# METHOD_OPTIONS

Type: dict_record

method options for plt_grph

Example:-

    METHOD_OPTIONS:
        py_module: grph

## py_module

Type: one_of(grph)

Python module required to process this script file

Example:-

    py_module: grph

# PARALLEL

Type: one_of_record

one of many possible servers

Example:-

    PARALLEL:
        SINGLE: {}

## SINGLE

Type: dict_record

single process server spec.

Example:-

    SINGLE: {}

## MPI_WORKERS

Type: dict_record

MPI local server spec.

Example:-

    MPI_WORKERS:
        n_workers: auto

### 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

# FILE_PATHS

Type: dict_record

file paths

Example:-

    FILE_PATHS:
        output_folder: auto
        log_folder: auto
        output_file_ext: ['svg']
        delete_old_files_flag: False
        solutions:
            pop: ./path_to_final_pop_solution.pyml
            indiv: ./path_to_final_indiv_solution.pyml

## output_folder

Type: output_folder / auto

Output folder - results of computation stored here

Example:-

    output_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

## solutions

Type: dict

Solutions to compare

Example:-

    solutions:
        pop: ./path_to_final_pop_solution.pyml
        indiv: ./path_to_final_indiv_solution.pyml

# DATA_FIELDS

Type: dict_record

data fields for popy.dat.fields object

Example:-

    DATA_FIELDS:
        type_field: TYPE
        id_field: ID
        time_field: TIME

## type_field

Type: str

Field name in data file that contains row type info, e.g. obs/dose etc

Example:-

    type_field: TYPE

## id_field

Type: str

Field name in data file that contains identity string for each data row e.g. obs/dose etc

Example:-

    id_field: ID

## time_field

Type: str

Field name in data file that contains time or event for each data row

Example:-

    time_field: TIME

# OUTPUT_GRAPHS

Type: list_record

List of graphs to output.

Example:-

    OUTPUT_GRAPHS:
        - SPAG_GRPH:
            graph_title: My rather excellent graph
            y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
            y_var_src_list: ['orig', 'sim']
            y_var_label_list: ['drug in plasma', 'bio marker in plasma']
            y_var_colour_list: ['b', 'g']
            y_var_symbol_list: ['-', '-']
            x_var: TIME
            x_axis_label: Time (hours)
            x_scale: linear
            y_var_list: ['CONC_DRUG', 'CONC_DRUG_sim']
            y_scale_list: ['linear', 'log']
            options_list: ['legend', 'grid', 'dose_lines']

        - COMB_SPAG_GRPH:
            graph_title: My rather excellent graph
            y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
            y_var_src_list: ['orig', 'sim']
            y_var_label_list: ['drug in plasma', 'bio marker in plasma']
            y_var_colour_list: ['b', 'g']
            y_var_symbol_list: ['-', '-']
            x_var: TIME
            x_axis_label: Time (hours)
            x_scale: linear
            y_var_list: ['CONC_DRUG', 'CONC_DRUG_sim']
            y_scale_list: ['linear', 'log']
            options_list: ['legend', 'grid', 'dose_lines']

## SPAG_GRPH

Type: dict_record

Plot data for all individuals on separate graphs.

Example:-

    SPAG_GRPH:
        graph_title: My rather excellent graph
        y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
        y_var_src_list: ['orig', 'sim']
        y_var_label_list: ['drug in plasma', 'bio marker in plasma']
        y_var_colour_list: ['b', 'g']
        y_var_symbol_list: ['-', '-']
        x_var: TIME
        x_axis_label: Time (hours)
        x_scale: linear
        y_var_list: ['CONC_DRUG', 'CONC_DRUG_sim']
        y_scale_list: ['linear', 'log']
        options_list: ['legend', 'grid', 'dose_lines']

### graph_title

Type: str

Title of graph.

Example:-

    graph_title: My rather excellent graph

### y_axis_label_list

Type: list(str)

List of labels for y variables that appear on axes.

