# Import libraries
import numpy as np
import pandas as pd
from time import time
from sklearn.metrics import f1_score

# Read student data
student_data = pd.read_csv("student-data.csv")
print "Student data read successfully!"

"""
Explanation: Machine Learning Engineer Nanodegree
Supervised Learning
Project 2: Building a Student Intervention System
Welcome to the second project of the Machine Learning Engineer Nanodegree! In this notebook, some template code has already been provided for you, and it will be your job to implement the additional functionality necessary to successfully complete this project. Sections that begin with 'Implementation' in the header indicate that the following block of code will require additional functionality which you must provide. Instructions will be provided for each section and the specifics of the implementation are marked in the code block with a 'TODO' statement. Please be sure to read the instructions carefully!
In addition to implementing code, there will be questions that you must answer which relate to the project and your implementation. Each section where you will answer a question is preceded by a 'Question X' header. Carefully read each question and provide thorough answers in the following text boxes that begin with 'Answer:'. Your project submission will be evaluated based on your answers to each of the questions and the implementation you provide.  

Note: Code and Markdown cells can be executed using the Shift + Enter keyboard shortcut. In addition, Markdown cells can be edited by typically double-clicking the cell to enter edit mode.

Question 1 - Classification vs. Regression
Your goal for this project is to identify students who might need early intervention before they fail to graduate. Which type of supervised learning problem is this, classification or regression? Why?
Answer: 
It's a classification problem. Because, we need to classify students into two groups, whether they need intervention or they don't need intervention.
Exploring the Data
Run the code cell below to load necessary Python libraries and load the student data. Note that the last column from this dataset, 'passed', will be our target label (whether the student graduated or didn't graduate). All other columns are features about each student.
End of explanation
"""


# TODO: Calculate number of students
n_students = len(student_data)

# TODO: Calculate number of features
n_features = len(student_data.columns[student_data.columns != 'passed'])

# TODO: Calculate passing students
n_passed = len(student_data[student_data['passed'] == 'yes'])

# TODO: Calculate failing students
n_failed = len(student_data[student_data['passed'] == 'no'])

# TODO: Calculate graduation rate
grad_rate = n_passed/float(n_students) * 100

# Print the results
print "Total number of students: {}".format(n_students)
print "Number of features: {}".format(n_features)
print "Number of students who passed: {}".format(n_passed)
print "Number of students who failed: {}".format(n_failed)
print "Graduation rate of the class: {:.2f}%".format(grad_rate)

"""
Explanation: Implementation: Data Exploration
Let's begin by investigating the dataset to determine how many students we have information on, and learn about the graduation rate among these students. In the code cell below, you will need to compute the following:
- The total number of students, n_students.
- The total number of features for each student, n_features.
- The number of those students who passed, n_passed.
- The number of those students who failed, n_failed.
- The graduation rate of the class, grad_rate, in percent (%).
End of explanation
"""


# Extract feature columns
feature_cols = list(student_data.columns[:-1])

# Extract target column 'passed'
target_col = student_data.columns[-1] 

# Show the list of columns
print "Feature columns:\n{}".format(feature_cols)
print "\nTarget column: {}".format(target_col)

# Separate the data into feature data and target data (X_all and y_all, respectively)
X_all = student_data[feature_cols]
y_all = student_data[target_col]

# Show the feature information by printing the first five rows
print "\nFeature values:"
print X_all.head()

"""
Explanation: Preparing the Data
In this section, we will prepare the data for modeling, training and testing.
Identify feature and target columns
It is often the case that the data you obtain contains non-numeric features. This can be a problem, as most machine learning algorithms expect numeric data to perform computations with.
Run the code cell below to separate the student data into feature and target columns to see if any features are non-numeric.
End of explanation
"""


def preprocess_features(X):
    ''' Preprocesses the student data and converts non-numeric binary variables into
        binary (0/1) variables. Converts categorical variables into dummy variables. '''
    
