piegy 1.0.0__tar.gz

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+ BSD 3-Clause License
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+
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+ Copyright (c) 2025, Chenning Xu
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+
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+ Redistribution and use in source and binary forms, with or without
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+ modification, are permitted provided that the following conditions are met:
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+
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+ 1. Redistributions of source code must retain the above copyright notice, this
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+ list of conditions and the following disclaimer.
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+
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+ 2. Redistributions in binary form must reproduce the above copyright notice,
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+ this list of conditions and the following disclaimer in the documentation
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+ and/or other materials provided with the distribution.
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+
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+ 3. Neither the name of the copyright holder nor the names of its
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+ contributors may be used to endorse or promote products derived from
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+ this software without specific prior written permission.
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+
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+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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+ include README.md
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+ include LICENSE.txt
piegy-1.0.0/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: piegy
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+ Version: 1.0.0
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+ Summary: Payoff-Driven Stochastic Spatial Model for Evolutionary Game Theory
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+ Author-email: Chenning Xu <cxu7@caltech.edu>
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+ License: BSD 3-Clause License
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+
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+ Copyright (c) 2025, Chenning Xu
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+
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+ Redistribution and use in source and binary forms, with or without
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+ modification, are permitted provided that the following conditions are met:
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+
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+ 1. Redistributions of source code must retain the above copyright notice, this
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+ list of conditions and the following disclaimer.
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+
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+ 2. Redistributions in binary form must reproduce the above copyright notice,
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+ this list of conditions and the following disclaimer in the documentation
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+ and/or other materials provided with the distribution.
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+
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+ 3. Neither the name of the copyright holder nor the names of its
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+ contributors may be used to endorse or promote products derived from
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+ this software without specific prior written permission.
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+
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+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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+
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+ Project-URL: Source, https://github.com/Chenning04/piegy.git
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+ Project-URL: Documentation, https://piegy.readthedocs.io/en/
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+ Keywords: Game Theory,Evolutionary Game Theory,Spatial Model,Stochastic Model,Payoff Driven
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+ Classifier: Development Status :: 4 - Beta
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+ Classifier: Intended Audience :: Developers
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: Intended Audience :: Education
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+ Classifier: License :: OSI Approved :: BSD License
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Programming Language :: Python :: 3.10
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+ Classifier: Programming Language :: Python :: 3.11
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+ Classifier: Operating System :: OS Independent
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+ Requires-Python: >=3.6
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE.txt
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+ Requires-Dist: numpy
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+ Requires-Dist: matplotlib
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+ Requires-Dist: imageio>=2.37.0
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+ Requires-Dist: moviepy>=2.1.1
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+ Requires-Dist: seaborn>=0.13.2
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+ Dynamic: license-file
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+
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+ # piegy
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+
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+ The package full name is: Payoff-Driven Stochastic Spatial Model for Evolutionary Game Theory
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+
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+ Provides a stochastic spatial model for simulating the interaction and evolution of two species in either 1D or 2D space, as well as analytic tools.
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+
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+ ## Installation
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+
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+ ```bash
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+ pip install piegy
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+ ```
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+
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+ ## Documentation and Source
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+
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+ See source code at: [GitHub-piegy repo](https://github.com/Chenning04/piegy.git).
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+ The *piegy* documentation at: [piegy docs](https://piegy.readthedocs.io/en/).
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+
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+ ## How the Model Works
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+
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+ Our model can be summarized as "classical game theory endowed with a spatial structure and payoff-driven migration rules". Consider two species, predators and preys (denote by *U* and *V*), in a rectangular region. We divide the region into N by M patches and simulate their interaction within a patch by classical game theory (i.e., payoff matrices and carrying capacity). Interactions across patches are simulated by payoff-driven migration rules. An individual migrates to a neighboring patch with probability weighted by payoff in the neighbors.
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+
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+ We use the Gillepie algorithm as the fundamental event-selection algorithm. At each time step, one event is selected and let happen; and step sizes are continuous, dependent on the current state in the space. Data are recorded every some specified time interval.
