metacountregressor 0.1.65__tar.gz → 0.1.67__tar.gz

metacountregressor-0.1.65/README.md → metacountregressor-0.1.67/PKG-INFO

@@ -1,3 +1,17 @@
+Metadata-Version: 2.1
+Name: metacountregressor
+Version: 0.1.67
+Summary: Extensions for a Python package for estimation of count models.
+Home-page: https://github.com/zahern/CountDataEstimation
+Author: Zeke Ahern
+Author-email: zeke.ahern@hdr.qut.edu.au
+License: QUT
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: numpy>=1.13.1
+Requires-Dist: scipy>=1.0.0
+
 <div style="display: flex; align-items: center;">
     <img src="https://github.com/zahern/data/raw/main/m.png" alt="My Image" style="width: 200px; margin-right: 20px;">
     <p><span style="font-size: 60px;"><strong>MetaCountRegressor</strong></span></p>

metacountregressor-0.1.67/README.rst

@@ -0,0 +1,357 @@
+.. container::
+
+   ::
+
+      <img src="https://github.com/zahern/data/raw/main/m.png" alt="My Image" style="width: 200px; margin-right: 20px;">
+      <p><span style="font-size: 60px;"><strong>MetaCountRegressor</strong></span></p>
+
+Quick Setup
+'''''''''''
+
+The Below code demonstrates how to set up automatic optimization
+assisted by the harmony search algorithm. References to the Differential
+Evolution and Simulated Annealing has been mentioned (change
+accordingly)
+
+Quick install: Requires Python 3.10
+-----------------------------------
+
+Install ``metacountregressor`` using pip as follows:
+
+\```bash pip install metacountregressor
+
+.. code:: ipython3
+
+    import pandas as pd
+    import numpy as np
+    from metacountregressor.solution import ObjectiveFunction
+    from metacountregressor.metaheuristics import (harmony_search,
+                                                differential_evolution,
+                                                simulated_annealing)
+
+Basic setup.
+^^^^^^^^^^^^
+
+The initial setup involves reading in the data and selecting an
+optimization algorithm. As the runtime progresses, new solutions will be
+continually evaluated. Finally, at the end of the runtime, the best
+solution will be identified and printed out. In the case of multiple
+objectives all of the best solutions will be printed out that belong to
+the Pareto frontier.
+
+.. code:: ipython3
+
+    # Read data from CSV file
+    df = pd.read_csv(
+    "https://raw.githubusercontent.com/zahern/data/main/Ex-16-3.csv")
+    X = df
+    y = df['FREQ']  # Frequency of crashes
+    X['Offset'] = np.log(df['AADT']) # Explicitley define how to offset the data, no offset otherwise
+    # Drop Y, selected offset term and  ID as there are no panels
+    X = df.drop(columns=['FREQ', 'ID', 'AADT'])  
+    
+    #some example argument, these are defualt so the following line is just for claritity. See the later agruments section for detials.
+    arguments = {'algorithm': 'hs', 'test_percentage': 0.15, 'test_complexity': 6, 'instance_number':1,
+                 'val_percentage':0.15, 'obj_1': 'bic', '_obj_2': 'RMSE_TEST', "MAX_TIME": 6}
+    # Fit the model with metacountregressor
+    obj_fun = ObjectiveFunction(X, y, **arguments)
+    #replace with other metaheuristics if desired
+    results = harmony_search(obj_fun)
+    
+    
+
+Arguments to feed into the Objective Function:
+----------------------------------------------
+
+Note: Please Consider the main arguments to change.
+
+-  ``algorithm``: This parameter has multiple choices for the algorithm,
+   such as �hs�, �sa�, and �de�. Only one choice should be defined as a
+   string value.
+-  ``test_percentage``: This parameter represents the percentage of data
+   used for in-sample prediction of the model. The value 0.15
+   corresponds to 15% of the data.
+-  ``val_percentage``: This parameter represents the percentage of data
+   used to validate the model. The value 0.15 corresponds to 15% of the
+   data.
+-  ``test_complexity``: This parameter defines the complexity level for
+   testing. The value 6 tests all complexities. Alternatively, you can
