Merge pull request #14 from benmaier/dev

updates

CHANGELOG.md

@@ -7,6 +7,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Unreleased
 
+## [v0.1.4] - 2020-05-18
+
+### Added
+
+- A new small-world network styling method based on 1d lattice distance (in epipack.networks)
+- methods to compute Jacobian and next generation matrices (NGMs) in `MatrixEpiModel`, as well as R0 from said NGMs (TODO: add docs)
+- tests for these methods
+- `epipack.distributions` module, which deals with fitting empirical distributions to sums of exponentially distributed random variables (still in dev mode, also TODO: add docs)
+- tests for this module
+- methods to `EpiModel` that save events that have been set. This will be used to generate model flowcharts with graphviz at some point
+- the possibility to pass a function to ``StochasticEpiModel.simulate`` that checks for a custom stop condition
+
 ## [v0.1.3] - 2020-04-07
 
 ### Fixed
@@ -88,7 +100,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 - initialized
 
-[Unreleased]: https://github.com/benmaier/epipack/compare/v0.1.3...HEAD
+[Unreleased]: https://github.com/benmaier/epipack/compare/v0.1.4...HEAD
+[v0.1.4]: https://github.com/benmaier/epipack/compare/v0.1.2...v0.1.4]
 [v0.1.3]: https://github.com/benmaier/epipack/compare/v0.1.2...v0.1.3]
 [v0.1.2]: https://github.com/benmaier/epipack/compare/v0.1.1...v0.1.2]
 [v0.1.1]: https://github.com/benmaier/epipack/compare/v0.1.0...v0.1.1]

README.md

@@ -92,7 +92,6 @@ So far, the package's functionality was tested on Mac OS X and CentOS only.
 * `sympy==1.6`
 * `pyglet<1.6`
 * `matplotlib>=3.0.0`
-* `bfmplot>=0.0.7`
 * `ipython>=7.14.0`
 * `ipywidgets>=7.5.1`
 

README.rst

@@ -101,7 +101,6 @@ installed by ``pip`` during the installation process
 -  ``sympy==1.6``
 -  ``pyglet<1.6``
 -  ``matplotlib>=3.0.0``
--  ``bfmplot>=0.0.7``
 -  ``ipython>=7.14.0``
 -  ``ipywidgets>=7.5.1``
 

cookbook/modular_hierarchical_network_reaction_diffusion/sw_layout_reaction_diffusion_simple_vis.py

@@ -0,0 +1,72 @@
+from epipack import MatrixEpiModel, get_2D_lattice_links
+from epipack.vis import visualize_reaction_diffusion, get_grid_layout
+import numpy as np
+import networkx as nx
+import cMHRN
+from time import time
+from epipack.networks import get_small_world_layout
+
+# load edges from txt file and construct Graph object
+N, edges = cMHRN.fast_mhrn(8,3,7,0.18,True)
+
+
+
+start = time()
+
+# get the network properties
+links = [ ( u, v, 1.0 ) for u, v in edges ]
+
+network = get_small_world_layout(N,links)
+
+
+
+
+
+
+base_compartments = "SIR"
+
+compartments = [ (node, C) for node in range(N) for C in base_compartments ]
+model = MatrixEpiModel(compartments)
+
+infection_rate = 3
+recovery_rate = 1
+mobility_rate = 0.05
+
+quadratic_processes = []
+linear_processes = []
+
+print("defining processes")
+
+for node in range(N):
+    quadratic_processes.append(
+            (  (node, "S"), (node, "I"), infection_rate, (node, "I"), (node, "I") ),
+        )
+
+    linear_processes.append(
+              ( (node, "I"), recovery_rate, (node, "R") ) 
+        )
+
+for u, v, w in links:
+    for C in base_compartments:
+
+        linear_processes.extend([
+                  ( (u, C), w*mobility_rate, (v, C) ),
+                  ( (v, C), w*mobility_rate, (u, C) ),
+            ])
+
+print("set processes")
+
+model.set_processes(quadratic_processes+linear_processes,allow_nonzero_column_sums=True)
+
+initial_conditions = { ( node, "S" ): 1.0 for node in range(N) } 
+initial_conditions[(0, "S")] = 0.8
+initial_conditions[(0, "I")] = 0.2
+model.set_initial_conditions(initial_conditions,allow_nonzero_column_sums=True)
+
+t = np.linspace(0,20,100)
+
+node_compartments = [ (node, "I" ) for node in range(N) ]
+
+dt = 0.04
+visualize_reaction_diffusion(model, network, dt, node_compartments, value_extent=[0,0.3])
+

docs/about.rst

@@ -103,7 +103,6 @@ installed by ``pip`` during the installation process
 -  ``sympy==1.6``
 -  ``pyglet<1.6``
 -  ``matplotlib>=3.0.0``
--  ``bfmplot>=0.0.7``
 -  ``ipython>=7.14.0``
 -  ``ipywidgets>=7.5.1``
 

docs/api/distributions.rst

@@ -0,0 +1,8 @@
+Distributions
+-------------
+
+.. automodule:: epipack.distributions
+    :members:
+    :undoc-members:
+    :show-inheritance:
+

docs/conf.py

@@ -83,7 +83,7 @@ def __getattr__(cls, name):
 
 # General information about the project.
 project = u'epipack'
-copyright = u'2020,  Benjamin F. Maier'
+copyright = u'2020-2021,  Benjamin F. Maier'
 author = u' Benjamin F. Maier'
 
 # The version info for the project you're documenting, acts as replacement for

docs/index.rst

@@ -69,6 +69,7 @@ epipack
    api/numeric_matrix_epi_models
    api/symbolic_matrix_epi_models
    api/plottools
+   api/distributions
 
 .. .. toctree::
 ..    :maxdepth: 2