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+
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+ ## Analytic Tools
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+
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+ The *piegy* package also provides a wide range of analytic and supportive tools alongside the main model, such as plotting, numerical tools, data saving & reading, etc. We also provide the *piegy.videos* module for more direct visualizations like how population distribution change over time.
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+
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+ ## Examples
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+
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+ To get started, simply get our demo model and run simulation:
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+
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+ ```python
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+ from piegy import model, figures
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+
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+ sim = model.demo_model()
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+ model.run(sim)
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+
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+ dynamics = figures.UV_dyna(sim)
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+ U_hmap, V_hmap = figures.UV_heatmap(sim)
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+ ```
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+
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+ The figures reveal the population dynamics and steady state distribution.
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+
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+
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+ ## Acknowledgments
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+
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+ - Thanks Professor Daniel Cooney at University of Illinois Urbana-Champaign. This package is developed alongside a project with Prof. Cooney and received enormous help from him.
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+ - Special thanks to the open-source community for making this package possible.
piegy-1.0.0/README.md ADDED
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+ # piegy
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+
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+ The package full name is: Payoff-Driven Stochastic Spatial Model for Evolutionary Game Theory
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+
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+ Provides a stochastic spatial model for simulating the interaction and evolution of two species in either 1D or 2D space, as well as analytic tools.
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+
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+ ## Installation
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+
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+ ```bash
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+ pip install piegy
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+ ```
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+
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+ ## Documentation and Source
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+
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+ See source code at: [GitHub-piegy repo](https://github.com/Chenning04/piegy.git).
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+ The *piegy* documentation at: [piegy docs](https://piegy.readthedocs.io/en/).
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+
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+ ## How the Model Works
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+
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+ Our model can be summarized as "classical game theory endowed with a spatial structure and payoff-driven migration rules". Consider two species, predators and preys (denote by *U* and *V*), in a rectangular region. We divide the region into N by M patches and simulate their interaction within a patch by classical game theory (i.e., payoff matrices and carrying capacity). Interactions across patches are simulated by payoff-driven migration rules. An individual migrates to a neighboring patch with probability weighted by payoff in the neighbors.
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+
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+ We use the Gillepie algorithm as the fundamental event-selection algorithm. At each time step, one event is selected and let happen; and step sizes are continuous, dependent on the current state in the space. Data are recorded every some specified time interval.
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+
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+ ## Analytic Tools
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+
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+ The *piegy* package also provides a wide range of analytic and supportive tools alongside the main model, such as plotting, numerical tools, data saving & reading, etc. We also provide the *piegy.videos* module for more direct visualizations like how population distribution change over time.
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+
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+ ## Examples
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+
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+ To get started, simply get our demo model and run simulation:
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+
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+ ```python
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+ from piegy import model, figures
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+
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+ sim = model.demo_model()
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+ model.run(sim)
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+
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+ dynamics = figures.UV_dyna(sim)
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+ U_hmap, V_hmap = figures.UV_heatmap(sim)
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+ ```
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+
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+ The figures reveal the population dynamics and steady state distribution.
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+
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+
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+ ## Acknowledgments
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+
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+ - Thanks Professor Daniel Cooney at University of Illinois Urbana-Champaign. This package is developed alongside a project with Prof. Cooney and received enormous help from him.
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+ - Special thanks to the open-source community for making this package possible.