    # Initialize new output DataFrame
    output = pd.DataFrame(index = X.index)

    # Investigate each feature column for the data
    for col, col_data in X.iteritems():
        
        # If data type is non-numeric, replace all yes/no values with 1/0
        if col_data.dtype == object:
            col_data = col_data.replace(['yes', 'no'], [1, 0])

        # If data type is categorical, convert to dummy variables
        if col_data.dtype == object:
            # Example: 'school' => 'school_GP' and 'school_MS'
            col_data = pd.get_dummies(col_data, prefix = col)  
        
        # Collect the revised columns
        output = output.join(col_data)
    
    return output

X_all = preprocess_features(X_all)
print "Processed feature columns ({} total features):\n{}".format(len(X_all.columns), list(X_all.columns))

"""
Explanation: Preprocess Feature Columns
As you can see, there are several non-numeric columns that need to be converted! Many of them are simply yes/no, e.g. internet. These can be reasonably converted into 1/0 (binary) values.
Other columns, like Mjob and Fjob, have more than two values, and are known as categorical variables. The recommended way to handle such a column is to create as many columns as possible values (e.g. Fjob_teacher, Fjob_other, Fjob_services, etc.), and assign a 1 to one of them and 0 to all others.
These generated columns are sometimes called dummy variables, and we will use the pandas.get_dummies() function to perform this transformation. Run the code cell below to perform the preprocessing routine discussed in this section.
End of explanation
"""


# TODO: Import any additional functionality you may need here
from sklearn.cross_validation import train_test_split

# TODO: Set the number of training points
num_train = 300

# Set the number of testing points
num_test = X_all.shape[0] - num_train

# TODO: Shuffle and split the dataset into the number of training and testing points above
X_train, X_test, y_train, y_test = train_test_split(X_all, y_all, train_size=num_train, random_state=22)

# Show the results of the split
print "Training set has {} samples.".format(X_train.shape[0])
print "Testing set has {} samples.".format(X_test.shape[0])

"""
Explanation: Implementation: Training and Testing Data Split
So far, we have converted all categorical features into numeric values. For the next step, we split the data (both features and corresponding labels) into training and test sets. In the following code cell below, you will need to implement the following:
- Randomly shuffle and split the data (X_all, y_all) into training and testing subsets.
  - Use 300 training points (approximately 75%) and 95 testing points (approximately 25%).
  - Set a random_state for the function(s) you use, if provided.
  - Store the results in X_train, X_test, y_train, and y_test.
End of explanation
"""


def train_classifier(clf, X_train, y_train):
    ''' Fits a classifier to the training data. '''
    
    # Start the clock, train the classifier, then stop the clock
    start = time()
    clf.fit(X_train, y_train)
    end = time()
    
    # Print the results
    print "Trained model in {:.4f} seconds".format(end - start)

    
def predict_labels(clf, features, target):
    ''' Makes predictions using a fit classifier based on F1 score. '''
    
    # Start the clock, make predictions, then stop the clock
    start = time()
    y_pred = clf.predict(features)
    end = time()
    
    # Print and return results
    print "Made predictions in {:.4f} seconds.".format(end - start)
    return f1_score(target.values, y_pred, pos_label='yes')


def train_predict(clf, X_train, y_train, X_test, y_test):
    ''' Train and predict using a classifer based on F1 score. '''
    
    # Indicate the classifier and the training set size
    print "Training a {} using a training set size of {}. . .".format(clf.__class__.__name__, len(X_train))
    
    # Train the classifier
    train_classifier(clf, X_train, y_train)
    # acc = accuracy_score(y_true, y_pred)
    # Print the results of prediction for both training and testing
    print "F1 score for training set: {:.4f}.\n".format(predict_labels(clf, X_train, y_train))
    print "F1 score for test set: {:.4f}.\n\n".format(predict_labels(clf, X_test, y_test))
    # print "accuracy for test set: {:.4f}.".format(predict_labels(clf, X_test, y_test))"