+   provide a list of numbers to consider different complexities. The
+   complexities are further explained later in this document.
+-  ``instance_number``: This parameter is used to give a name to the
+   outputs.
+-  ``obj_1``: This parameter has multiple choices for obj_1, such as
+   �bic�, �aic�, and �hqic�. Only one choice should be defined as a
+   string value.
+-  ``_obj_2``: This parameter has multiple choices for objective 2, such
+   as �RMSE_TEST�, �MSE_TEST�, and �MAE_TEST�.
+-  ``_max_time``: This parameter specifies the maximum number of seconds
+   for the total estimation before stopping.
+-  ``distribution``: This parameter is a list of distributions to
+   consider. Please select all of the available options and put them
+   into a list of valid options if you want to to consider the
+   distribution type for use when modellign with random parameters. The
+   valid options include: �Normal�, �LnNormal�, �Triangular�, and
+   �Uniform�.
+-  ``transformations``: This parameters is a list of transformations to
+   consider. Plesee select all of the available options and put them
+   into a list of valid options if you want to consider the
+   transformation type. The valid options include �Normal�, �LnNormal�,
+   �Triangular�, �Uniform�.
+-  ``method_ll``: This is a specificication on the type of solvers are
+   avilable to solve the lower level maximum likilihood objective. The
+   valid options include: �Normal�, �LnNormal�, �Triangular�, and
+   �Uniform�.
+
+An Example of changing the arguments.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Modify the arguments according to your preferences using the commented
+code as a guide.
+
+.. code:: ipython3
+
+    #Solution Arguments
+    arguments = {
+            'algorithm': 'hs', #alternatively input 'de', or 'sa'
+            'is_multi': 1,
+            'test_percentage': 0.2, # used in multi-objective optimisation only. Saves 20% of data for testing.
+            'val_percenetage:': 0.2, # Saves 20% of data for testing.
+            'test_complexity': 6, # Complexity level for testing (6 tests all) or a list to consider potential differences in complexity
+            'instance_number': 'name', # used for creeating a named folder where your models are saved into from the directory
+            'distribution': ['Normal', 'LnNormal', 'Triangular', 'Uniform'],
+            'Model': [0,1],  # or equivalently ['POS', 'NB']
+            'transformations': ['no', 'sqrt', 'archsinh'],
+            'method_ll': 'BFGS_2',
+            '_max_time': 10
+        }
+    obj_fun = ObjectiveFunction(X, y, **arguments)
+    results = harmony_search(obj_fun)
+
+Initial Solution Configurement
+------------------------------
+
+Listed below is an example of how to specify an initial solution within
+the framework. This initial solution will be used to calculate the
+fitness and considered in the objective-based search. However, as the
+search progresses, different hypotheses may be proposed, and alternative
+modeling components may completely replace the initial solution.
+
+.. code:: ipython3
+
+     #Model Decisions, Specify for Intial Optimization
+    manual_fit_spec = {
+        'fixed_terms': ['SINGLE', 'LENGTH'],
+        'rdm_terms': ['AADT:normal'],
+        'rdm_cor_terms': ['GRADEBR:uniform', 'CURVES:triangular'],
+        'grouped_terms': [],
+        'hetro_in_means': ['ACCESS:normal', 'MINRAD:normal'],
+        'transformations': ['no', 'no', 'log', 'no', 'no', 'no', 'no'],
+        'dispersion': 1
+    }
+    #Search Arguments
+    arguments = {
+        'algorithm': 'hs',
+        'test_percentage': 0.2,
+        'test_complexity': 6,
+        'instance_number': 'name',
+        'Manual_Fit': manual_fit_spec
+    }
+    obj_fun = ObjectiveFunction(X, y, **arguments)
+
+simarly to return the results feed the objective function into a
+metaheuristic solution algorithm. An example of this is provided below:
+
+.. code:: ipython3
+
+    results = harmony_search(obj_fun)
