Analysis

This class stores a series of methods to make plots and output data generated with COMORBUSS, this class can load data from a community object or from an hdf5 file.

do_plot(self, t, dt, data, colors, seeds, filename=None, size=(5, 4), title=None, events=False, events_type=0, skip=[], start_day=None, end_day=None, bands=True, colorsmap=None, start=True, close=True, dates=True, xlim=None, ylim=None, xlabel=False, ylabel=False, log_y=False, show_legend=True, legend_args={}, show_bands_legend=True, bands_legend_args={}, plt_args={})

Internal method used to plot one or more curve.

**plot_args:

Parameters:

Name	Type	Description	Default
filename	str	File name to save the graph, if not informed will only show the plot.	None
size	tuple	Size to generate the plot. Defaults to (5, 4).	(5, 4)
title	str	Title to be printed on the plot.	None
events	bool	Overlay simulation events on the plot. Defaults to False.	False
events_type	int	Type of logs to overlay as events. Defaults to MSG_EVENTS.	0
skip	list	List of curves to skip plotting. Use the same string used in the legend of the plot to skip curves.	[]
start_day	float	Plot only the interval from start_day. Defaults to 0.	None
end_day	float	Plot only the interval to end_day. Defaults to last day.	None
bands	bool	Plot standard deviation bands and 95% percentiles if data has multiple seeds. Defaults to True.	True
colorsmap	arr[str]	If provided, the list of string is used to initialize colormaps, used in the shading of bands	None
close	bool	If False doesn't show, save or close the plot so that the user can add more information to plot using the plt attribute from the class. Defaults to False.	True
dates	bool	Use dates instead of days in the x axis. Defaults to True.	True
xlabel	str	Label for the x axis.	False
ylabel	str	Label for the y axis.	False
log_y	bool	Sets the y scale to log. Defaults to False	False
show_legend	bool	Hides legends if False. Defaults to True.	True
legend_args	dict	Arguments to be passed to pyplot.legend when drawing the legend.	{}
show_bands_legend	bool	Hides bands legends if False. Defaults to True.	True
bands_legend_args	dict	Arguments to be passed to pyplot.legend when drawing the bands legend.	{}
plt_args	dict	Additional arguments to be passed to pyplot.plot when drawing the curves.	{}

Internal parameters:

Parameters:

Name	Type	Description	Default
t	[type]	[description]	required
dt	[type]	[description]	required
data	[type]	[description]	required
colors	[type]	[description]	required
seeds	[type]	[description]	required

from_comm(comm, **loader_args) classmethod

Initialize an Analysis object from a community object.

Parameters:

Name	Type	Description	Default
comm	community	Community to extract data.	required

Returns:

Type	Description
Analysis	An Analysis object.

from_hdf5(hdf5_file='', seed='', **loader_args) classmethod

Initialize an Analysis object from an hdf5 file.

Parameters:

Name	Type	Description	Default
if	seed == ""	seed = list(results["realizations"].keys())[0]file (str): Path to the hdf5 file, if not informed a prompt will be open for the user to select the file.	required
seed	int	An execution seed in the hdf5 file to be loaded, if not informed will load the first in the file.	''

Returns:

Type	Description
Analysis	An Analysis object.

placement_statistics(self, placement, txtfile=None, filename=None, plot_hist=True, size=(5, 4), include_guests=False, seeds=None)

Show placement visitation statistics.

Parameters:

Name	Type	Description	Default
placement	int or str	Placement id or placement name to show statistics.	required
txtfile	str	File name to save text output, if not informed will only show it.	None
plot_hist	bool	Plots a histogram of the number of visits. Defaults to True.	True
filename	str	File name to save the histogram, if not informed will only show the plot.	None
size	tuple	Size to generate the plot. Defaults to (5, 4).	(5, 4)
include_guests	bool	Includes guests as visitors. Defaults to False.	False
seeds	list	List of seeds to plot, if None will plot all seeds available.	None

plot_age_group_histogram(self, data='infected', percentage=False, filename=None, size=(5, 4), title=None, seed=-1, close=True)

Plots a specift count of particles per age group. Can only plot one seed.