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+ [build-system]
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+ requires = ['setuptools>=61.0', 'wheel']
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+ build-backend = 'setuptools.build_meta'
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+
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+ [project]
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+ name = 'piegy'
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+ version = '1.0.0'
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+ description = 'Payoff-Driven Stochastic Spatial Model for Evolutionary Game Theory'
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+ readme = 'README.md'
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+ requires-python = '>=3.6'
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+ license = {file = "LICENSE.txt"}
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+ authors = [
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+ {name = 'Chenning Xu', email = 'cxu7@caltech.edu'}
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+ ]
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+ keywords = ['Game Theory', 'Evolutionary Game Theory', 'Spatial Model', 'Stochastic Model', 'Payoff Driven']
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+ dependencies = [
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+ 'numpy',
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+ 'matplotlib',
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+ 'imageio>=2.37.0',
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+ 'moviepy>=2.1.1',
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+ 'seaborn>=0.13.2'
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+ ]
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+ classifiers = [
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+ "Development Status :: 4 - Beta",
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+ "Intended Audience :: Developers",
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+ "Intended Audience :: Science/Research",
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+ "Intended Audience :: Education",
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+ "License :: OSI Approved :: BSD License",
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+ "Programming Language :: Python :: 3",
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+ "Programming Language :: Python :: 3.10",
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+ "Programming Language :: Python :: 3.11",
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+ "Operating System :: OS Independent"
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+ ]
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+
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+
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+ [project.urls]
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+ Source = 'https://github.com/Chenning04/piegy.git'
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+ Documentation = 'https://piegy.readthedocs.io/en/'
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+
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+ [tool.setuptools]
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+ package-dir = {'' = 'src'}
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+
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+ [tool.setuptools.packages.find]
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+ where = ['src']
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+
piegy-1.0.0/setup.cfg ADDED
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+ [egg_info]
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+ tag_build =
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+ tag_date = 0
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+
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+ '''
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+ Payoff-Driven Stochastic Spatial Model for Evolutionary Game Theory
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+ -----------------------------------------------------------
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+
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+ Provides:
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+ 1. A stochastic spatial model for simulating the interaction and evolution of two species in either 1D or 2D space
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+ 2. Plot & video functions to visualize simulation results.
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+ 3. Module to test influence of certain variables on results.
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+ 4. Data saving & reading module.
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+ 4. Additional analytical tools.
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+
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+ Websites:
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+ - The *piegy* documentation: https://piegy.readthedocs.io/en/
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+ - GitHub repository at: https://github.com/Chenning04/piegy.git
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+ - PyPI page: https://pypi.org/project/piegy/
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+
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+
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+ Last update: May 12, 2025
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+ '''
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+
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+ from .__version__ import __version__
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+
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+ from .model import simulation, run, demo_model
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+ from .videos import make_video, SUPPORTED_FIGURES
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+ from .data_tools import save_data, read_data
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+
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+ from .analysis import rounds_expected, scale_maxtime, check_convergence, combine_sim
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+
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+ from .figures import (UV_heatmap, UV_bar, UV_dyna, UV_hist, UV_std, UV_expected_val, UV_expected,
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+ pi_heatmap, pi_bar, pi_dyna, pi_hist, pi_std, UV_pi)
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+
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+ from .test_var import (test_var1, var_UV1, var_pi1, var_convergence1, get_dirs1,
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+ test_var2, var_UV2, var_pi2, var_convergence2, get_dirs2)
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+
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+
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+ model_members = ['simulation', 'run', 'get_demo_model']
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+
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+ videos_members = ['make_video', 'SUPPORTED_FIGURES']
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+
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+ data_members = ['save_data', 'read_data']
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+
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+ analysis_members = ['expected_rounds', 'scale_maxtime', 'check_convergence', 'combine_sim']
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+
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+ figures_members = ['UV_heatmap', 'UV_bar', 'UV_dyna', 'UV_hist', 'UV_std', 'UV_expected_val', 'UV_expected',
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+ 'pi_heatmap', 'pi_bar', 'pi_dyna', 'pi_hist', 'pi_std', 'UV_pi']
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+
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+ test_var_members = ['test_var1', 'var_UV1', 'var_pi1', 'var_convergence1', 'get_dirs1',
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+ 'test_var2', 'var_UV2', 'var_pi2', 'var_convergence2', 'get_dirs2']
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+
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+
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+ __all__ = model_members + videos_members + data_members + figures_members + analysis_members + test_var_members
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+
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+
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+
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+
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+
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+
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+
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+ # Below might be better suited for documents
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+ '''
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+ To run a simulation, start by defining some parameter. Here is a complete set of params::
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+
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+ >>> N = 5
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+ >>> M = 5
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+ >>> maxtime = 300
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+ >>> sim_time = 3
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+ >>> I = [[[22, 44] for i in range(N)] for j in range(M)]
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+ >>> X = [[[-0.1, 0.4, 0, 0.2] for i in range(N)] for j in range(M)]
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+ >>> X[1][1] = [0.1, 0.6, 0.2, 0.4]
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+ >>> P = [[[0.5, 0.5, 100, 100, 0.001, 0.001] for i in range(N)] for j in range(M)]
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+ >>> boundary = True
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+ >>> print_pct = 5
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+ >>> seed = None
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+
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+ These parameters essentially define the spatial size, initial population, payoff matrices...
