added docs

README.md

@@ -76,7 +76,7 @@ for drawing and drawing is not essential. If you want to use `tacoma.drawing`, p
 
 ## Documentation
 
-The documentation is currently available at http://rocs.hu-berlin.de/~tacoma. It is full of
+The documentation is currently available at http://tacoma.benmaier.org . It is full of
 typos and non-exhaustive but I think the important points are in there.
 
 

docs/conf.py

@@ -30,7 +30,7 @@ def __getattr__(cls, name):
 MOCK_MODULES = ['numpy', 'scipy', 'matplotlib', 'matplotlib.pyplot', 'matplotlib.collections',
                 'lmfit', 'networkx', 'community', 
                 'scipy.optimize', 'scipy.stats', 'scipy.special', 'scipy.integrate',
-                'scipy.sparse',
+                'scipy.sparse', 'scipy.sparse.linalg', 'scipy.linalg',
                 'numpy.polynomial', 'numpy.polynomial.polynomial', 'wget',
                 'lmfit',
                ]

docs/epidemic_spreading/epidemic_classes.rst

@@ -402,3 +402,48 @@ Plot the results as
     - The simulation works on both :class:`_tacoma.edge_lists` and
       :class:`_tacoma.edge_changes`.
 
+coverage-SIS
+------------
+
+This class behaves similar to the SIS dynamics introduced above. However,
+it comes with an additional condition to end the simulation. The coverage
+:math:`\mathcal C(t)` is defined as the ratio of nodes which have been infected
+at least once during simulation. The simulation ends as soon as a critical
+coverage :math:`\mathcal C_c(t)` is reached or the number of infected is zero. 
+This variation of the SIS process
+is usually used to measure the life time of the process as a susceptibility
+parameter to find the epidemic threshold.
+
+.. code:: python
+
+    cSIS = tc.coverage_SIS(
+                   N, #number of nodes
+                   t_simulation, # maximum time of the simulation (set this to a high value)
+                   infection_rate, 
+                   recovery_rate,
+                   number_of_initially_infected = 1, # optional, default: 1
+                   number_of_initially_vaccinated = 0, # optional, default: 0
+                   critical_coverage = 0.75, # optional, default: 0.75
+                   seed = 792, # optional, default: randomly initiated
+                  )
+
+
+The instance of the `coverage_SIS` class is then passed to the corresponding
+Gillespie function :func:`tacoma.api.gillespie_epidemics` for the simulation.
+
+.. code:: python
+
+    tc.gillespie_epidemics(temporal_network, cSIS)
+
+Note that per default, observables are not saved during simulation, since
+this kind of simulation is usually only performed to measure the lifetime
+as a susceptibility parameter. Access the following observables after
+simulation.
+
+- ``coverage_SIS.lifetime`` : The time it took to reach either of the termination
+  conditions
+- ``coverage_SIS.number_of_events`` : The total number of events (infection, recovery)
+  it took to reach either of the termination
+  conditions.
+
+

docs/reference/_generate/_tacoma.QS_SIS.rst

@@ -0,0 +1,34 @@
+\_tacoma.QS\_SIS
+================
+
+.. currentmodule:: _tacoma
+
+.. autoclass:: QS_SIS
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~QS_SIS.__init__
+      ~QS_SIS.ended_in_absorbing_state
+      ~QS_SIS.get_infection_observables
+      ~QS_SIS.get_random_configuration
+      ~QS_SIS.set_initial_configuration
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~QS_SIS.configurations
+      ~QS_SIS.last_active_time
+      ~QS_SIS.t_simulation
+
+

docs/reference/_generate/_tacoma.coverage_SIS.rst

@@ -0,0 +1,34 @@
+\_tacoma.coverage\_SIS
+======================
+
+.. currentmodule:: _tacoma
+
+.. autoclass:: coverage_SIS
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~coverage_SIS.__init__
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~coverage_SIS.I
+      ~coverage_SIS.R0
+      ~coverage_SIS.SI
+      ~coverage_SIS.lifetime
+      ~coverage_SIS.number_of_events
+      ~coverage_SIS.t_simulation
+      ~coverage_SIS.time
+
+