"""
Explanation: Training and Evaluating Models
In this section, you will choose 3 supervised learning models that are appropriate for this problem and available in scikit-learn. You will first discuss the reasoning behind choosing these three models by considering what you know about the data and each model's strengths and weaknesses. You will then fit the model to varying sizes of training data (100 data points, 200 data points, and 300 data points) and measure the F<sub>1</sub> score. You will need to produce three tables (one for each model) that shows the training set size, training time, prediction time, F<sub>1</sub> score on the training set, and F<sub>1</sub> score on the testing set.
The following supervised learning models are currently available in scikit-learn that you may choose from:
- Gaussian Naive Bayes (GaussianNB)
- Decision Trees
- Ensemble Methods (Bagging, AdaBoost, Random Forest, Gradient Boosting)
- K-Nearest Neighbors (KNeighbors)
- Stochastic Gradient Descent (SGDC)
- Support Vector Machines (SVM)
- Logistic Regression
Question 2 - Model Application
List three supervised learning models that are appropriate for this problem. For each model chosen
- Describe one real-world application in industry where the model can be applied. (You may need to do a small bit of research for this — give references!) 
- What are the strengths of the model; when does it perform well? 
- What are the weaknesses of the model; when does it perform poorly?
- What makes this model a good candidate for the problem, given what you know about the data?
Answer: 
I chose Support Vector Machines, AdaBoosting and Gaussian Naive Bayes algorithms.
Support Vector Classifier


General Applications

text (and hypertext) categorization such as email classification and web searching
image classification
bioinformatics (Protein classification, Cancer classification)
hand-written character recognition



Strengths

Avoids localization problems
Can use the kernel trick
Accurate with small & clean datasets 
Effecient since it only uses a subset of the data



Weaknesses

Sensitive to noise (may need to drop some features that are causing noise)
It only considers two classes at a time
Can be painful to train with large datasets



Reasons for Choosing

SVMs can do well when with a small set as long as the number of data points is larger than the number of features being considered.



AdaBoost Classifier

General Applications
An AdaBoost classifier is to interpolot between many weak learners to create a more accurate model.


Strengths
Improves classification accuracy
Can be used with many different classifiers
Not prone to overfitting which is helpful given our dataset's limited size


Weaknesses
Effected by noisy data
Longer training time since boosting trains multiple instances of the estimator


Reasons for Choosing
In the case that the above 2 classifiers don't work well, we can use the AdaBoost classifier with SVC or simply go with the default estimator (Decision Trees).



Gaussian Naive Bayes

General Applications
Spam mail filter
Classifying emails based on content


Strengths
Easy and fast to use
Accurate if the models assumption holds up


Weaknesses
When assumptions don't hold and accuracy will be off. (Assumption being that the pressence of features are independent of each other.)


Reasons for Choosing
One could argue that in our use case, I felt like features are independent of each other, although they could be depenent.



Setup
Run the code cell below to initialize three helper functions which you can use for training and testing the three supervised learning models you've chosen above. The functions are as follows:
- train_classifier - takes as input a classifier and training data and fits the classifier to the data.
- predict_labels - takes as input a fit classifier, features, and a target labeling and makes predictions using the F<sub>1</sub> score.
- train_predict - takes as input a classifier, and the training and testing data, and performs train_clasifier and predict_labels.
 - This function will report the F<sub>1</sub> score for both the training and testing data separately.
End of explanation
"""


# TODO: Import the three supervised learning models from sklearn
from sklearn import svm
from sklearn.ensemble import AdaBoostClassifier
from sklearn.naive_bayes import GaussianNB


# TODO: Initialize the three models
clf_A = svm.SVC(random_state=24)
clf_B = AdaBoostClassifier(random_state=42)
clf_C = GaussianNB()

# TODO: Set up the training set sizes
X_train_100 = X_train[:100]
y_train_100 = y_train[:100]

X_train_200 = X_train[:200]
y_train_200 = y_train[:200]

