From ae3be261bd3aff9053c0d4206af195a7860402fc Mon Sep 17 00:00:00 2001 From: Giulio Rossetti Date: Mon, 12 Oct 2020 11:18:20 +0200 Subject: [PATCH] :memo: update SEIR/SEIS references --- docs/reference/models/epidemics/SEIR.rst | 7 +- docs/reference/models/epidemics/SEIR_ct.rst | 108 ++++++++++++++++++++ docs/reference/models/epidemics/SEIS.rst | 7 +- docs/reference/models/epidemics/SEIS_ct.rst | 106 +++++++++++++++++++ docs/reference/reference.rst | 2 + 5 files changed, 224 insertions(+), 6 deletions(-) create mode 100644 docs/reference/models/epidemics/SEIR_ct.rst create mode 100644 docs/reference/models/epidemics/SEIS_ct.rst diff --git a/docs/reference/models/epidemics/SEIR.rst b/docs/reference/models/epidemics/SEIR.rst index a76ae80..1ae1d08 100644 --- a/docs/reference/models/epidemics/SEIR.rst +++ b/docs/reference/models/epidemics/SEIR.rst @@ -1,6 +1,6 @@ -**** -SEIR -**** +********* +SEIR (DT) +********* In the SEIR model [#]_, during the course of an epidemics, a node is allowed to change its status from **Susceptible** (S) to **Exposed** (E) to **Infected** (I), then to **Removed** (R). @@ -9,6 +9,7 @@ The model is instantiated on a graph having a non-empty set of infected nodes. SEIR assumes that if, during a generic iteration, a susceptible node comes into contact with an infected one, it becomes infected after an exposition period with probability beta, than it can switch to removed with probability gamma (the only transition allowed are S→E→I→R). +This implementation assumes discrete time dynamics for the E->I and I->R transitions. -------- Statuses diff --git a/docs/reference/models/epidemics/SEIR_ct.rst b/docs/reference/models/epidemics/SEIR_ct.rst new file mode 100644 index 0000000..28fee32 --- /dev/null +++ b/docs/reference/models/epidemics/SEIR_ct.rst @@ -0,0 +1,108 @@ +********* +SEIR (CT) +********* + + +In the SEIR model [#]_, during the course of an epidemics, a node is allowed to change its status from **Susceptible** (S) to **Exposed** (E) to **Infected** (I), then to **Removed** (R). + +The model is instantiated on a graph having a non-empty set of infected nodes. + +SEIR assumes that if, during a generic iteration, a susceptible node comes into contact with an infected one, it becomes infected after an exposition period with probability beta, than it can switch to removed with probability gamma (the only transition allowed are S→E→I→R). + +This implementation assumes continuous time dynamics for the E->I and I->R transitions. + +-------- +Statuses +-------- + +During the simulation a node can experience the following statuses: + +=========== ==== +Name Code +=========== ==== +Susceptible 0 +Infected 1 +Exposed 2 +Removed 3 +=========== ==== + +---------- +Parameters +---------- + +===== ===== =============== ======= ========= ===================== +Name Type Value Type Default Mandatory Description +===== ===== =============== ======= ========= ===================== +beta Model float in [0, 1] True Infection probability +gamma Model float in [0, 1] True Removal probability +alpha Model float in [0, 1] True Latent period +===== ===== =============== ======= ========= ===================== + +The initial infection status can be defined via: + + - **fraction_infected**: Model Parameter, float in [0, 1] + - **Infected**: Status Parameter, set of nodes + +The two options are mutually exclusive and the latter takes precedence over the former. + +------- +Methods +------- + +The following class methods are made available to configure, describe and execute the simulation: + +^^^^^^^^^ +Configure +^^^^^^^^^ +.. autoclass:: ndlib.models.epidemics.SEIR_ct_Model.SEIRctModel +.. automethod:: ndlib.models.epidemics.SEIR_ct_Model.SEIRctModel.__init__(graph) + +.. automethod:: ndlib.models.epidemics.SEIR_ct_Model.SEIRctModel.set_initial_status(self, configuration) +.. automethod:: ndlib.models.epidemics.SEIR_ct_Model.SEIRctModel.reset(self) + +^^^^^^^^ +Describe +^^^^^^^^ + +.. automethod:: ndlib.models.epidemics.SEIR_ct_Model.SEIRctModel.get_info(self) +.. automethod:: ndlib.models.epidemics.SEIR_ct_Model.SEIRctModel.get_status_map(self) + +^^^^^^^^^^^^^^^^^^ +Execute Simulation +^^^^^^^^^^^^^^^^^^ +.. automethod:: ndlib.models.epidemics.SEIR_ct_Model.SEIRctModel.iteration(self) +.. automethod:: ndlib.models.epidemics.SEIR_ct_Model.SEIRctModel.iteration_bunch(self, bunch_size) + + +------- +Example +------- + +In the code below is shown an example of instantiation and execution of an SEIR simulation on a random graph: we set the initial set of infected nodes as % of the overall population, a probability of infection of 1%, a removal probability of 0.5% and an incubation period of 5% (e.g. 20 iterations). + +.. code-block:: python + + import networkx as nx + import ndlib.models.ModelConfig as mc + import ndlib.models.epidemics as ep + + # Network topology + g = nx.erdos_renyi_graph(1000, 0.1) + + # Model selection + model = ep.SEIRctModel(g) + + # Model Configuration + cfg = mc.Configuration() + cfg.add_model_parameter('beta', 0.01) + cfg.add_model_parameter('gamma', 0.005) + cfg.add_model_parameter('alpha', 0.05) + cfg.add_model_parameter("fraction_infected", 0.05) + model.set_initial_status(cfg) + + # Simulation execution + iterations = model.iteration_bunch(200) + + + +.. [#] J.L. Aron and