metacountregressor 0.1.91__tar.gz → 0.1.95__tar.gz

{metacountregressor-0.1.91 → metacountregressor-0.1.95}/PKG-INFO

@@ -1,17 +1,31 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: metacountregressor
-Version: 0.1.91
-Summary: Extensions for a Python package for estimation of count models.
+Version: 0.1.95
+Summary: Extensive Testing for Estimation of Data Count Models
 Home-page: https://github.com/zahern/CountDataEstimation
 Author: Zeke Ahern
-Author-email: zeke.ahern@hdr.qut.edu.au
-License: QUT
+Author-email: z.ahern@qut.edu.au
+License: MIT
 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
 Requires-Dist: requests
+Requires-Dist: latextable
+Requires-Dist: pandas
+Requires-Dist: scikit_learn>=1.4.1.post1
+Requires-Dist: statsmodels
+Requires-Dist: psutil
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 <div style="display: flex; align-items: center;">
     <img src="https://github.com/zahern/data/raw/main/m.png" alt="My Image" style="width: 100px; margin-right: 20px;">
@@ -23,10 +37,24 @@ Requires-Dist: requests
 
 The tutorial provides more extensive examples on how to run the code and perform experiments. Further documentation is currently in development.
 
-##### Quick Setup
+# For an Application Setup Download the following GUI
+[Download Application](https://github.com/zahern/MetaCount/tree/master/metacountregressor/application_gui/dist/meta_app)
+
+The application involves setting up a problem instance to run the models.
+
+### Entire [Git Repository](https://github.com/zahern/MetaCount.git) is available to clone.
+#### Steps
+1. Clone Project
+2. Navigate to "metacountregressor/application_gui/dist/meta_app"
+3. Run meta_app.exe
+4. Navigate to metacountregressor/app_main.py
+5. Run app_main.py
+
+
+## Setup For Python Package Approach
 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: Requires Python 3.10
 
 Install `metacountregressor` using pip as follows:
 
@@ -274,6 +302,8 @@ Let's begin by fitting very simple models and use the structure of these models
 
 
 ```python
+
+'''Setup Data'''
 df = pd.read_csv(
 "https://raw.githubusercontent.com/zahern/data/main/Ex-16-3.csv")
 X = df
@@ -281,25 +311,158 @@ 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'])  
-
+'''Aguments for Solution'''
 arguments = {
-        'algorithm': 'hs', #alternatively input 'de', or 'sa'
-        'is_multi': 1,
+        'is_multi': 1, #is two objectives considered
         '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
+        'instance_number': 'hs_run', # used for creeating a named folder where your models are saved into from the directory
         'distribution': ['Normal'],
-        'Model': [0],  # or equivalently ['POS', 'NB']
+        'Model': [0, 1],  # or equivalently ['POS', 'NB']
         'transformations': ['no', 'sqrt', 'archsinh'],
         '_max_time': 10000
-    }
+} '''Arguments for the solution algorithm'''
+argument_hs = {
+    '_hms': 20, #harmony memory size,
+    '_mpai': 1, #adjustement inded
+    '_par': 0.3,
+    '_hmcr': .5
+}
 obj_fun = ObjectiveFunction(X, y, **arguments)
-results = harmony_search(obj_fun)
+results = harmony_search(obj_fun, None, argument_hs)
 print(results)
 ```
 
