Language: en

METHOD_OPTIONS¶

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']
    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']

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:
    - COMB_QUANT_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_BIO_MARKER']
        y_scale_list: ['linear', 'log']
        options_list: ['legend', 'grid', 'dose_lines']
        bin_indexer: {EQUAL_SPACE: {n_bins: auto}}
        quantile_list: [0.05, 0.5, 0.95]
        min_bin_count: 10

    - 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_BIO_MARKER']
        y_scale_list: ['linear', 'log']
        options_list: ['legend', 'grid', 'dose_lines']

    - 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_BIO_MARKER']
        y_scale_list: ['linear', 'log']
        options_list: ['legend', 'grid', 'dose_lines']

    - FE_BAR_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: ['-', '-']
        scaling: prop
        orientation: vertical

COMB_QUANT_GRPH¶

Type: dict_record

Plot orig and simulation data using histograms on one graph.

Example:-

COMB_QUANT_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_BIO_MARKER']
    y_scale_list: ['linear', 'log']
    options_list: ['legend', 'grid', 'dose_lines']
    bin_indexer: {EQUAL_SPACE: {n_bins: auto}}
    quantile_list: [0.05, 0.5, 0.95]
    min_bin_count: 10

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_BIO_MARKER']

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']

bin_indexer¶

Type: one_of_record

Possible bin indexing methods.

Example:-

bin_indexer:
    EQUAL_SPACE: {n_bins: auto}

EQUAL_SPACE¶

Type: dict_record

Equally spaced index builder.

Example:-

EQUAL_SPACE:
    n_bins: auto

n_bins¶

Type: int / auto

Number of equally spaced bins in index.

Example:-

n_bins: auto

UNEQUAL_SPACE¶

Type: dict_record

fixed, irregularly spaced user defined bin edges.

Example:-

UNEQUAL_SPACE:
    bin_edge_list: [2.0, 4.0, 8.0]

bin_edge_list¶

Type: list(float)

List of user-defined bin edges.

Example:-

bin_edge_list: [2.0, 4.0, 8.0]

K_MEANS¶

Type: dict_record

Deduce bin centres automatically using k-means algorithm for a pre-determined number of bins.

Example:-

K_MEANS:
    n_bins: 10
    init_method: random

n_bins¶

Type: int

Number of bins.

Example:-

n_bins: 10

init_method¶

Type: one_of(random)

Initialisation method for k-means algorithm.

Example:-

init_method: random

quantile_list¶

Type: list(float)

List of quantiles to plot for each bin of the histogram.

Example:-

quantile_list: [0.05, 0.5, 0.95]

min_bin_count¶

Type: int

Number of data points required to plot an individual bin.

Example:-

min_bin_count: 10

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_BIO_MARKER']
    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_BIO_MARKER']

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']

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_BIO_MARKER']
    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_BIO_MARKER']

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']

FE_BAR_GRPH¶

Type: dict_record

Plot bar chart of f[X] values.

Example:-

FE_BAR_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: ['-', '-']
    scaling: prop
    orientation: vertical

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: ['-', '-']

scaling¶

Type: one_of(log,prop)

Scaling with respect to ground truth.

Example:-

scaling: prop

orientation¶

Type: one_of(vertical,horizontal)

Orientation of the bars.

Example:-

orientation: vertical

Grph Script

Vpc Script

Documentation

METHOD_OPTIONS¶

py_module¶

PARALLEL¶

SINGLE¶

MPI_WORKERS¶

n_workers¶

FILE_PATHS¶

output_folder¶

log_folder¶

output_file_ext¶

solutions¶

DATA_FIELDS¶

type_field¶

id_field¶

time_field¶

OUTPUT_GRAPHS¶

COMB_QUANT_GRPH¶

graph_title¶

y_axis_label_list¶

y_var_src_list¶

y_var_label_list¶

y_var_colour_list¶

y_var_symbol_list¶

x_var¶

x_axis_label¶

x_scale¶

y_var_list¶

y_scale_list¶

options_list¶

bin_indexer¶

EQUAL_SPACE¶

n_bins¶

UNEQUAL_SPACE¶

bin_edge_list¶

K_MEANS¶

n_bins¶

init_method¶

quantile_list¶

min_bin_count¶

COMB_SPAG_GRPH¶

graph_title¶

y_axis_label_list¶

y_var_src_list¶

y_var_label_list¶

y_var_colour_list¶

y_var_symbol_list¶

x_var¶

x_axis_label¶

x_scale¶

y_var_list¶

y_scale_list¶

options_list¶

SPAG_GRPH¶

graph_title¶

y_axis_label_list¶

y_var_src_list¶

y_var_label_list¶

y_var_colour_list¶

y_var_symbol_list¶

x_var¶

x_axis_label¶

x_scale¶

y_var_list¶

y_scale_list¶

options_list¶

FE_BAR_GRPH¶

graph_title¶

y_axis_label_list¶

y_var_src_list¶

y_var_label_list¶

y_var_colour_list¶

y_var_symbol_list¶

scaling¶

orientation¶

Additional Information

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