Available counts:

• infected: number of infected particles.
• vaccinated: number of vaccinated particles.
• deceased: number of deceased particles.
• particles: total number of particles

Parameters:

Name	Type	Description	Default
data	str	Type of count to plot. Defaults to "infected".	'infected'
percentage	bool	Y axis as a percentage. Defaults to False.	False
filename	str	File name to save the graph, if not informed will only show the plot.	None
size	tuple	Size for the plot. Defaults to (5, 4).	(5, 4)
title	str	Title to be printed on the plot.	None
seed	str	Seed to be plotted, if None will plot last loaded.	-1
close	bool	If False doesn't show, save or close the plot so that the user can add more information to plot using the plt attribute from the class. Defaults to False.	True

plot_contact_matrix_age_group(self, filename=None, slice_rng=slice(1, None, None), size=(10, 4), title=None, seed=-1, close=True)

Plot a contacts matrix per age group. Contacts are unique in a day, encounters are not (particle A can have multiple encounters with particle B in a single day, but only one contact).

Parameters:

Name	Type	Description	Default
filename	str	File name to save the graph, if not informed will only show the plot.	None
slice_rng	slice	Slice of days (steps?) to plot. Defaults to slice(1, None).	slice(1, None, None)
size	tuple	Size for the plot. Defaults to (10, 4).	(10, 4)
title	str	Title to be printed on the plot.	None
seed	str	Seed to be plotted, if None will plot last loaded.	-1
close	bool	If False doesn't show, save or close the plot so that the user can add more information to plot using the plt attribute from the class. Defaults to False.	True

plot_diagnosed(self, seeds=None, cumulative=True, **plot_args)

Plots the number of encounters.

Important

This plot uses the do_plot method, see plot_args to see all available arguments.

Parameters:

Name	Type	Description	Default
seeds	list	List of seeds to plot, if None will plot all seeds available.	None
cumulative	bool	Plot the cumulative diagnostics curve as well. Defaults to True.	True
**plot_args	kwargs	Arguments for the do_plot method (see plot_args).	{}

plot_encounters(self, seeds=None, plot_per_day=True, **plot_args)

Plots the number of encounters.

Important

This plot uses the do_plot method, see plot_args to see all available arguments.

Parameters:

Name	Type	Description	Default
seeds	list	List of seeds to plot, if None will plot all seeds available.	None
plot_per_day	bool	Consolidate the data on a one day resolution.	True
**plot_args	kwargs	Arguments for the do_plot method (see plot_args).	{}

plot_encounters_age_group(self, filename=None, slice_rng=slice(1, None, None), size=(5, 4), title=None, seed=-1, close=True)

Plots number of encounters per age group on a slice of time.

Parameters:

Name	Type	Description	Default
filename	str	File name to save the graph, if not informed will only show the plot.	None
slice_rng	slice	Slice of (steps?) to plot. Defaults to slice(1, None).	slice(1, None, None)
size	tuple	Size for the plot. Defaults to (5, 4).	(5, 4)
title	str	Title to be printed on the plot.	None
seed	str	Seed to be plotted, if None will plot last loaded.	-1
close	bool	If False doesn't show, save or close the plot so that the user can add more information to plot using the plt attribute from the class. Defaults to False.	True

plot_encounters_matrix_age_group(self, filename=None, slice_rng=slice(1, None, None), size=(10, 4), title=None, seed=-1, close=True)

Plot an encounters matrix per age group. Contacts are unique in a day, encounters are not (particle A can have multiple encounters with particle B in a single day, but only one contact).

