress_bar_length: 0

### n_workers

Type: int / auto

Number of workers to use on this machine, defaults to number of processors, but could be more or fewer.

Example:-

    n_workers: auto

### cpu_load

Type: float

Desired load on CPU as a decimal greater than 0.0 (0%) and less than or equal to 1.0 (100%)

Example:-

    cpu_load: 1.0

### progress_bar_length

Type: int

Length of progress bar on screen (default=0, off)

Example:-

    progress_bar_length: 0

# DESCRIPTION

Type: dict_record

Description fields for script.

Example:-

    DESCRIPTION:
        name: my_pkpd_model
        title: My PKPD model
        author: My Name
        abstract: |
            Abstract describing the model
        keywords: ['pkpd']

## name

Type: str

Unique name used to distinguish script

Example:-

    name: my_pkpd_model

## title

Type: str

A longer text string that could serve as a title

Example:-

    title: My PKPD model

## author

Type: str

Author of the model

Example:-

    author: My Name

## abstract

Type: verbatim

Abstract paragraph describing model

Example:-

    abstract: |
        Abstract describing the model

## keywords

Type: list

Keywords list used to categorise models.

Example:-

    keywords: ['pkpd']

# FILE_PATHS

Type: dict_record

File paths for comp script

Example:-

    FILE_PATHS:
        output_folder: auto
        temp_folder: auto
        log_folder: auto
        output_file_ext: ['svg']
        delete_old_files_flag: False
        gen_script_path: my_pkpd_model_gen.pyml
        gen_output_folder: my_pkpd_model_gen.pyml_output
        fit_script_path: my_pkpd_model_fit.pyml
        fit_output_folder: my_pkpd_model_fit.pyml_output
        solutions:
            fit_obs: input_observations_soln.pyml
            gen_pred: my_pkpd_model_gen.pyml_output/generated_data/solution.pyml
            gen_sim_pred: my_pkpd_model_gen.pyml_output/my_pkpd_model_sim.pyml_output/gen_pred/solution.pyml
            final_fit_ipred: my_pkpd_model_fit.pyml_output/solN/solution.pyml
            final_fit_sim_ipred: my_pkpd_model_fit.pyml_output/my_pkpd_model_sim.pyml_output/final_fit_ipred/solution.pyml

## output_folder

Type: output_folder / auto

Output folder - results of computation stored here

Example:-

    output_folder: auto

## temp_folder

Type: output_folder / auto

Temp folder - temporary files stored here

Example:-

    temp_folder: auto

## log_folder

Type: output_folder / auto

Log folder - log files stored here

Example:-

    log_folder: auto

## output_file_ext

Type: list_of(pdf,png,svg)

Output file extension - determines graphical output file format.

Example:-

    output_file_ext: ['svg']

## delete_old_files_flag

Type: bool

Option to delete any existing files before running.

Example:-

    delete_old_files_flag: False

## gen_script_path

Type: input_file / auto

Path to gen_script.

Example:-

    gen_script_path: my_pkpd_model_gen.pyml

## gen_output_folder

Type: output_folder / auto

Gen script output folder.

Example:-

    gen_output_folder: my_pkpd_model_gen.pyml_output

## fit_script_path

Type: input_file / auto

Path to fit_script.

Example:-

    fit_script_path: my_pkpd_model_fit.pyml

## fit_output_folder

Type: output_folder / auto

Fit script output folder.

Example:-

    fit_output_folder: my_pkpd_model_fit.pyml_output

## solutions

Type: dict

Solutions to compare

Example:-

    solutions:
        fit_obs: input_observations_soln.pyml
        gen_pred: my_pkpd_model_gen.pyml_output/generated_data/solution.pyml
        gen_sim_pred: my_pkpd_model_gen.pyml_output/my_pkpd_model_sim.pyml_output/gen_pred/solution.pyml
        final_fit_ipred: my_pkpd_model_fit.pyml_output/solN/solution.pyml
        final_fit_sim_ipred: my_pkpd_model_fit.pyml_output/my_pkpd_model_sim.pyml_output/final_fit_ipred/solution.pyml

# COMP_OPTIONS

Type: dict_record

Options for comp script

Example:-

    COMP_OPTIONS:
        compute_gen_objective_value: True
        compute_fit_objective_value: True

## compute_gen_objective_value

Type: bool

Compute objective value of generated data given generated parameters.

Example:-

    compute_gen_objective_value: True

## compute_fit_objective_value

Type: bool

Compute objective value of generated data using fitted parameters.

Example:-

    compute_fit_objective_value: True

# OUTPUT_SCRIPTS

Type: dict_record

scripts to output for further processing

Example:-

    OUTPUT_SCRIPTS:
        GRPH: {output_mode: none, grph_list: ['OBS_vs_TIME']}

## GRPH

Type: dict_record

options to pass to grph script.

Example:-

    GRPH:
        output_mode: none
        grph_list: ['OBS_vs_TIME']

### output_mode

Type: one_of(none,create,run)

Output options.

Example:-

    output_mode: none

### grph_list

Type: list(str)

Graph types to plt

Example:-

    grph_list: ['OBS_vs_TIME']