Getting Started with Kaggle

# Load a csv file as a dataframe using Pandas library.
titanic = pandas.read_csv("titanic_train.csv")

# Print the first 5 rows of the data frame.
print(titanic.head(5))

# Get description of the dataframe
print(titanic.describe())

# To access a column
titanic["Age"]

# fillna() function fill the column with missing values
# median() is self-explanatory
titanic["Age"] = titanic["Age"].fillna(titanic["Age"].median())

# Find all the unique genders -- the column appears to contain only male and female.
print(titanic["Sex"].unique())

# Replace all the occurences of male with the number 0. The objective is to convert all non-numeric values to numeric values
titanic.loc[titanic["Sex"] == "male", "Sex"] = 0

# Import the linear regression class
from sklearn.linear_model import LinearRegression
# Sklearn also has a helper that makes it easy to do cross validation
from sklearn.cross_validation import KFold

# The columns we'll use to predict the target
predictors = ["Pclass", "Sex", "Age", "SibSp", "Parch", "Fare", "Embarked"]

# Initialize our algorithm class
alg = LinearRegression()
# Generate cross validation folds for the titanic dataset.  It return the row indices corresponding to train and test.
# We set random_state to ensure we get the same splits every time we run this.
kf = KFold(titanic.shape[0], n_folds=3, random_state=1)

predictions = []
for train, test in kf:
    # The predictors we're using the train the algorithm.  Note how we only take the rows in the train folds.
    train_predictors = (titanic[predictors].iloc[train,:])
    # The target we're using to train the algorithm.
    train_target = titanic["Survived"].iloc[train]
    # Training the algorithm using the predictors and target.
    alg.fit(train_predictors, train_target)
    # We can now make predictions on the test fold
    test_predictions = alg.predict(titanic[predictors].iloc[test,:])
    predictions.append(test_predictions)
    
# Now calculating accuracy

import numpy as np

# The predictions are in three separate numpy arrays.  Concatenate them into one.  
# We concatenate them on axis 0, as they only have one axis.
predictions = np.concatenate(predictions, axis=0)

# Map predictions to outcomes (only possible outcomes are 1 and 0)
predictions[predictions > .5] = 1
predictions[predictions <=.5] = 0

totalPredictions = predictions.size

# How many matches in actual and predicted values
totalMatch = np.sum(predictions == titanic["Survived"])

accuracy = totalMatch*1.0 / totalPredictions

from sklearn import cross_validation

# Initialize our algorithm
alg = LogisticRegression(random_state=1)
# Compute the accuracy score for all the cross validation folds.  (much simpler than what we did before!)
scores = cross_validation.cross_val_score(alg, titanic[predictors], titanic["Survived"], cv=3)
# Take the mean of the scores (because we have one for each fold)
print(scores.mean())

titanic_test = pandas.read_csv("titanic_test.csv")

# Do some cleaning of data
titanic_test = pandas.read_csv("titanic_test.csv")

titanic_test["Age"] = titanic_test["Age"].fillna(titanic["Age"].median())

titanic_test.loc[titanic_test["Sex"] == "male", "Sex"] = 0
titanic_test.loc[titanic_test["Sex"] == "female", "Sex"] = 1

titanic_test["Embarked"] = titanic_test["Embarked"].fillna("S")
titanic_test.loc[titanic_test["Embarked"] == "S", "Embarked"] = 0
titanic_test.loc[titanic_test["Embarked"] == "C", "Embarked"] = 1
titanic_test.loc[titanic_test["Embarked"] == "Q", "Embarked"] = 2

titanic_test["Fare"] = titanic_test["Fare"].fillna(titanic_test["Fare"].median())

# Initialize the algorithm class
alg = LogisticRegression(random_state=1)

# Train the algorithm using all the training data
alg.fit(titanic[predictors], titanic["Survived"])

# Make predictions using the test set.
predictions = alg.predict(titanic_test[predictors])

# Create a new data frame with only the columns Kaggle wants from the dataset.
submission = pandas.DataFrame({
        "PassengerId": titanic_test["PassengerId"],
        "Survived": predictions
    })
    

from sklearn import cross_validation
from sklearn.ensemble import RandomForestClassifier

predictors = ["Pclass", "Sex", "Age", "SibSp", "Parch", "Fare", "Embarked"]

# Initialize our algorithm with the default paramters
# n_estimators is the number of trees we want to make
# min_samples_split is the minimum number of rows we need to make a split
# min_samples_leaf is the minimum number of samples we can have at the place where a tree branch ends (the bottom points of the tree)
alg = RandomForestClassifier(random_state=1, n_estimators=10, min_samples_split=2, min_samples_leaf=1)

kf = cross_validation.KFold(titanic.shape[0], n_folds=3, random_state=1)
scores = cross_validation.cross_val_score(alg, titanic[predictors], titanic["Survived"], cv=kf)

# What an elegant way to get mean!
print(scores.mean())

# Generating a familysize column
titanic["FamilySize"] = titanic["SibSp"] + titanic["Parch"]

# The .apply method generates a new series
titanic["NameLength"] = titanic["Name"].apply(lambda x: len(x))

import re

# A function to get the title from a name.
def get_title(name):
    # Use a regular expression to search for a title.  Titles always consist of capital and lowercase letters, and end with a period.
    title_search = re.search(' ([A-Za-z]+)\.', name)
    # If the title exists, extract and return it.
    if title_search:
        return title_search.group(1)
    return ""

# Get all the titles and print how often each one occurs.
titles = titanic["Name"].apply(get_title)
print(pandas.value_counts(titles))

