TransTree#

class TransTree(sim, to_networkx=False, **kwargs)[source]#

Bases: Analyzer

A class for holding a transmission tree. There are several different representations of the transmission tree: “infection_log” is copied from the people object and is the simplest representation. “detailed h” includes additional attributes about the source and target. If NetworkX is installed (required for most methods), “graph” includes an NX representation of the transmission tree.

Parameters:

  • sim (Sim) – the sim object

  • to_networkx (bool) – whether to convert the graph to a NetworkX object

Example:

sim = cv.Sim().run()
sim.run()
tt = sim.make_transtree()
tt.plot()
tt.plot_histograms()

New in version 2.1.0: tt.detailed is a dataframe rather than a list of dictionaries; for the latter, use tt.detailed.to_dict('records').

Methods

day(day=None, which=None)[source]#

Convenience function for converting an input to an integer day

count_targets(start_day=None, end_day=None)[source]#

Count the number of targets each infected person has. If start and/or end days are given, it will only count the targets of people who got infected between those dates (it does not, however, filter on the date the target got infected).

Parameters:

  • start_day (int/str) – the day on which to start counting people who got infected

  • end_day (int/str) – the day on which to stop counting people who got infected

count_transmissions()[source]#

Iterable over edges corresponding to transmission events

This excludes edges corresponding to seeded infections without a source

make_detailed(people, reset=False)[source]#

Construct a detailed transmission tree, with additional information for each person

r0(recovered_only=False)[source]#

Return average number of transmissions per person

This doesn’t include seed transmissions. By default, it also doesn’t adjust for length of infection (e.g. people infected towards the end of the simulation will have fewer transmissions because their infection may extend past the end of the simulation, these people are not included). If ‘recovered_only=True’ then the downstream transmissions will only be included for people that recover before the end of the simulation, thus ensuring they all had the same amount of time to transmit.

plot(fig_args=None, plot_args=None, do_show=None, fig=None)[source]#

Plot the transmission tree.

Parameters:

  • fig_args (dict) – passed to pl.figure()

  • plot_args (dict) – passed to pl.plot()

  • do_show (bool) – whether to show the plot

  • fig (fig) – if supplied, use this figure

animate(*args, **kwargs)[source]#

Animate the transmission tree.

Parameters:

  • animate (bool) – whether to animate the plot (otherwise, show when finished)

  • verbose (bool) – print out progress of each frame

  • markersize (int) – size of the markers

  • sus_color (list) – color for susceptibles

  • fig_args (dict) – arguments passed to pl.figure()

  • axis_args (dict) – arguments passed to pl.subplots_adjust()

  • plot_args (dict) – arguments passed to pl.plot()

  • delay (float) – delay between frames in seconds

  • colors (list) – color of each person

  • cmap (str) – colormap for each person (if colors is not supplied)

  • fig (fig) – if supplied, use this figure

Returns:

the figure object

Return type:

fig

plot_histograms(start_day=None, end_day=None, bins=None, width=0.8, fig_args=None, fig=None)[source]#

Plots a histogram of the number of transmissions.

Parameters:

  • start_day (int/str) – the day on which to start counting people who got infected

  • end_day (int/str) – the day on which to stop counting people who got infected

  • bins (list) – bin edges to use for the histogram

  • width (float) – width of bars

  • fig_args (dict) – passed to pl.figure()

  • fig (fig) – if supplied, use this figure