X_train_300 = X_train
y_train_300 = y_train

# TODO: Execute the 'train_predict' function for each classifier and each training set size
train_predict(clf_A, X_train_100, y_train_100, X_test, y_test)
train_predict(clf_A, X_train_200, y_train_200, X_test, y_test)
train_predict(clf_A, X_train, y_train, X_test, y_test)

train_predict(clf_B, X_train_100, y_train_100, X_test, y_test)
train_predict(clf_B, X_train_200, y_train_200, X_test, y_test)
train_predict(clf_B, X_train, y_train, X_test, y_test)

train_predict(clf_C, X_train_100, y_train_100, X_test, y_test)
train_predict(clf_C, X_train_200, y_train_200, X_test, y_test)
train_predict(clf_C, X_train, y_train, X_test, y_test)

"""
Explanation: Implementation: Model Performance Metrics
With the predefined functions above, you will now import the three supervised learning models of your choice and run the train_predict function for each one. Remember that you will need to train and predict on each classifier for three different training set sizes: 100, 200, and 300. Hence, you should expect to have 9 different outputs below — 3 for each model using the varying training set sizes. In the following code cell, you will need to implement the following:
- Import the three supervised learning models you've discussed in the previous section.
- Initialize the three models and store them in clf_A, clf_B, and clf_C.
 - Use a random_state for each model you use, if provided.
 - Note: Use the default settings for each model — you will tune one specific model in a later section.
- Create the different training set sizes to be used to train each model.
 - Do not reshuffle and resplit the data! The new training points should be drawn from X_train and y_train.
- Fit each model with each training set size and make predictions on the test set (9 in total).
Note: Three tables are provided after the following code cell which can be used to store your results.
End of explanation
"""


# TODO: Import 'GridSearchCV' and 'make_scorer'
from sklearn.grid_search import GridSearchCV
from sklearn.metrics import make_scorer
# TODO: Create the parameters list you wish to tune
parameters = {'kernel': ['linear', 'poly', 'rbf', 'sigmoid'], 'C': range(1, 11)}

# TODO: Initialize the classifier
clf = svm.SVC(random_state=24)

# TODO: Make an f1 scoring function using 'make_scorer' 
f1_scorer = make_scorer(score_func=f1_score, pos_label='yes')

# TODO: Perform grid search on the classifier using the f1_scorer as the scoring method
grid_obj = GridSearchCV(clf, param_grid=parameters, scoring=f1_scorer)

# TODO: Fit the grid search object to the training data and find the optimal parameters
grid_obj = grid_obj.fit(X_train, y_train)

# Get the estimator
clf = grid_obj.best_estimator_

# Report the final F1 score for training and testing after parameter tuning
print "Tuned model has a training F1 score of {:.4f}.".format(predict_labels(clf, X_train, y_train))
print "Tuned model has a testing F1 score of {:.4f}.".format(predict_labels(clf, X_test, y_test))