I.B. Schwartz. Seasonality and period-doubling bifurcations in an epidemic model. Journal Theoretical Biology, 110:665-679, 1984 diff --git a/docs/reference/models/epidemics/SEIS.rst b/docs/reference/models/epidemics/SEIS.rst index 3dcb85b..f880f02 100644 --- a/docs/reference/models/epidemics/SEIS.rst +++ b/docs/reference/models/epidemics/SEIS.rst @@ -1,6 +1,6 @@ -**** -SEIS -**** +********* +SEIS (DT) +********* In the SEIS model, during the course of an epidemics, a node is allowed to change its status from **Susceptible** (S) to **Exposed** (E) to **Infected** (I), then again to **Susceptible** (S). @@ -9,6 +9,7 @@ The model is instantiated on a graph having a non-empty set of infected nodes. SEIS assumes that if, during a generic iteration, a susceptible node comes into contact with an infected one, it becomes infected after an exposition period with probability beta, than it can switch back to susceptible with probability lambda (the only transition allowed are S→E→I→S). +This implementation assumes discrete time dynamics for the E->I and I->S transitions. -------- Statuses diff --git a/docs/reference/models/epidemics/SEIS_ct.rst b/docs/reference/models/epidemics/SEIS_ct.rst new file mode 100644 index 0000000..98123f7 --- /dev/null +++ b/docs/reference/models/epidemics/SEIS_ct.rst @@ -0,0 +1,106 @@ +********* +SEIS (CT) +********* + + +In the SEIS model, during the course of an epidemics, a node is allowed to change its status from **Susceptible** (S) to **Exposed** (E) to **Infected** (I), then again to **Susceptible** (S). + +The model is instantiated on a graph having a non-empty set of infected nodes. + +SEIS assumes that if, during a generic iteration, a susceptible node comes into contact with an infected one, it becomes infected after an exposition period with probability beta, than it can switch back to susceptible with probability lambda (the only transition allowed are S→E→I→S). + +This implementation assumes continuous time dynamics for the E->I and I->S transitions. + +-------- +Statuses +-------- + +During the simulation a node can experience the following statuses: + +=========== ==== +Name Code +=========== ==== +Susceptible 0 +Infected 1 +Exposed 2 +=========== ==== + +---------- +Parameters +---------- + +====== ===== =============== ======= ========= ===================== +Name Type Value Type Default Mandatory Description +====== ===== =============== ======= ========= ===================== +beta Model float in [0, 1] True Infection probability +lambda Model float in [0, 1] True Removal probability +alpha Model float in [0, 1] True Latent period +====== ===== =============== ======= ========= ===================== + +The initial infection status can be defined via: + + - **fraction_infected**: Model Parameter, float in [0, 1] + - **Infected**: Status Parameter, set of nodes + +The two options are mutually exclusive and the latter takes precedence over the former. + +------- +Methods +------- + +The following class methods are made available to configure, describe and execute the simulation: + +^^^^^^^^^ +Configure +^^^^^^^^^ +.. autoclass:: ndlib.models.epidemics.SEIS_ct_Model.SEISctModel +.. automethod:: ndlib.models.epidemics.SEIS_ct_Model.SEISctModel.__init__(graph) + +.. automethod:: ndlib.models.epidemics.SEIS_ct_Model.SEISctModel.set_initial_status(self, configuration) +.. automethod:: ndlib.models.epidemics.SEIS_ct_Model.SEISctModel.reset(self) + +^^^^^^^^ +Describe +^^^^^^^^ + +.. automethod:: ndlib.models.epidemics.SEIS_ct_Model.SEISctModel.get_info(self) +.. automethod:: ndlib.models.epidemics.SEIS_ct_Model.SEISctModel.get_status_map(self) + +^^^^^^^^^^^^^^^^^^ +Execute Simulation +^^^^^^^^^^^^^^^^^^ +.. automethod:: ndlib.models.epidemics.SEIS_ct_Model.SEISctModel.iteration(self) +.. automethod:: ndlib.models.epidemics.SEIS_ct_Model.SEISctModel.iteration_bunch(self, bunch_size) + + +------- +Example +------- + +In the code below is shown an example of instantiation and execution of an SEIS simulation on a random graph: +we set the initial set of infected nodes as 5% of the overall population, a probability of infection of 1%, a removal probability of 0.5% and an latent period of 5% (e.g. 20 iterations). + +.. code-block:: python + + import networkx as nx + import ndlib.models.ModelConfig as mc + import ndlib.models.epidemics as ep + + # Network topology + g = nx.erdos_renyi_graph(1000, 0.1) + + # Model selection + model = ep.SEISctModel(g) + + # Model Configuration + cfg = mc.Configuration() + cfg.add_model_parameter('beta', 0.01) + cfg.add_model_parameter('lambda', 0.005) + cfg.add_model_parameter('alpha', 0.05) + cfg.add_model_parameter("fraction_infected", 0.05) + model.set_initial_status(cfg) + + # Simulation execution + iterations = model.iteration_bunch(200) + + diff --git a/docs/reference/reference.rst b/docs/reference/reference.rst index ab83017..ae85c98 100644 --- a/docs/reference/reference.rst +++ b/docs/reference/reference.rst @@ -39,7 +39,9 @@ In ``NDlib`` are implemented the following **Epidemic** models: models/epidemics/SIS.rst models/epidemics/SIR.rst models/epidemics/SEIR.rst + models/epidemics/SEIR_ct.rst models/epidemics/SEIS.rst + models/epidemics/SEIS_ct.rst models/epidemics/SWIR.rst models/epidemics/Threshold.rst models/epidemics/GeneralisedThreshold.rst