Commit 5da1cee9 authored by Tiago Peixoto's avatar Tiago Peixoto
Browse files

dynamics: change notation from 'infected' to 'infections'

parent ef39caab
......@@ -204,7 +204,7 @@ class SIState(EpidemicStateBase):
Susceptible to exposed transition probability. This only has an
effect if ``exposed=True``.
v0 : ``int`` or :class:`~graph_tool.Vertex` (optional, default: ``None``)
Initial infected vertex. If not provided, and if the global state is
Initial infectious vertex. If not provided, and if the global state is
also not provided via paramter ``s``, a random vertex will be chosen.
s : :class:`~graph_tool.VertexPropertyMap` (optional, default: ``None``)
Initial global state. If not provided, all vertices will be
......@@ -219,8 +219,8 @@ class SIState(EpidemicStateBase):
-----
This implements an SI epidemic process [pastor-satorras-epidemic-2015]_,
where nodes in the susceptible state (value 0) are infected by neighbours
in the infected state (value 1).
where nodes in the susceptible state (value 0) are infectious by neighbours
in the infectious state (value 1).
If a node :math:`i` is updated at time :math:`t`, the transition
probabilities from state :math:`s_i(t)` to state :math:`s_i(t+1)` are
......@@ -263,7 +263,7 @@ class SIState(EpidemicStateBase):
[...]
>>> xlabel(r"Time")
Text(...)
>>> ylabel(r"Infected nodes")
>>> ylabel(r"Infectious nodes")
Text(...)
>>> tight_layout()
>>> savefig("SI.svg")
......@@ -271,7 +271,7 @@ class SIState(EpidemicStateBase):
.. figure:: SI.svg
:align: center
Number of infected nodes vs. time for an SI dynamics.
Number of infectious nodes vs. time for an SI dynamics.
References
----------
......@@ -311,7 +311,7 @@ class SISState(DiscreteStateBase):
Susceptible to exposed transition probability. This only has an
effect if ``exposed=True``.
v0 : ``int`` or :class:`~graph_tool.Vertex` (optional, default: ``None``)
Initial infected vertex. If not provided, and if the global state is
Initial infectious vertex. If not provided, and if the global state is
also not provided via paramter ``s``, a random vertex will be chosen.
s : :class:`~graph_tool.VertexPropertyMap` (optional, default: ``None``)
Initial global state. If not provided, all vertices will be
......@@ -327,7 +327,7 @@ class SISState(DiscreteStateBase):
This implements an SIS epidemic process
[pastor-satorras-epidemic-2015]_, where nodes in the susceptible state
(value 0) are infected by neighbours in the infected state (value 1),
(value 0) are infectious by neighbours in the infectious state (value 1),
which can then eventually recover to a susceptible state.
If a node :math:`i` is updated at time :math:`t`, the transition
......@@ -372,7 +372,7 @@ class SISState(DiscreteStateBase):
[...]
>>> xlabel(r"Time")
Text(...)
>>> ylabel(r"Infected nodes")
>>> ylabel(r"Infectious nodes")
Text(...)
>>> tight_layout()
>>> savefig("SIS.svg")
......@@ -380,7 +380,7 @@ class SISState(DiscreteStateBase):
.. figure:: SIS.svg
:align: center
Number of infected nodes vs. time for an SIS dynamics.
Number of infectious nodes vs. time for an SIS dynamics.
References
----------
......@@ -420,7 +420,7 @@ class SIRState(DiscreteStateBase):
Susceptible to exposed transition probability. This only has an
effect if ``exposed=True``.
v0 : ``int`` or :class:`~graph_tool.Vertex` (optional, default: ``None``)
Initial infected vertex. If not provided, and if the global state is
Initial infectious vertex. If not provided, and if the global state is
also not provided via paramter ``s``, a random vertex will be chosen.
s : :class:`~graph_tool.VertexPropertyMap` (optional, default: ``None``)
Initial global state. If not provided, all vertices will be
......@@ -436,7 +436,7 @@ class SIRState(DiscreteStateBase):
This implements an SIR epidemic process
[pastor-satorras-epidemic-2015]_, where nodes in the susceptible state
(value 0) are infected by neighbours in the infected state (value 1),
(value 0) are infectious by neighbours in the infectious state (value 1),
which can then eventually recover to a recovered state (value 2).
If a node :math:`i` is updated at time :math:`t`, the transition
......@@ -482,7 +482,7 @@ class SIRState(DiscreteStateBase):
<...>
>>> plot(S, label="Susceptible")
[...]
>>> plot(X, label="Infected")
>>> plot(X, label="Infectious")
[...]
>>> plot(R, label="Recovered")
[...]
......@@ -498,7 +498,7 @@ class SIRState(DiscreteStateBase):
.. figure:: SIR.svg
:align: center
Number of susceptible, infected, and recovered nodes vs. time for an
Number of susceptible, infectious, and recovered nodes vs. time for an
SIR dynamics.
References
......@@ -542,7 +542,7 @@ class SIRSState(DiscreteStateBase):
Susceptible to exposed transition probability. This only has an
effect if ``exposed=True``.
v0 : ``int`` or :class:`~graph_tool.Vertex` (optional, default: ``None``)
Initial infected vertex. If not provided, and if the global state is
Initial infectious vertex. If not provided, and if the global state is
also not provided via paramter ``s``, a random vertex will be chosen.
s : :class:`~graph_tool.VertexPropertyMap` (optional, default: ``None``)
Initial global state. If not provided, all vertices will be
......@@ -558,7 +558,7 @@ class SIRSState(DiscreteStateBase):
This implements an SIRS epidemic process
[pastor-satorras-epidemic-2015]_, where nodes in the susceptible state
(value 0) are infected by neighbours in the infected state (value 1),
(value 0) are infectious by neighbours in the infectious state (value 1),
which can then eventually recover to a recovered state (value 2), and
finally back to the susceptible state.
......@@ -609,7 +609,7 @@ class SIRSState(DiscreteStateBase):
<...>
>>> plot(S, label="Susceptible")
[...]
>>> plot(X, label="Infected")
>>> plot(X, label="Infectious")
[...]
>>> plot(R, label="Recovered")
[...]
......@@ -625,7 +625,7 @@ class SIRSState(DiscreteStateBase):
.. figure:: SIRS.svg
:align: center
Number of susceptible, infected, and recovered nodes vs. time for an
Number of susceptible, infectious, and recovered nodes vs. time for an
SIRS dynamics.
References
......
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