Parameters:

Name	Type	Description	Default
filename	str	File name to save the graph, if not informed will only show the plot.	None
slice_rng	slice	Slice of days (steps?) to plot. Defaults to slice(1, None).	slice(1, None, None)
size	tuple	Size for the plot. Defaults to (10, 4).	(10, 4)
title	str	Title to be printed on the plot.	None
seed	str	Seed to be plotted, if None will plot last loaded.	-1
close	bool	If False doesn't show, save or close the plot so that the user can add more information to plot using the plt attribute from the class. Defaults to False.	True

plot_homes_hist(self, data='Symptoms', bins=10, filename=None, size=(5, 4), title=None, seed=-1)

Plots histograms of the percentage of particles on each category on all homes. Can only plot one seed.

Available data:

• symptoms: Plots percentages of mild symptomatic, severe symptomatic, asymptomatic and not infected;
• infections: Plots percentages of Infected ans not infected.

Parameters:

Name	Type	Description	Default
data	str	Data to be plotted, "Symptoms" or "Infections". Defaults to "Symptoms".	'Symptoms'
bins	int	Number of bins in the histogram. Defaults to 10.	10
filename	str	File name to save the graph, if not informed will only show the plot.	None
size	tuple	Size for the plot. Defaults to (5, 4).	(5, 4)
title	str	Title to be printed on the plot.	None
seed	str	Seed to be plotted, if None will plot last loaded.	-1

Exceptions:

Type	Description
RuntimeWarning	Invalid data selected or data unavailible.

plot_homes_infection_hist(self, filename=None, size=(5, 4), seed=-1, title=None, bins=10, close=True)

Plots a histogram of the percentage of infection that occurred inside each home. Can only plot one seed.

Parameters:

Name	Type	Description	Default
filename	str	File name to save the graph, if not informed will only show the plot.	None
size	tuple	Size to generate the plot. Defaults to (5, 4).	(5, 4)
title	str	Title to be printed on the plot.	None
seed	str	Seed to be plotted, if None will plot last loaded.	-1
bins	int	Number of bins in the histogram. Defaults to 100.	10
close	bool	If False doesn't show, save or close the plot so that the user can add more information to plot using the plt attribute from the class. Defaults to False.	True

plot_inf_probability(self, filename=None, seed=-1, bins=100, size=(5, 4), title=None, remove_zeros=False, close=True)

Plot a histogram of the maximum infection probability of all particles. Can only plot one seed.

Parameters:

Name	Type	Description	Default
filename	str	File name to save the graph, if not informed will only show the plot.	None
bins	int	Number of bins in the histogram. Defaults to 100.	100
size	tuple	Size to generate the plot. Defaults to (5, 4).	(5, 4)
title	str	Title to be printed on the plot.	None
seed	str	Seed to be plotted, if None will plot last loaded.	-1
remove_zeros	bool	Ignore particles with infection probability equals to zero. Defaults to False.	False
close	bool	If False doesn't show, save or close the plot so that the user can add more information to plot using the plt attribute from the class. Defaults to False.	True

plot_inf_source_symptoms(self, filename=None, seed=-1, hide_zeros=False, size=(5, 4), title=None, pie=True, close=True)

Plot vector symptom data. Can only plot one seed.

Parameters:

Name	Type	Description	Default
filename	str	File name to save the graph, if not informed will only show the plot.	None
hide_zeros	bool	Hide placements with no infections. Defaults to False.	False
size	tuple	Size to generate the plot. Defaults to (10, 4).	(5, 4)
title	str	Title to be printed on the plot.	None
seed	str	Seed to be plotted, if None will plot last loaded.	-1
close	bool	If False doesn't show, save or close the plot so that the user can add more information to plot using the plt attribute from the class. Defaults to False.	True

plot_inf_tree(self, filename=None, size=(20, 20), seed=-1, color=None, title=None, close=True)

Plots the infection tree. Can only plot one seed.

Available color markers: * placement: placement where the infection occurred.

