pypomp 0.0.1__tar.gz

pypomp-0.0.1/.gitignore

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pypomp-0.0.1/LICENSE

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+Copyright (c) 2018 The Python Packaging Authority
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

pypomp-0.0.1/PKG-INFO

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+Metadata-Version: 2.3
+Name: pypomp
+Version: 0.0.1
+Summary: Modeling and inference using partially observed Markov process (POMP) models
+Project-URL: Homepage, https://github.com/ionides/pomp-py
+Project-URL: Issues, https://github.com/ionides/pomp-py/issues
+Author-email: Kevin Tan <kevtan@wharton.upenn.edu>, Jun Chen <chenjunc@umich.edu>, Jesse Wheeler <jeswheel@umich.edu>, Edward Ionides <ionides@umich.edu>
+Maintainer-email: Edward Ionides <ionides@umich.edu>, Kevin Tan <kevtan@wharton.upenn.edu>
+License-File: LICENSE
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+
+# pypomp
+
+Python code for modeling and inference using partially observed Markov process (POMP) models, featuring automatic differentiation.
+
+### Expected package users
+
+* Scientists wanting to perform data analysis on a dynamic system via partially observed Markov processes (POMP), also  called state-space models (SSM) or hidden Markov models (HMM) in other contexts.
+
+  * This package design and intended use is similar to the popular [**pomp** R package](https://kingaa.github.io/pomp/). As such, many of the expected use cases and motivating examples of this package can be found on the [pomp package bibliography page](https://kingaa.github.io/pomp/biblio.html).
+  
+* Researchers wishing to develop novel inference methodology for POMP models.
+
+  * Like the **pomp** R package, this package provides a framework for implementing computer representations of arbitrary POMP models. This ability provides an environment for researchers to develop, test, and deploy novel algorithms that are applicable to POMP models. 
+
+### Package Development 
+
+* The **pypomp** package is currently at early stages of development. All version numbers below 0.1 are pre-release.
+
+* All contributions are welcome! Contributions should keep in mind the intended uses of this package, and its intended users.
+
+* The **pypomp** package is run by the [pypomp organization](https://github.com/pypomp).
+

pypomp-0.0.1/README.md

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+# pypomp
+
+Python code for modeling and inference using partially observed Markov process (POMP) models, featuring automatic differentiation.
+
+### Expected package users
+
+* Scientists wanting to perform data analysis on a dynamic system via partially observed Markov processes (POMP), also  called state-space models (SSM) or hidden Markov models (HMM) in other contexts.
+
+  * This package design and intended use is similar to the popular [**pomp** R package](https://kingaa.github.io/pomp/). As such, many of the expected use cases and motivating examples of this package can be found on the [pomp package bibliography page](https://kingaa.github.io/pomp/biblio.html).
+  
+* Researchers wishing to develop novel inference methodology for POMP models.
+
+  * Like the **pomp** R package, this package provides a framework for implementing computer representations of arbitrary POMP models. This ability provides an environment for researchers to develop, test, and deploy novel algorithms that are applicable to POMP models. 
+
+### Package Development 
+
+* The **pypomp** package is currently at early stages of development. All version numbers below 0.1 are pre-release.
+
+* All contributions are welcome! Contributions should keep in mind the intended uses of this package, and its intended users.
+
+* The **pypomp** package is run by the [pypomp organization](https://github.com/pypomp).
+

pypomp-0.0.1/pypomp/fit.py

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+from .pomp_class import *
+
+
+
+def fit(pomp_object=None, J=100, Jh=1000, theta=None, rinit=None, rprocess=None, dmeasure=None, rprocesses=None,
+        dmeasures=None, ys=None, sigmas=None, sigmas_init=None, covars=None, M=10, a=0.9, method='Newton', itns=20,
+        beta=0.9, eta=0.0025, c=0.1,
+        max_ls_itn=10, thresh_mif=100, thresh_tr=100, verbose=False, scale=False, ls=False, alpha=0.1, monitor=True,
+        mode="IFAD"):
+    if pomp_object is not None:
+        if mode == "IF2" or mode == "IFAD":
+            if sigmas is not None and sigmas_init is not None:
+                return pomp_object.fit(sigmas, sigmas_init, M, a, J, Jh, method, itns, beta, eta, c, max_ls_itn,
+                                       thresh_mif, thresh_tr, verbose, scale, ls, alpha, monitor, mode)
+            else:
+                raise ValueError("Invalid Argument Input with Missing sigmas or sigmas_init")
+        elif mode == "GD":
+            return pomp_object.fit(sigmas, sigmas_init, M, a, J, Jh, method, itns, beta, eta, c, max_ls_itn, thresh_mif,
+                                   thresh_tr, verbose, scale, ls, alpha, monitor, mode)
+        else:
+            raise ValueError("Invalid Mode Input")
+    elif rinit is not None and rprocess is not None and dmeasure is not None and theta is not None and ys is not None:
+        if mode == "IF2" or mode == "IFAD":
+            if rprocesses is not None and dmeasures is not None and sigmas is not None and sigmas_init is not None:
+                return fit_internal(theta, ys, rinit, rprocess, dmeasure, rprocesses, dmeasures, sigmas, sigmas_init,
+                                    covars, M, a, J, Jh, method, itns, beta, eta, c, max_ls_itn, thresh_mif, thresh_tr,
+                                    verbose, scale, ls, alpha, monitor, mode)
+            else:
+                raise ValueError("Invalid Argument Input with Missing workhorse or sigmas")
+        elif mode == "GD":
+            return fit_internal(theta, ys, rinit, rprocess, dmeasure, rprocesses, dmeasures, sigmas, sigmas_init,
+                                covars, M, a, J, Jh, method, itns, beta, eta, c, max_ls_itn, thresh_mif, thresh_tr,
+                                verbose, scale, ls, alpha, monitor, mode)
+        else:
+            raise ValueError("Invalid Mode Input")
+    else:
+        raise ValueError("Invalid Argument Input with Missing Required Argument")