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+ For a detailed explanation, see simulation object.
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+
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+ Then create a 'simulation' object with those parameters::
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+
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+ >>> sim = simulation(N, M, maxtime, sim_time, I, X, P, boundary, print_pct, seed)
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+
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+ This 'sim' object will be the basis of our simulation. It carries all the necessary parameters
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+ and storage bin for the results.
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+
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+ Now let's run the simulation (assuming you imported)::
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+
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+ >>> multi_test(sim)
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+
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+ And that's the simulation! It takes 30s ~ 1min. You can see the progress.
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+
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+ Now, to see the results, let's use figures::
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+
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+ >>> fig = UV_heatmap(sim)
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+
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+
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+ '''
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+ __version__ = '1.0.0'
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+
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+ '''
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+ version history:
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+
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+ 0.1.0: first publishing, May 11, 2025
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+ 0.1.1: fix dependency errors
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+ 0.1.2: fixing module not find error
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+ 0.1.3: restructuring package
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+ 0.1.4 ~ 0.1.6: fixing moviepy import issue
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+ 0.1.7: changed name back to 'piegy'
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+ 0.1.8: updated installation in README
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+ 0.1.9: first round of full debugging
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+
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+ 1.0.0: first version in PyPI
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+
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+ '''
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+ '''
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+ This file contains pre-processing, post-processing, and analytical tools for simulations.
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+
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+ Public Funcions:
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+ - check_convergence: Check whether a simulation result converges. i.e. whether U, V's fluctuation are very small.
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+ - combine_sim: Combine two simulation objects and return a new one (the first two unchanged).
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+ Intended usage: say you have sim1, sim2 with same parameters except for sim_time, say 10 and 20.
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+ Then combine_sim takes a weighted average (with ratio 1:2) of results and return a new sim3.
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+ So that you now have sim3 with 30 sim_time.
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+
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+ Private Functions:
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+ - rounds_expected: Roughly calculates how many rounds are expected in a single simulation (which reflects runtime).
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+ NOTE: Not well-developed. Not recommending to use.
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+ - scale_maxtime: Given two simulation objects, scale first one's maxtime towards the second, so that the two have the same expected rounds.
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+ Intended to possibly decrease maxtime and save runtime.
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+ NOTE: Not well-developed. Not recommending to use.
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+
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+ '''
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+
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+ from . import model as model
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+ from . import figures as figures
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+ from .tools import figure_tools as figure_t
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+
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+ import numpy as np
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+ import math
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+
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+
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+
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+
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+ def rounds_expected(sim):
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+ '''
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+ NOTE: Not well-developed. Not recommending to use.
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+
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+ Predict how many rounds will run in single_test. i.e., how many for loops from time = 0 to sim.maxtime.
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+ Calculated based on expected_UV.