+## Example: Assistance by Differential Evololution and Simulated Annealing
+Similiar to the above example we only need to change the hyperparamaters, the obj_fun can remane the same
+
+
+```python
+argument_de = {'_AI': 2,
+            '_crossover_perc': .2,
+            '_max_iter': 1000,
+            '_pop_size': 25
+}
+de_results = differential_evolution(obj_fun, None, **argument_de)
+print(de_results)
+
+
+args_sa = {'alpha': .99,
+        'STEPS_PER_TEMP': 10,
+        'INTL_ACPT': 0.5,
+        '_crossover_perc': .3,
+        'MAX_ITERATIONS': 1000,
+        '_num_intl_slns': 25,
+}
+
+sa_results = simulated_annealing(obj_fun, None, **args_sa)
+print(sa_results)
+```
+
+## Comparing to statsmodels
+The following example illustrates how the output compares to well-known packages, including Statsmodels."
+
+
+```python
+# Load modules and data
+import statsmodels.api as sm
+
+data = sm.datasets.sunspots.load_pandas().data
+#print(data.exog)
+data_exog = data['YEAR']
+data_exog = sm.add_constant(data_exog)
+data_endog = data['SUNACTIVITY']
+
+# Instantiate a gamma family model with the default link function.
+import numpy as np
+
+gamma_model = sm.NegativeBinomial(data_endog, data_exog)
+gamma_results = gamma_model.fit()
+
+print(gamma_results.summary())
+
+
+
+
+#NOW LET's COMPARE THIS TO METACOUNTREGRESSOR
+
+
+
+
+ #Model Decisions, 
+manual_fit_spec = {
+    'fixed_terms': ['const','YEAR'],
+    'rdm_terms': [],
+    'rdm_cor_terms': [],
+    'grouped_terms': [],
+    'hetro_in_means': [],
+    'transformations': ['no', 'no'],
+    'dispersion': 1 #Negative Binomial 
+}
+
+
+#Arguments
+arguments = {
+    'algorithm': 'hs',
+    'test_percentage': 0,
+    'test_complexity': 6,
+    'instance_number': 'name',
+    'Manual_Fit': manual_fit_spec
+}
+obj_fun = ObjectiveFunction(data_exog, data_endog, **arguments)
+
+
+
+
+
+
+
+```
+
+    Optimization terminated successfully.
+             Current function value: 4.877748
+             Iterations: 22
+             Function evaluations: 71
+             Gradient evaluations: 70
+                         NegativeBinomial Regression Results                      
+    ==============================================================================
+    Dep. Variable:            SUNACTIVITY   No. Observations:                  309
+    Model:               NegativeBinomial   Df Residuals:                      307
+    Method:                           MLE   Df Model:                            1
+    Date:                Tue, 13 Aug 2024   Pseudo R-squ.:                0.004087
+    Time:                        14:13:22   Log-Likelihood:                -1507.2
+    converged:                       True   LL-Null:                       -1513.4
+    Covariance Type:            nonrobust   LLR p-value:                 0.0004363
+    ==============================================================================
+                     coef    std err          z      P>|z|      [0.025      0.975]
+    ------------------------------------------------------------------------------
+    const          0.2913      1.017      0.287      0.774      -1.701       2.284
+    YEAR           0.0019      0.001      3.546      0.000       0.001       0.003
+    alpha          0.7339      0.057     12.910      0.000       0.622       0.845
+    ==============================================================================
+    0.1.88
+    Setup Complete...
+    Benchmaking test with Seed 42
+    1
+    --------------------------------------------------------------------------------
+    Log-Likelihood:  -1509.0683662284273
+    --------------------------------------------------------------------------------
+    bic: 3035.84
+    --------------------------------------------------------------------------------
+    MSE: 10000000.00
+    +--------+--------+-------+----------+----------+------------+
+    | Effect | $\tau$ | Coeff | Std. Err | z-values | Prob |z|>Z |
+    +========+========+=======+==========+==========+============+
+    | const  | no     | 0.10  |   0.25   |   0.39   | 0.70       |
+    +--------+--------+-------+----------+----------+------------+
+    | YEAR   | no     | 0.00  |   0.00   |  20.39   | 0.00***    |
+    +--------+--------+-------+----------+----------+------------+
+    | nb     |        | 1.33  |   0.00   |  50.00   | 0.00***    |
+    +--------+--------+-------+----------+----------+------------+
+    
+
 ## Paper
 
 The following tutorial is in conjunction with our latest paper. A link the current paper can be found here [MetaCountRegressor](https://www.overleaf.com/read/mszwpwzcxsng#c5eb0c)

{metacountregressor-0.1.91 → metacountregressor-0.1.95}/README.rst

@@ -9,21 +9,42 @@ Tutorial also available as a jupyter notebook
 =============================================
 
 `Download Example
-Notebook <https://github.com/zahern/CountDataEstimation/blob/main/README.ipynb>`__
+Notebook <https://github.com/zahern/CountDataEstimation/blob/main/Tutorial.ipynb>`__
 
 The tutorial provides more extensive examples on how to run the code and
 perform experiments. Further documentation is currently in development.
 
-Quick Setup
-'''''''''''
+For an Application Setup Download the following GUI
+===================================================
+
+`Download
+Application <https://github.com/zahern/MetaCount/tree/master/metacountregressor/application_gui/dist/meta_app>`__
+
+The application involves setting up a problem instance to run the
+models.
+
+Entire `Git Repository <https://github.com/zahern/MetaCount.git>`__ is available to clone.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Steps
+^^^^^
+
+1. Clone Project
+2. Navigate to �metacountregressor/application_gui/dist/meta_app�
+3. Run meta_app.exe
+4. Navigate to metacountregressor/app_main.py
+5. Run app_main.py
+
+Setup For Python Package Approach
+---------------------------------
 
 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: Requires Python 3.10
+-----------------------------
 
 Install ``metacountregressor`` using pip as follows:
 
@@ -376,6 +397,8 @@ factors for our search.
 
 .. code:: ipython3
 
+    
+    '''Setup Data'''
     df = pd.read_csv(
     "https://raw.githubusercontent.com/zahern/data/main/Ex-16-3.csv")
     X = df
@@ -383,24 +406,164 @@ factors for our search.
     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'])  
-    
+    '''Aguments for Solution'''
     arguments = {
-            'algorithm': 'hs', #alternatively input 'de', or 'sa'
-            'is_multi': 1,
+            'is_multi': 1, #is two objectives considered
             '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
+            'instance_number': 'hs_run', # used for creeating a named folder where your models are saved into from the directory
             'distribution': ['Normal'],
-            'Model': [0],  # or equivalently ['POS', 'NB']
+            'Model': [0, 1],  # or equivalently ['POS', 'NB']
             'transformations': ['no', 'sqrt', 'archsinh'],
             '_max_time': 10000
-        }
+    } '''Arguments for the solution algorithm'''
+    argument_hs = {
+        '_hms': 20, #harmony memory size,
+        '_mpai': 1, #adjustement inded
+        '_par': 0.3,
+        '_hmcr': .5
+    }
     obj_fun = ObjectiveFunction(X, y, **arguments)
-    results = harmony_search(obj_fun)
+    results = harmony_search(obj_fun, None, argument_hs)
     print(results)
 