Example:-

    y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']

### y_var_src_list

Type: list(str)

List of y variable types, orig = original data set sim = simulated data

Example:-

    y_var_src_list: ['orig', 'sim']

### y_var_label_list

Type: list(str)

List of y variable labels, which appear in the legend.

Example:-

    y_var_label_list: ['drug in plasma', 'bio marker in plasma']

### y_var_colour_list

Type: list(str)

List of colours for y variable plot lines.

Example:-

    y_var_colour_list: ['b', 'g']

### y_var_symbol_list

Type: list(str)

List of plot line styles for y variable plot lines.

Example:-

    y_var_symbol_list: ['-', '-']

### x_var

Type: str

x axis variable name.

Example:-

    x_var: TIME

### x_axis_label

Type: str

x axis label text.

Example:-

    x_axis_label: Time (hours)

### x_scale

Type: one_of(linear,log)

x axis scale - can be either ‘linear’ or ‘log’.

Example:-

    x_scale: linear

### y_var_list

Type: list(str)

List of y variable names to be plotted on graph.

Example:-

    y_var_list: ['CONC_DRUG', 'CONC_DRUG_sim']

### y_scale_list

Type: list(str)

List of scales (linear or log) for multiple y axes.

Example:-

    y_scale_list: ['linear', 'log']

### options_list

Type: list_of(legend,legend_above,grid,dose_lines,share_axes,45degree_line,sim_xy)

List of visual options to apply to individual plots.

Example:-

    options_list: ['legend', 'grid', 'dose_lines']

## COMB_SPAG_GRPH

Type: dict_record

Plot data for all individuals one one graph.

Example:-

    COMB_SPAG_GRPH:
        graph_title: My rather excellent graph
        y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
        y_var_src_list: ['orig', 'sim']
        y_var_label_list: ['drug in plasma', 'bio marker in plasma']
        y_var_colour_list: ['b', 'g']
        y_var_symbol_list: ['-', '-']
        x_var: TIME
        x_axis_label: Time (hours)
        x_scale: linear
        y_var_list: ['CONC_DRUG', 'CONC_DRUG_sim']
        y_scale_list: ['linear', 'log']
        options_list: ['legend', 'grid', 'dose_lines']

### graph_title

Type: str

Title of graph.

Example:-

    graph_title: My rather excellent graph

### y_axis_label_list

Type: list(str)

List of labels for y variables that appear on axes.

Example:-

    y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']

### y_var_src_list

Type: list(str)

List of y variable types, orig = original data set sim = simulated data

Example:-

    y_var_src_list: ['orig', 'sim']

### y_var_label_list

Type: list(str)

List of y variable labels, which appear in the legend.

Example:-

    y_var_label_list: ['drug in plasma', 'bio marker in plasma']

### y_var_colour_list

Type: list(str)

List of colours for y variable plot lines.

Example:-

    y_var_colour_list: ['b', 'g']

### y_var_symbol_list

Type: list(str)

List of plot line styles for y variable plot lines.

Example:-

    y_var_symbol_list: ['-', '-']

### x_var

Type: str

x axis variable name.

Example:-

    x_var: TIME

### x_axis_label

Type: str

x axis label text.

Example:-

    x_axis_label: Time (hours)

### x_scale

Type: one_of(linear,log)

x axis scale - can be either ‘linear’ or ‘log’.

Example:-

    x_scale: linear

### y_var_list

Type: list(str)

List of y variable names to be plotted on graph.

Example:-

    y_var_list: ['CONC_DRUG', 'CONC_DRUG_sim']

### y_scale_list

Type: list(str)

List of scales (linear or log) for multiple y axes.

Example:-

    y_scale_list: ['linear', 'log']

### options_list

Type: list_of(legend,legend_above,grid,dose_lines,share_axes,45degree_line,sim_xy)

List of visual options to apply to individual plots.

Example:-

    options_list: ['legend', 'grid', 'dose_lines']