# Map each title to an integer.  Some titles are very rare, and are compressed into the same codes as other titles.
title_mapping = {"Mr": 1, "Miss": 2, "Mrs": 3, "Master": 4, "Dr": 5, "Rev": 6, "Major": 7, "Col": 7, "Mlle": 8, "Mme": 8, "Don": 9, "Lady": 10, "Countess": 10, "Jonkheer": 10, "Sir": 9, "Capt": 7, "Ms": 2}
for k,v in title_mapping.items():
    titles[titles == k] = v

# Verify that we converted everything.
print(pandas.value_counts(titles))

# Add in the title column.
titanic["Title"] = titles

import operator

# A dictionary mapping family name to id
family_id_mapping = {}

# A function to get the id given a row
def get_family_id(row):
    # Find the last name by splitting on a comma
    last_name = row["Name"].split(",")[0]
    # Create the family id
    family_id = "{0}{1}".format(last_name, row["FamilySize"])
    # Look up the id in the mapping
    if family_id not in family_id_mapping:
        if len(family_id_mapping) == 0:
            current_id = 1
        else:
            # Get the maximum id from the mapping and add one to it if we don't have an id
            current_id = (max(family_id_mapping.items(), key=operator.itemgetter(1))[1] + 1)
        family_id_mapping[family_id] = current_id
    return family_id_mapping[family_id]

# Get the family ids with the apply method
family_ids = titanic.apply(get_family_id, axis=1)

# There are a lot of family ids, so we'll compress all of the families under 3 members into one code.
family_ids[titanic["FamilySize"] < 3] = -1

# Print the count of each unique id.
print(pandas.value_counts(family_ids))

titanic["FamilyId"] = family_ids

import numpy as np
from sklearn.feature_selection import SelectKBest, f_classif

predictors = ["Pclass", "Sex", "Age", "SibSp", "Parch", "Fare", "Embarked", "FamilySize", "Title", "FamilyId", "NameLength"]

# Perform feature selection
selector = SelectKBest(f_classif, k=5)
selector.fit(titanic[predictors], titanic["Survived"])

# Get the raw p-values for each feature, and transform from p-values into scores
scores = -np.log10(selector.pvalues_)

# Plot the scores.  See how "Pclass", "Sex", "Title", and "Fare" are the best?
plt.bar(range(len(predictors)), scores)
plt.xticks(range(len(predictors)), predictors, rotation='vertical')
plt.show()

# Pick only the four best features.
predictors = ["Pclass", "Sex", "Fare", "Title"]

alg = RandomForestClassifier(random_state=1, n_estimators=50, min_samples_split=8, min_samples_leaf=4)

scores = cross_validation.cross_val_score(alg, titanic[predictors], titanic["Survived"], cv=3)

print(scores.mean())

from sklearn.ensemble import GradientBoostingClassifier
import numpy as np

# The algorithms we want to ensemble.
# We're using the more linear predictors for the logistic regression, and everything with the gradient boosting classifier.
algorithms = [
    [GradientBoostingClassifier(random_state=1, n_estimators=25, max_depth=3), ["Pclass", "Sex", "Age", "Fare", "Embarked", "FamilySize", "Title", "FamilyId"]],
    [LogisticRegression(random_state=1), ["Pclass", "Sex", "Fare", "FamilySize", "Title", "Age", "Embarked"]]
]

# Initialize the cross validation folds
kf = KFold(titanic.shape[0], n_folds=3, random_state=1)

predictions = []
for train, test in kf:
    train_target = titanic["Survived"].iloc[train]
    full_test_predictions = []
    # Make predictions for each algorithm on each fold
    for alg, predictors in algorithms:
        # Fit the algorithm on the training data.
        alg.fit(titanic[predictors].iloc[train,:], train_target)
        # Select and predict on the test fold.  
        # The .astype(float) is necessary to convert the dataframe to all floats and avoid an sklearn error.
        test_predictions = alg.predict_proba(titanic[predictors].iloc[test,:].astype(float))[:,1]
        full_test_predictions.append(test_predictions)
    # Use a simple ensembling scheme -- just average the predictions to get the final classification.
    test_predictions = (full_test_predictions[0] + full_test_predictions[1]) / 2
    # Any value over .5 is assumed to be a 1 prediction, and below .5 is a 0 prediction.
    test_predictions[test_predictions <= .5] = 0
    test_predictions[test_predictions > .5] = 1
    predictions.append(test_predictions)

# Put all the predictions together into one array.
predictions = np.concatenate(predictions, axis=0)

# Compute accuracy by comparing to the training data.
accuracy = sum(predictions[predictions == titanic["Survived"]]) / len(predictions)
print(accuracy)

predictors = ["Pclass", "Sex", "Age", "Fare", "Embarked", "FamilySize", "Title", "FamilyId"]

algorithms = [
    [GradientBoostingClassifier(random_state=1, n_estimators=25, max_depth=3), predictors],
    [LogisticRegression(random_state=1), ["Pclass", "Sex", "Fare", "FamilySize", "Title", "Age", "Embarked"]]
]

full_predictions = []
for alg, predictors in algorithms:
    # Fit the algorithm using the full training data.
    alg.fit(titanic[predictors], titanic["Survived"])
    # Predict using the test dataset.  We have to convert all the columns to floats to avoid an error.
    predictions = alg.predict_proba(titanic_test[predictors].astype(float))[:,1]
    full_predictions.append(predictions)

# The gradient boosting classifier generates better predictions, so we weight it higher.
predictions = (full_predictions[0] * 3 + full_predictions[1]) / 4

threshold = 0.5
predictions = np.where(predictions > threshold, 1,0).astype(int)

#This is a submission dataframe
submission = pandas.DataFrame({
        "PassengerId": titanic_test["PassengerId"],
        "Survived": predictions
    })
    
# Generating csv file    
submission.to_csv("kaggle.csv", index=False)