Interactive¶

Interactive Jupyter widgets for SymbolicEpiModels.

class epipack.interactive.GeneralInteractiveWidget(**kwargs)[source]¶

Bases: ipywidgets.widgets.widget_box.HBox

An interactive widget that lets you control parameters that are passed to a custom function which returns a result dictionary.

Based on this tutorial: https://kapernikov.com/ipywidgets-with-matplotlib/

Parameters

result_function (func) -- A function that returns a result dictionary when passed parameter values as result_function(**parameter_values).
parameter_values (dict) -- A dictionary that maps parameter names to single, fixed values or ranges (instances of epipack.interactive.Range or epipack.interactive.LogRange).
t (numpy.ndarray) -- The time points corresponding to values in the result dictionary.
return_keys (list, default = None) -- A list of result keys that should be shown. If None, all compartments will be displayed.
figsize (tuple, default = (4,4)) -- Width and height of the created figure.

palette (str, default = 'dark') --

A palette from epipack.colors. Choose from

[ 'dark', 'light', 'dark pastel', 'light pastel',
  'french79', 'french79 pastel', 'brewer light',
  'brewer dark', 'brewer dark pastel', 'brewer light pastel'
]

continuous_update (bool, default = False) -- If False, curves will be updated only if the mouse button is released. If True, curves will be continuously updated.
show_grid (bool, default = False) -- Whether or not to display a grid
ylabel (str, default = 'frequency') -- What to name the yaxis
label_converter (func, default = str) -- A function that returns a string when passed a result key or parameter name.

result_function¶

A function that returns a result dictionary when passed parameter values as result_function(**parameter_values).

Type: func

fixed_parameters¶

A dictionary that maps parameter names to fixed values

Type: dict

t¶

The time points corresponding to values in the result dictionary.

Type: numpy.ndarray

return_keys¶

A list of result dictionary keys of which the result will be displayed.

Type: list

colors¶

A list of hexstrings.

Type: list

fig¶

The figure that will be displayed.

Type: matplotlib.Figure

ax¶

The axis that will be displayed.

Type: matplotlib.Axis

lines¶

Maps compartments to line objects

Type: dict

children¶

Contains two displayed boxes (controls and output)

Type: list

continuous_update¶

If False, curves will be updated only if the mouse button is released. If True, curves will be continuously updated.

Type: bool, default = False

lbl¶

A function that returns a string when passed a result key or parameter name.

Type: func, default = str

update_parameters(*args, **kwargs)[source]¶: Update the current values of parameters as given by slider positions.

update_plot(parameters)[source]¶: Recompute and -draw the epidemic curves with updated parameter values

update_xscale(change)[source]¶: Update the scale of the x-axis. For "log", pass an object change that has change.new=True

update_yscale(change)[source]¶: Update the scale of the y-axis. For "log", pass an object change that has change.new=True

class epipack.interactive.InteractiveIntegrator(**kwargs)[source]¶

Bases: ipywidgets.widgets.widget_box.HBox

An interactive widget that lets you control parameters of a SymbolicEpiModel and shows you the output.

Based on this tutorial: https://kapernikov.com/ipywidgets-with-matplotlib/

Parameters

model (epipack.symbolic_epi_models.SymbolicEpiModel) -- An instance of SymbolicEpiModel that has been initiated with initial conditions
parameter_values (dict) -- A dictionary that maps parameter symbols to single, fixed values or ranges (instances of epipack.interactive.Range or epipack.interactive.LogRange).
t (numpy.ndarray) -- The time points over which the model will be integrated
return_compartments (list, default = None) -- A list of compartments that should be displayed. If None, all compartments will be displayed.
return_derivatives (list, default = None) -- A list of derivatives that should be displayed If None, no derivatives will be displayed.
figsize (tuple, default = (4,4)) -- Width and height of the created figure.

palette (str, default = 'dark') --

A palette from epipack.colors. Choose from

[ 'dark', 'light', 'dark pastel', 'light pastel',
  'french79', 'french79 pastel', 'brewer light',
  'brewer dark', 'brewer dark pastel', 'brewer light pastel'
]

integrator (str, default = 'dopri5') -- Either euler or dopri5.
continuous_update (bool, default = False) -- If False, curves will be updated only if the mouse button is released. If True, curves will be continuously updated.
show_grid (bool, default = False) -- Whether or not to display a grid

model¶

An instance of SymbolicEpiModel that has been initiated with initial conditions.

Type: epipack.symbolic_epi_models.SymbolicEpiModel

fixed_parameters¶

A dictionary that maps parameter symbols to single, fixed values

Type: dict

t¶

The time points over which the model will be integrated

Type: numpy.ndarray

return_compartments¶

A list of compartments that will be displayed.

Type: list

colors¶

A list of hexstrings.

Type: list

fig¶

The figure that will be displayed.

Type: matplotlib.Figure

ax¶

The axis that will be displayed.

Type: matplotlib.Axis

lines¶

Maps compartments to line objects

Type: dict

children¶

Contains two displayed boxes (controls and output)

Type: list

continuous_update¶

If False, curves will be updated only if the mouse button is released. If True, curves will be continuously updated.

Type: bool, default = False

update_parameters(*args, **kwargs)[source]¶: Update the current values of parameters as given by slider positions.

update_plot(parameters)[source]¶: Recompute and -draw the epidemic curves with updated parameter values

update_xscale(change)[source]¶: Update the scale of the x-axis. For "log", pass an object change that has change.new=True

update_yscale(change)[source]¶: Update the scale of the y-axis. For "log", pass an object change that has change.new=True

class epipack.interactive.LogRange(min, max, step_count=100, value=None, base=10)[source]¶

Bases: dict

Defines a value range for an interactive logarithmic value slider.

Parameters

min (float) -- Minimal value of parameter range
max (float) -- Maximal value of parameter range
step_count (int, default = 100) -- Divide the exponent space into that many intervals
base (float, default = 10) -- Base of the logarithm
value (float, default = None) -- Initial value. If None, defaults to the geometric mean of min and max.

class epipack.interactive.Range(min, max, step_count=100, value=None)[source]¶

Bases: dict

Defines a value range for an interactive linear value slider.

Parameters

min (float) -- Minimal value of parameter range
max (float) -- Maximal value of parameter range
step_count (int, default = 100) -- Divide the parameter space into that many intervals
value (float, default = None) -- Initial value. If None, defaults to the mean of min and max.

epipack.interactive.get_box_layout()[source]¶: Return default box layout