+    print(results)
+
+Notes:
+------
+
+Capabilities of the software include:
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+-  Handling of Panel Data
+-  Support for Data Transformations
+-  Implementation of Models with Correlated and Non-Correlated Random
+   Parameters
+-  A variety of mixing distributions for parameter estimations,
+   including normal, lognormal, truncated normal, Lindley, Gamma,
+   triangular, and uniform distributions Capability to handle
+   heterogeneity in the means of the random parameters
+-  Use of Halton draws for simulated maximum likelihood estimation
+-  Support for grouped random parameters with unbalanced groups
+-  Post-estimation tools for assessing goodness of fit, making
+   predictions, and conducting out-of-sample validation
+-  Multiple parameter optimization routines, such as the BFGS method
+-  Comprehensive hypothesis testing using single objectives, such as
+   in-sample BIC and log-likelihood
+-  Extensive hypothesis testing using multiple objectives, such as
+   in-sample BIC and out-of-sample MAE (Mean Absolute Error), or
+   in-sample AIC and out-of-sample MSPE (mean-square prediction errorr)
+-  Features that allow analysts to pre-specify variables, interactions,
+   and mixing distributions, among others
+-  Meta-heuristic Guided Optimization, including techniques like
+   Simulated Annealing, Harmony Search, and Differential Evolution
+-  Customization of Hyper-parameters to solve problems tailored to your
+   dataset
+-  Out-of-the-box optimization capability using default metaheuristics
+
+Intreting the output of the model:
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+A regression table is produced. The following text elements are
+explained: - Std. Dev.: This column appears for effects that are related
+to random paramters and displays the assument distributional assumption
+next to it - Chol: This term refers to Cholesky decomposition element,
+to show the correlation between two random paramaters. The combination
+of the cholesky element on iyself is equivalent to a normal random
+parameter. - hetro group #: This term represents the heterogeneity group
+number, which refers all of the contributing factors that share
+hetrogentiy in the means to each other under the same numbered value. -
+:math:`\tau`: This column, displays the type of transformation that was
+applied to the specific contributing factor in the data.
+
+Arguments:
+----------
+
+In reference to the arguments that can be fed into the solution alrogithm, a dictionary system is utilised with relecant names these include
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The following list describes the arguments available in this function.
+By default, all of the capabilities described are enabled unless
+specified otherwise as an argument. For list arguments, include all
+desired elements in the list to ensure the corresponding options are
+considered. Example code will be provided later in this guide.
+
+1. **``complexity_level``**: This argument accepts an integer 1-6 or a
+   list based of integegers between 0 to 5 eg might be a possible
+   configuration [0, 2, 3]. Each integer represents a hierarchy level
+   for estimable models associated with each explanatory variable. Here
+   is a summary of the hierarchy:
+
+   -  0: Null model
+   -  1: Simple fixed effects model
+   -  2: Random parameters model
+   -  3: Random correlated parameters model
+   -  4: Grouped random parameters model
+   -  5: Heterogeneity in the means random parameter model
+
+   **Note:** For the grouped random parameters model, groupings need to
+   be defined prior to estimation. This can be achieved by including the
+   following key-value pair in the arguments of the
+   ``ObjectiveFunction``: ``'group': "Enter Column Grouping in data"``.
+   Replace ``"Enter Column Grouping in data"`` with the actual column
+   grouping in your dataset.
+
+   Similarly, for panel data, the panel column needs to be defined using