"""
Explanation: Tabular Results
Edit the cell below to see how a table can be designed in Markdown. You can record your results from above in the tables provided.
 Classifer 1 - SVM  
| Training Set Size | Training Time | Prediction Time (test) | F1 Score (train) | F1 Score (test) |
| :---------------: | :---------------------: | :--------------------: | :--------------: | :-------------: |
| 100               | 0.0019 sec              | 0.0012 sec             | 0.8780           | 0.7681          |
| 200               | 0.0040 sec              | 0.0019 sec             | 0.8849           | 0.8514          |
| 300               | 0.0070 sec              | 0.0016 sec             | 0.8705           | 0.8497          |
 Classifer 2 - AdaBoost  
| Training Set Size | Training Time | Prediction Time (test) | F1 Score (train) | F1 Score (test) |
| :---------------: | :---------------------: | :--------------------: | :--------------: | :-------------: |
| 100               | 0.1115 sec              | 0.0044 sec             | 0.9573           | 0.6230          |
| 200               | 0.1216 sec              | 0.0046 sec             | 0.8898           | 0.8058          |
| 300               | 0.1351 sec              | 0.0046 sec             | 0.8537           | 0.7770          |
 Classifer 3 - Gaussian NB  
| Training Set Size | Training Time | Prediction Time (test) | F1 Score (train) | F1 Score (test) |
| :---------------: | :---------------------: | :--------------------: | :--------------: | :-------------: |
| 100               | 0.0012 sec              | 0.0003 sec             | 0.2154           | 0.2326          |
| 200               | 0.0012 sec              | 0.0004 sec             | 0.7954           | 0.6970          |
| 300               | 0.0011 sec              | 0.0004 sec             | 0.7789           | 0.7353          |
Choosing the Best Model
In this final section, you will choose from the three supervised learning models the best model to use on the student data. You will then perform a grid search optimization for the model over the entire training set (X_train and y_train) by tuning at least one parameter to improve upon the untuned model's F<sub>1</sub> score. 
Question 3 - Choosing the Best Model
Based on the experiments you performed earlier, in one to two paragraphs, explain to the board of supervisors what single model you chose as the best model. Which model is generally the most appropriate based on the available data, limited resources, cost, and performance?
Answer: 
The chosen model for this project is one that implements a Support Vector Machine (SVM) algorithim.
Support Vector Machines can be used for Classification (labeling) or Regression (numeric) predications. Since we are trying to find out if an intervention is necessary or not, we will make use of specific type of SVMs called Support Vector Classifier (SVC) to get the results we are looking for.
The SVM takes data about past students (age, gender, family, etc), and uses them to create predictions about new student cases. These predictions are made by creating a function that draws a boundary between the students who graduated and those who did not. The boundary should be drawn so as to maximize the the space between itself and each of the classifications (graduation results), this space is called a "margin".

Often, though, it's not easy to draw a decision boundary in low dimensions (i.e. A line is not a good enough boundry), so the SVM separates the passing and failing students by turning the dimensions we're working with from a plane into a higher dimension such as a cube (see below). Once the SVM changes its way of looking at the data, it can then use a plane to seperate the data instead of just a line.

By using the technique mentioned above, our SVC algorithim predicts if a student will graduate or not with an acceptable accuracy.
Question 4 - Model in Layman's Terms
In one to two paragraphs, explain to the board of directors in layman's terms how the final model chosen is supposed to work. Be sure that you are describing the major qualities of the model, such as how the model is trained and how the model makes a prediction. Avoid using advanced mathematical or technical jargon, such as describing equations or discussing the algorithm implementation.
Answer: 
The chosen model is called Support Vector Machine (SVM). This algorithim works by trying to split the data in the cleanest way. This means that SVMs try to draw a line between different outcomes (aka Classifications) from the training data (aka student records available) in order to learn to predict the outcomes of a new student case.
SVMs are a great choice when the resources are limited and the number of considerations (aka Features, ex: absences) in our data is relatively large. This is the case with in this project since the number of features is 40+ (after data processing) and the number of entries is 300+ which is relatively low. SVMs still however provide a quick training and prediction times compared to other algorithims that were considered.
Implementation: Model Tuning
Fine tune the chosen model. Use grid search (GridSearchCV) with at least one important parameter tuned with at least 3 different values. You will need to use the entire training set for this. In the code cell below, you will need to implement the following:
- Import sklearn.grid_search.gridSearchCV and sklearn.metrics.make_scorer.
- Create a dictionary of parameters you wish to tune for the chosen model.
 - Example: parameters = {'parameter' : [list of values]}.
- Initialize the classifier you've chosen and store it in clf.
- Create the F<sub>1</sub> scoring function using make_scorer and store it in f1_scorer.
 - Set the pos_label parameter to the correct value!
- Perform grid search on the classifier clf using f1_scorer as the scoring method, and store it in grid_obj.
- Fit the grid search object to the training data (X_train, y_train), and store it in grid_obj.
End of explanation
"""