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+ '''
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+
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+ N = sim.N
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+ M = sim.M
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+ U_expected, V_expected = figures.UV_expected_val(sim)
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+
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+ rates = []
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+ patch0 = None # simulate patch i, j
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+ patch0_nb = [] # simulate neighbors of patch i, j
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+
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+ # loop through N, M, create a sample patch to calculate rates, store them
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+ for i in range(N):
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+ for j in range(M):
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+ patch0 = model.patch(U_expected[i][j], V_expected[i][j], sim.X[i][j], sim.P[i][j])
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+
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+ nb_indices = None
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+ if sim.boundary:
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+ nb_indices = model.find_nb_zero_flux(N, M, i, j)
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+ else:
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+ nb_indices = model.find_nb_periodical(N, M, i, j)
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+
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+ for k in range(4):
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+ if nb_indices[k] != None:
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+ i_nb = nb_indices[k][0]
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+ j_nb = nb_indices[k][1]
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+ patch0_nb_k = model.patch(U_expected[i_nb][j_nb], V_expected[i_nb][j_nb], sim.X[i_nb][j_nb], sim.P[i_nb][j_nb])
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+ patch0_nb_k.update_pi_k()
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+ patch0_nb.append(patch0_nb_k)
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+
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+ else:
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+ patch0_nb.append(None)
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+
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+ patch0.nb = patch0_nb
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+ patch0.update_pi_k()
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+ patch0.update_mig()
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+
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+ rates += patch0.pi_death_rates
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+ rates += patch0.mig_rates
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+
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+ delta_t_expected = (1 / sum(rates)) * math.log(1 / 0.5)
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+ r_expected = round(sim.maxtime / delta_t_expected)
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+
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+ return r_expected
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+
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+
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+
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+
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+ def scale_maxtime(sim1, sim2, scale_interval = True):
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+ '''
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+ NOTE: Not well-developed. Not recommending to use.
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+
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+ Scale sim1's maxtime towards sim2's, so they will run similar number of rounds in single_test, and hence similar runtime.
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+ Intended to reduce the effect of changing params on runtime.
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+
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+ Input:
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+ - scale_interval decides whether to scale sim1's interval as well, so that the same number of data will be stored.
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+ '''
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+
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+ r_expected1 = rounds_expected(sim1)
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+ r_expected2 = rounds_expected(sim2)
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+ ratio = r_expected2 / r_expected1
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+
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+ new_maxtime = sim1.maxtime * ratio
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+ old_max_record = sim1.maxtime / sim1.interval
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+
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+ if scale_interval:
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+ sim1.interval = new_maxtime / old_max_record
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+
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+ sim1.change_maxtime(new_maxtime)
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+
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+
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+
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+
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+ def check_convergence(sim, interval = 20, start = 0.8, fluc = 0.07):
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+ '''
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+ Check whether a simulation converges or not.
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+ Based on whether the fluctuation of U, V, pi all < 'fluc' in the later 'tail' portion of time.
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+
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+ Essentially find the max and min values (of population) in every small interval, and then check whether their difference > min * fluc.
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+
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+ Inputs:
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+ - sim: a simulation object
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+ - interval: int, how many records to take average over,
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+ and then compare this "local mean" with "whole-tail mean" and expect the difference to be less than fluc.
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+ - start: (0, 1) float, decides where you expect to check convergence from. Smaller start needs earlier convergence.
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+ - fluc: (0, 1) float. How much fluctuation is allowed between the average value of a small interval and the mean.