Parameters:

Name	Type	Description	Default
filename	str	File name to save the graph, if not informed will only show the plot.	None
size	tuple	Size for the plot. Defaults to (20, 20).	(20, 20)
seed	str	Seed to be plotted, if None will plot last loaded.	-1
color	str	A color marker. Defaults to None.	None
title	str	Title for the plot. Defaults to None.	None
close	bool	If False doesn't show, save or close the plot so that the user can add more information to plot using the plt attribute from the class. Defaults to False.	True

plot_infection_placement(self, filename=None, seeds=None, size=(5, 4), skip=[], close=True, title=None)

Plot infection placement data.

Parameters:

Name	Type	Description	Default
filename	str	File name to save the graph, if not informed will only show the plot.	None
size	tuple	Size to generate the plot. Defaults to (10, 4).	(5, 4)
title	str	Title to be printed on the plot.	None
seeds	list	List of seeds to plot, if None will plot all seeds available.	None
skip	list	List of placements names to skip plotting.	[]
close	bool	If False doesn't show, save or close the plot so that the user can add more information to plot using the plt attribute from the class. Defaults to False.	True

plot_isolation_percentage(self, filename=None, size=(5, 4), seeds=None, dates=True, start_day=None, end_day=None, title=None, events=False, events_type=0)

Plot a isolation curve in time.

Parameters:

Name	Type	Description	Default
filename	str	File name to save the graph, if not informed will only show the plot.	None
size	tuple	Size to generate the plot. Defaults to (5, 4).	(5, 4)
title	str	Title to be printed on the plot.	None
seeds	list	List of seeds to plot, if None will plot all seeds available.	None
dates	bool	Use dates instead of days in the x axis. Defaults to True.	True
start_day	float	Plot only the interval from start_day. Defaults to 0.	None
end_day	float	Plot only the interval to end_day. Defaults to last day.	None
events	bool	Overlay simulation events on the plot. Defaults to False.	False
events_type	int	Type of logs to overlay as events. Defaults to MSG_EVENTS.	0

plot_quarantine(self, seeds=None, **plot_args)

Plots the number of encounters.

Important

This plot uses the do_plot method, see plot_args to see all available arguments.

Parameters:

Name	Type	Description	Default
seeds	list	List of seeds to plot, if None will plot all seeds available.	None
**plot_args	kwargs	Arguments for the do_plot method (see plot_args).	{}

plot_R(self, seeds=None, **plot_args)

Save a R graph.

Important

This plot uses the do_plot method, see plot_args to see all available arguments.

Parameters:

Name	Type	Description	Default
seeds	list	List of seeds to plot, if None will plot all seeds available.	None
**plot_args	kwargs	Arguments for the do_plot method (see plot_args).	{}

plot_secondary_infections_hist(self, filename=None, size=(5, 4), title=None, seed=-1, close=True)

Plot a secondary infections histogram. Can only plot one seed.

Parameters:

Name	Type	Description	Default
filename	str	File name to save the graph, if not informed will only show the plot.	None
size	tuple	Size to generate the plot. Defaults to (5, 4).	(5, 4)
title	str	Title to be printed on the plot.	None
seed	str	Seed to be plotted, if None will plot last loaded.	-1
close	bool	If False doesn't show, save or close the plot so that the user can add more information to plot using the plt attribute from the class. Defaults to False.	True

plot_SEIR(self, seeds=None, **plot_args)

Save a SEIR graph.

Important

This plot uses the do_plot method, see plot_args to see all available arguments.

Parameters:

Name	Type	Description	Default
seeds	list	List of seeds to plot, if None will plot all seeds available.	None
**plot_args	kwargs	Arguments for the do_plot method (see plot_args).	{}

plot_SEIR_stack(self, filename=None, size=(5, 4), seed=-1, show_legend=True, dates=True, events_type=0, title=None)

Save a stacked SEIR graph. Can only plot one seed.

