CV19 module

class cv19.Graph

Bases: object

class Graph This class is used to create and manipulated graphs It makes a heavy use of the node class A graph is made of nodes and edges. This class allows to store a value for each node and different “weights” for each edge. Also, edges are directed.

Exampe of usage: g = Graph()

for i, inode in enumerate([‘A’,’B’,’C’,’D’]):

print(i) g.add_node(inode, 0)

nms = [‘x’, ‘y’] g.add_edge(‘A’, ‘B’, nms, [1, 100]) g.add_edge(‘A’, ‘C’, nms, [2, 200]) g.add_edge(‘B’, ‘D’, nms, [3, 300]) g.add_edge(‘D’, ‘B’, nms, [4, 400]) g.add_edge(‘D’, ‘C’, nms, [5, 500]) g.add_edge(‘C’, ‘C’, nms, [6, 600])

# A node can be connected to itself. g.add_edge(‘B’, ‘B’, nms, [333, 333])

g.show()

vert_dict: dict

a dict containing the vertices

num_vertices : int

the number of nodes (or vertices) in a graph

add_node(node, value) get_node() get_node_value() set_node() get_node_ids() get_nodes_to() get_nodes_from()

add_edge(frm, to, names=[], values=0)

warning: does not verify if edge already exists

add_node(nnode, value)

method: add_node

Adds a node to a graph. The node must have a value.

get_edge(frm, to, field)

get_node(n)

method: get_node

n: str

node: a node object

get_node_ids()

get_node_value(n)

method: get_node_value

n: str

value: float

get_nodes_from(nnode)

get_nodes_to(nnode)

node_activation(nnode, key)

node_upgrade(nnode, key)

set_node(n, value)

method: set_node

n: str

The ID or name of the node

value: float

The value to be assigned to the node

updates the Graph

show_connections()

show_weights()

class cv19.InfectionCurve

Bases: object

compute(p)

InfectionCurve(self, p): computes the Infection Curve based on a probabilistic model implemented in a simulation

Args:

config object from ParseConfig

Raises:

Returns:

Time series for the curves of: - Infected - Confirmed - Recovered - Confirmed at home - Confirmed at hospital - Confirmed at ICU - Dead

model_SEIR()

model_SIR(p)

plt_IC()

plots the infection curve

Args:

ic: time series fplot: filename for the plot

Raises:

Returns:

Nothing, just save the plot.

plt_IC_n()

plots the infection curve

Args:

ic: time series fplot: filename for the plot

Raises:

Returns:

Nothing, just save the plot.

class cv19.node(nnode, value)

Bases: object

class node This class is used to create and manipulated nodes.

add_neighbor(neighbor, names, values)

be_neighbor(neighbor, names, values)

get_connections()

get_id()

get_weight(neighbor)

class cv19.parser(defaults=None, dict_type=<class 'collections.OrderedDict'>, allow_no_value=False, *, delimiters=('=', ':'), comment_prefixes=('#', ';'), inline_comment_prefixes=None, strict=True, empty_lines_in_values=True, default_section='DEFAULT', interpolation=<object object>, converters=<object object>)

Bases: configparser.ConfigParser

parser class manipulation of parser from ini files

check_file(sys_args)

chek_file(args): Parse paramenters for the simulation from a .ini file

Args:

filename (str): the file name of the map to be read

Raises:

Returns:

readmap: a healpix map, class ?

load_filenames()

load_filenames(self): make filenames based on info in config file

Args:

None

Raises:

Returns:

list of filenames

load_parameters()

load_parameters(self): load parameters from config file

Args:

None

Raises:

Returns:

list of parameters as a named tuple

read_config_file()

chek_file(args): Parse paramenters for the simulation from a .ini file

Args:

filename (str): the file name of the map to be read

Raises:

Returns:

readmap: a healpix map, class ?

class cv19.table_draw

Bases: object

add_clean_column(columnname, column)

load(filename)

random_gen(xinfname, xsupname, yname)

method: random_gen

Generates a random sample from a given probability density The probability density must be in the table, in the table_draw class.

save_clean_CDF(filename)

tabular(x, y)

test_random_gen(nran, fplot)