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+ '''
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+
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+ if (start < 0) or (start > 1):
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+ raise ValueError("start should be a float in (0, 1)")
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+ if (fluc < 0) or (fluc > 1):
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+ raise ValueError("fluc should be a float in (0, 1)")
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+ if (type(interval) != int) or (interval < 1):
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+ raise ValueError("interval should be an int >= 1")
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+
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+ interval = figure_t.scale_interval(interval, sim.compress_itv)
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+
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+ start_index = int(sim.max_record * start) # where the tail starts
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+ num_interval = int((sim.max_record - start_index) / interval) # how many intervals in total
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+
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+ # find the max and min value of the small intervals
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+ # initiate as average of the first interval
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+ min_U = np.mean(sim.U[:, :, start_index : start_index + interval])
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+ max_U = np.mean(sim.U[:, :, start_index : start_index + interval])
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+ min_V = np.mean(sim.V[:, :, start_index : start_index + interval])
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+ max_V = np.mean(sim.V[:, :, start_index : start_index + interval])
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+
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+ for i in range(1, num_interval):
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+ # lower and upper bound of current interval
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+ lower = start_index + i * interval
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+ upper = lower + interval
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+
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+ ave_U = np.mean(sim.U[:, :, lower : upper])
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+ ave_V = np.mean(sim.V[:, :, lower : upper])
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+
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+ # Compare with min, max
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+ if ave_U > max_U:
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+ max_U = ave_U
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+ if ave_U < min_U:
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+ min_U = ave_U
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+
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+ if ave_V > max_V:
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+ max_V = ave_V
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+ if ave_V < min_V:
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+ min_V = ave_V
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+
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+ # check whether (max - min) > min * fluc
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+ if (max_U - min_U) > min_U * fluc:
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+ return False
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+ if (max_V - min_V) > min_V * fluc:
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+ return False
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+
168
+ return True
169
+
170
+
171
+
172
+
173
+ def combine_sim(sim1, sim2):
174
+ '''
175
+ Combine data of sim1 and sim2.
176
+ Intended usage: assume sim1 and sim2 has the same N, M, maxtime, interval, boundary, max_record, and I, X, P
177
+ combine_sim then combines the two results and calculate a new weighted average of the two data, return a new sim object.
178
+ Essentially allows breaking up many rounds of simulations into several smaller pieces, and then put together.
179
+
180
+ Inputs:
181
+ - sim1, sim2: both stochastic_model.simulation object. All input parameters the same except for sim_time, print_pct and seed.
182
+ Raises error if not.
183
+
184
+ Returns:
185
+
186
+ - sim3: a new simulation object whose U, V, U_pi, V_pi are weighted averages of sim1 and sim2
187
+ (weighted by sim_time).
188
+ sim3.print_pct is set to sim1's, seed set to None, sim_time set to sum of sim1's and sim2's. All other params same as sim1
189
+ '''
190
+ if not (sim1.N == sim2.N and
191
+ sim1.M == sim2.M and
192
+ sim1.maxtime == sim2.maxtime and
193
+ sim1.record_itv == sim2.record_itv and
194
+ sim1.boundary == sim2.boundary and
195
+ sim1.max_record == sim2.max_record and
196
+ np.array_equal(sim1.I, sim2.I) and
197
+ np.array_equal(sim1.X, sim2.X) and
198
+ np.array_equal(sim1.P, sim2.P)):
199
+
200
+ raise ValueError('sim1 and sim2 have different input parameters (N, M, maxtime, interval, boundary, max_record, or I, X, P).')
201
+
202
+ if sim1.seed == sim2.seed:
203
+ raise ValueError('Cannot combine two simulations with the same seed.')
204
+
205
+ # copy sim1, except for no data and a different sim_time
206
+ combined_sim_time = sim1.sim_time + sim2.sim_time
207
+ sim3 = sim1.copy(copy_data = False)
208
+ sim3.sim_time = combined_sim_time
209
+ sim3.seed = None
210
+
211
+ for i in range(sim3.N):
212
+ for j in range(sim3.M):
213
+ for k in range(sim3.max_record):
214
+ sim3.U[i][j][k] = (sim1.U[i][j][k] * sim1.sim_time + sim2.U[i][j][k] * sim2.sim_time) / combined_sim_time
215
+ sim3.V[i][j][k] = (sim1.V[i][j][k] * sim1.sim_time + sim2.V[i][j][k] * sim2.sim_time) / combined_sim_time
216
+ sim3.U_pi[i][j][k] = (sim1.U_pi[i][j][k] * sim1.sim_time + sim2.U_pi[i][j][k] * sim2.sim_time) / combined_sim_time
217
+ sim3.V_pi[i][j][k] = (sim1.V_pi[i][j][k] * sim1.sim_time + sim2.V_pi[i][j][k] * sim2.sim_time) / combined_sim_time
218
+
219
+ return sim3
220
+
221
+
222
+