+   the key-value pair:
+   ``'panel': "enter column string covering panels"``. Replace
+   ``"enter column string covering panels"`` with the appropriate column
+   string that represents the panel information in your dataset.
+
+2. **``distributions``**: This argument accepts a list of strings where
+   each string corresponds to a distribution. Valid options include:
+
+   -  �Normal�
+   -  �Lindley�
+   -  �Uniform�
+   -  �LogNormal�
+   -  �Triangular�
+   -  �Gamma�
+   -  �TruncatedNormal�
+   -  Any of the above, concatenated with �:� (e.g., �Normal:grouped�;
+      requires a grouping term defined in the model)
+
+3. **``Model``**: This argument specifies the model form. It can be a
+   list of integers representing different models to test:
+
+   -  0: Poisson
+   -  1: Negative-Binomial
+   -  2: Generalized-Poisson
+
+4. **``transformations``**: This argument accepts a list of strings
+   representing available transformations within the framework. Valid
+   options include:
+
+   -  �no�
+   -  �square-root�
+   -  �logarithmic�
+   -  �archsinh�
+   -  �as_factor�
+
+5. **``is_multi``**: This argument accepts an integer indicating whether
+   single or multiple objectives are to be tested (0 for single, 1 for
+   multiple).
+
+6. **``test_percentage``**: This argument is used for multi-objective
+   optimization. Define it as a decimal; for example, 0.2 represents 20%
+   of the data for testing.
+
+7. **``val_percentage``**: This argument saves data for validation.
+   Define it as a decimal; for example, 0.2 represents 20% of the data
+   for validation.
+
+8. **``_max_time``**: This argument is used to add a termination time in
+   the algorithm. It takes values as seconds. Note the time is only
+   dependenant on the time after intial population of solutions are
+   generated.
+
+Example
+=======
+
+Let�s start by fitting very simple models, use those model sto help and
+define the objectives, then perform more of an extensive search on the
+variables that are identified more commonly
+
+.. code:: ipython3
+
+    df = pd.read_csv(
+    "https://raw.githubusercontent.com/zahern/data/main/Ex-16-3.csv")
+    X = df
+    y = df['FREQ']  # Frequency of crashes
+    X['Offset'] = np.log(df['AADT']) # Explicitley define how to offset the data, no offset otherwise
+    # Drop Y, selected offset term and  ID as there are no panels
+    X = df.drop(columns=['FREQ', 'ID', 'AADT'])  
+    
+    arguments = {
+            'algorithm': 'hs', #alternatively input 'de', or 'sa'
+            'is_multi': 1,
+            'test_percentage': 0.2, # used in multi-objective optimisation only. Saves 20% of data for testing.
+            'val_percentage:': 0.2, # Saves 20% of data for testing.
+            'test_complexity': 3, # For Very simple Models
+            'obj_1': 'BIC', '_obj_2': 'RMSE_TEST',
+            'instance_number': 'name', # used for creeating a named folder where your models are saved into from the directory
+            'distribution': ['Normal'],
+            'Model': [0],  # or equivalently ['POS', 'NB']
+            'transformations': ['no', 'sqrt', 'archsinh'],
+            '_max_time': 10000
+        }
+    obj_fun = ObjectiveFunction(X, y, **arguments)
+    
+    results = harmony_search(obj_fun)
+    print(results)
+
+Contact
+-------
+
+If you have any questions, ideas to improve MetaCountRegressor, or want
+to report a bug, just open a new issue in `GitHub
+repository <https://github.com/zahern/CountDataEstimation>`__.
+
+Citing MetaCountRegressor
+-------------------------
+
+Please cite MetaCountRegressor as follows:
+
+Ahern, Z., Corry P., Paz A. (2023). MetaCountRegressor [Computer
+software]. https://pypi.org/project/metacounregressor/
+
+Or using BibTex as follows:
+
+\```bibtex @misc{Ahern2023, author = {Zeke Ahern and Paul Corry and
+Alexander Paz}, journal = {PyPi}, title = {metacountregressor · PyPI},
+url = {https://pypi.org/project/metacountregressor/0.1.47/}, year =
+{2023}, }