+Example: Assistance by Differential Evololution and Simulated Annealing
+-----------------------------------------------------------------------
+
+Similiar to the above example we only need to change the
+hyperparamaters, the obj_fun can remane the same
+
+.. code:: ipython3
+
+    argument_de = {'_AI': 2,
+                '_crossover_perc': .2,
+                '_max_iter': 1000,
+                '_pop_size': 25
+    }
+    de_results = differential_evolution(obj_fun, None, **argument_de)
+    print(de_results)
+    
+    
+    args_sa = {'alpha': .99,
+            'STEPS_PER_TEMP': 10,
+            'INTL_ACPT': 0.5,
+            '_crossover_perc': .3,
+            'MAX_ITERATIONS': 1000,
+            '_num_intl_slns': 25,
+    }
+    
+    sa_results = simulated_annealing(obj_fun, None, **args_sa)
+    print(sa_results)
+
+Comparing to statsmodels
+------------------------
+
+The following example illustrates how the output compares to well-known
+packages, including Statsmodels.�
+
+.. code:: ipython3
+
+    # Load modules and data
+    import statsmodels.api as sm
+    
+    data = sm.datasets.sunspots.load_pandas().data
+    #print(data.exog)
+    data_exog = data['YEAR']
+    data_exog = sm.add_constant(data_exog)
+    data_endog = data['SUNACTIVITY']
+    
+    # Instantiate a gamma family model with the default link function.
+    import numpy as np
+    
+    gamma_model = sm.NegativeBinomial(data_endog, data_exog)
+    gamma_results = gamma_model.fit()
+    
+    print(gamma_results.summary())
+    
+    
+    
+    
+    #NOW LET's COMPARE THIS TO METACOUNTREGRESSOR
+    
+    
+    
+    
+     #Model Decisions, 
+    manual_fit_spec = {
+        'fixed_terms': ['const','YEAR'],
+        'rdm_terms': [],
+        'rdm_cor_terms': [],
+        'grouped_terms': [],
+        'hetro_in_means': [],
+        'transformations': ['no', 'no'],
+        'dispersion': 1 #Negative Binomial 
+    }
+    
+    
+    #Arguments
+    arguments = {
+        'algorithm': 'hs',
+        'test_percentage': 0,
+        'test_complexity': 6,
+        'instance_number': 'name',
+        'Manual_Fit': manual_fit_spec
+    }
+    obj_fun = ObjectiveFunction(data_exog, data_endog, **arguments)
+    
+    
+    
+    
+    
+    
+    
+
+
+.. parsed-literal::
+
+    Optimization terminated successfully.
+             Current function value: 4.877748
+             Iterations: 22
+             Function evaluations: 71
+             Gradient evaluations: 70
+                         NegativeBinomial Regression Results                      
+    ==============================================================================
+    Dep. Variable:            SUNACTIVITY   No. Observations:                  309
+    Model:               NegativeBinomial   Df Residuals:                      307
+    Method:                           MLE   Df Model:                            1
+    Date:                Tue, 13 Aug 2024   Pseudo R-squ.:                0.004087
+    Time:                        14:13:22   Log-Likelihood:                -1507.2
+    converged:                       True   LL-Null:                       -1513.4
+    Covariance Type:            nonrobust   LLR p-value:                 0.0004363
+    ==============================================================================
+                     coef    std err          z      P>|z|      [0.025      0.975]
+    ------------------------------------------------------------------------------
+    const          0.2913      1.017      0.287      0.774      -1.701       2.284
+    YEAR           0.0019      0.001      3.546      0.000       0.001       0.003
+    alpha          0.7339      0.057     12.910      0.000       0.622       0.845
+    ==============================================================================
+    0.1.88
+    Setup Complete...
+    Benchmaking test with Seed 42
+    1
+    --------------------------------------------------------------------------------
+    Log-Likelihood:  -1509.0683662284273
+    --------------------------------------------------------------------------------
+    bic: 3035.84
+    --------------------------------------------------------------------------------
+    MSE: 10000000.00
+    +--------+--------+-------+----------+----------+------------+
+    | Effect | $\tau$ | Coeff | Std. Err | z-values | Prob |z|>Z |
+    +========+========+=======+==========+==========+============+
+    | const  | no     | 0.10  |   0.25   |   0.39   | 0.70       |
+    +--------+--------+-------+----------+----------+------------+
+    | YEAR   | no     | 0.00  |   0.00   |  20.39   | 0.00***    |
+    +--------+--------+-------+----------+----------+------------+
+    | nb     |        | 1.33  |   0.00   |  50.00   | 0.00***    |
+    +--------+--------+-------+----------+----------+------------+
+    
+
 Paper
 -----