Parameters:

Name	Type	Description	Default
filename	str	File name to save the graph, if not informed will only show the plot.	None
size	tuple	Size to generate the plot. Defaults to (5, 4).	(5, 4)
title	str	Title to be printed on the plot.	None
seed	str	Seed to be plotted, if None will plot last loaded.	-1
dates	bool	Use dates instead of days in the x axis. Defaults to True.	True
show_legend	bool	Hides legends if False. Defaults to True.	True

plot_service_infections(self, filename=None, seeds=None, size=(10, 4), skip=[], close=True, title=None)

Plots proportion of infections relating clients and workers inside each service

Returns:

Type	Description
	Three graphs, the first telling the proportion of infection derived from workers and clients, the second from workers to workers and clients, and the third from clients to workers and clients

PS: This code has been developed by Edmilson Roque - USP edmilson.roque.usp@gmail.com

plot_services_visitors(self, time_window='day', seeds=None, per_instance=False, **plot_args)

Plots the mean number of visitors on services in an week, whole simulation or a day window of time.

Important

This plot uses the do_plot method, see plot_args to see all available arguments.

Parameters:

Name	Type	Description	Default
time_window	str	"week", "day" or "simulation". Defaults to "day".	'day'
per_instance	bool	If True will divide the number of visitors by the number of instances. Defaults to False.	False
seeds	list	List of seeds to plot, if None will plot all seeds available.	None

plot_symptomatic_states(self, seeds=None, **plot_args)

Plots the number of particles in each symptomatic state in time.

Important

This plot uses the do_plot method, see plot_args to see all available arguments.

Parameters:

Name	Type	Description	Default
seeds	list	List of seeds to plot, if None will plot all seeds available.	None
**plot_args	kwargs	Arguments for the do_plot method (see plot_args).	{}

plot_symptoms(self, seeds=None, **plot_args)

Plots the percentage of symptomatic and asymptomatic particles in time.

Important

This plot uses the do_plot method, see plot_args to see all available arguments.

Parameters:

Name	Type	Description	Default
seeds	list	List of seeds to plot, if None will plot all seeds available.	None
**plot_args	kwargs	Arguments for the do_plot method (see plot_args).	{}

plot_time_between_hist(self, time_in=['time_infectious'], time_out=['time_recovered', 'time_dead'], bins=10, percentage=False, filename=None, size=(5, 4), title=None, seed=-1, close=True)

Plot a histogram of the duration between two times saved in the infection tree for all particles. Can only plot one seed.

Available times:

• time_exposed
• time_infectious
• time_activated
• time_recovered
• time_deceased
• time_vaccinated
• time_immune
• time_quarantined
• time_released_quarantine

Parameters:

Name	Type	Description	Default
time_in	list	A list of times to be accepted as a start time, if a particle has more than one the first in the list will be used. Defaults to ["time_infectious"].	['time_infectious']
time_out	list	A list of times to be accepted as a end time, if a particle has more than one the first in the list will be used. Defaults to ["time_recovered", "time_dead"].	['time_recovered', 'time_dead']
bins	int	Number of bins in the histogram. Defaults to 10.	10
percentage	bool	Y axis as a percentage. Defaults to False.	False
filename	str	File name to save the graph, if not informed will only show the plot.	None
size	tuple	Size for the plot. Defaults to (5, 4).	(5, 4)
title	str	Title to be printed on the plot.	None
seed	str	Seed to be plotted, if None will plot last loaded.	-1
close	bool	If False doesn't show, save or close the plot so that the user can add more information to plot using the plt attribute from the class. Defaults to False.	True

plot_total_infections_hist(self, filename=None, title=None, seeds=None, size=(5, 4), close=True)

Plots a histogram of the total number of infections at the end of the simulation for all seeds.

Parameters:

Name	Type	Description	Default
filename	str	File name to save the graph, if not informed will only show the plot.	None
size	tuple	Size for the plot. Defaults to (20, 20).	(5, 4)
seeds	list	List of seeds to plot, if None will plot all seeds available.	None
title	str	Title for the plot. Defaults to None.	None
close	bool	If False doesn't show, save or close the plot so that the user can add more information to plot using the plt attribute from the class. Defaults to False.	True