{metacountregressor-0.1.65 → metacountregressor-0.1.67/metacountregressor.egg-info}/PKG-INFO

@@ -1,22 +1,16 @@
 Metadata-Version: 2.1
 Name: metacountregressor
-Version: 0.1.65
-Summary: A python package for count regression of rare events assisted by metaheuristics
-Author: zahern
+Version: 0.1.67
+Summary: Extensions for a Python package for estimation of count models.
+Home-page: https://github.com/zahern/CountDataEstimation
+Author: Zeke Ahern
 Author-email: zeke.ahern@hdr.qut.edu.au
-Requires-Python: >=3.10,<3.11
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Requires-Dist: latextable (>=1.0.0,<2.0.0)
-Requires-Dist: matplotlib (>=3.7.1,<4.0.0)
-Requires-Dist: numpy (>=1.24.3,<2.0.0)
-Requires-Dist: pandas (>=2.0.2,<3.0.0)
-Requires-Dist: psutil (>=5.9.5,<6.0.0)
-Requires-Dist: scikit-learn (>=1.2.2,<2.0.0)
-Requires-Dist: scipy (>=1.10.1,<2.0.0)
-Requires-Dist: statsmodels (>=0.14.0,<0.15.0)
-Requires-Dist: tabulate (>=0.9.0,<0.10.0)
+License: QUT
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: numpy>=1.13.1
+Requires-Dist: scipy>=1.0.0
 
 <div style="display: flex; align-items: center;">
     <img src="https://github.com/zahern/data/raw/main/m.png" alt="My Image" style="width: 200px; margin-right: 20px;">
@@ -271,4 +265,3 @@ Or using BibTex as follows:
    year = {2023},
 }
 
-

metacountregressor-0.1.67/metacountregressor.egg-info/SOURCES.txt

@@ -0,0 +1,24 @@
+LICENSE.txt
+README.rst
+setup.cfg
+setup.py
+metacountregressor/__init__.py
+metacountregressor/_device_cust.py
+metacountregressor/halton.py
+metacountregressor/helperprocess.py
+metacountregressor/main.py
+metacountregressor/main_old.py
+metacountregressor/metaheuristics.py
+metacountregressor/pareto_file.py
+metacountregressor/pareto_logger__plot.py
+metacountregressor/setup.py
+metacountregressor/single_objective_finder.py
+metacountregressor/solution.py
+metacountregressor/test_generated_paper2.py
+metacountregressor.egg-info/PKG-INFO
+metacountregressor.egg-info/SOURCES.txt
+metacountregressor.egg-info/dependency_links.txt
+metacountregressor.egg-info/not-zip-safe
+metacountregressor.egg-info/requires.txt
+metacountregressor.egg-info/top_level.txt
+tests/test.py

metacountregressor-0.1.67/metacountregressor.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

metacountregressor-0.1.67/metacountregressor.egg-info/not-zip-safe

@@ -0,0 +1 @@
+

metacountregressor-0.1.67/metacountregressor.egg-info/requires.txt

@@ -0,0 +1,2 @@
+numpy>=1.13.1
+scipy>=1.0.0

metacountregressor-0.1.67/metacountregressor.egg-info/top_level.txt

@@ -0,0 +1 @@
+metacountregressor

metacountregressor-0.1.67/setup.cfg

@@ -0,0 +1,7 @@
+[metadata]
+description-file = README.md
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

metacountregressor-0.1.67/setup.py

@@ -0,0 +1,43 @@
+import codecs
+
+import setuptools
+
+# Read the README.md file for the long description
+with open('README.md', 'r', encoding='utf-8') as fh:
+    long_description = fh.read()
+
+with open('version.txt', 'r') as f:
+    current_version = f.read().strip()
+
+# Split the current version into its components
+version_parts = current_version.split('.')
+major, minor, patch = map(int, version_parts)
+
+# Increment the patch version
+patch += 1
+
+# Construct the new version string
+new_version = f"{major}.{minor}.{patch}"
+
+# Write the new version number back to the file
+with open('version.txt', 'w') as f:
+    f.write(new_version)
+
+setuptools.setup(
+    name='metacountregressor',
+    version=new_version,
+    description='Extensions for a Python package for estimation of count models.',
+    long_description=long_description,
+    long_description_content_type='text/markdown',  # Specify the content type as Markdown
+    url='https://github.com/zahern/CountDataEstimation',
+    author='Zeke Ahern',
+    author_email='zeke.ahern@hdr.qut.edu.au',
+    license='QUT',
+    packages=['metacountregressor'],
+    zip_safe=False,
+    python_requires='>=3.10',
+    install_requires=[
+        'numpy>=1.13.1',
+        'scipy>=1.0.0'
+    ]
+)