"Data analysis is Python's killer app" | ||
--Unknown |
This book is the follow-up to Python Data Analysis. The obvious question is, "what does this new book add?" as Python Data Analysis is pretty great (or so I like to believe) already. This book, Python Data Analysis Cookbook, is targeted at slightly more experienced Pythonistas. A year has passed, so we are using newer versions of software and software libraries that I didn't cover in Python Data Analysis. Also, I've had time to rethink and research, and as a result I decided the following:
I need to have a toolbox in order to make my life easier and increase reproducibility. I called the toolbox dautil and made it available via PyPi (which can be installed with
pip
/easy_install
).My soul-searching exercise led me to believe that I need to make it easier to obtain and install the required software. I published a Docker container (pydacbk) with some of the software we need via DockerHub. You can read more about the setup in Chapter 1, Laying the Foundation for Reproducible Data Analysis, and the online chapter. The Docker container is not ideal because it grew quite large, so I had to make some tough decisions. Since the container is not really part of the book, I think it will be appropriate if you contact me directly if you have any issues. However, please keep in mind that I can't change the image drastically.
This book uses the IPython Notebook, which has become a standard tool for analysis. I have given some related tips in the online chapter and other books I have written.
I am using Python 3 with very few exceptions because Python 2 will not be maintained after 2020.
Some people will tell you that you don't need books, just get yourself an interesting project and figure out the rest as you go along. Although there are plenty of resources out there, this may be a very frustrating road. If you want to make a delicious soup, for example, you can of course ask friends and family, search the Internet, or watch cooking shows. However, your friends and family are not available full time for you and the quality of Internet content varies. And in my humble opinion, Packt Publishing, the reviewers, and I have spent so much time and energy on this book, that I will be surprised if you don't get any value out of it.
You probably have seen Venn diagrams depicting data science as the intersection of mathematics/statistics, computer science, and domain expertise. Data analysis is timeless and was there before data science and even before computer science. You could do data analysis with a pen and paper and, in more modern times, with a pocket calculator.
Data analysis has many aspects, with goals such as making decisions or coming up with new hypotheses and questions. The hype, status, and financial rewards surrounding data science and big data remind me of the time when datawarehousing and business intelligence were the buzz words. The ultimate goal of business intelligence and datawarehousing was to build dashboards for management. This involved a lot of politics and organizational aspects, but on the technical side, it was mostly about databases. Data science, on the other hand, is not database-centric and leans heavily on machine learning. Machine learning techniques have become necessary because of the bigger volumes of data. The data growth is caused by the growth of the world population and the rise of new technologies, such as social media and mobile devices. The data growth is, in fact, probably the only trend that we can be sure of continuing. The difference between constructing dashboards and applying machine learning is analogous to the way search engines evolved.
Search engines (if you can call them that) were initially nothing more than well-organized collections of links created manually. Eventually, the automated approach won. Since, in time, more data will be created (and not destroyed), we can expect an increase in automated data analysis.
The history of the various Python software libraries is quite interesting. I am not a historian, so the following notes are written from my own perspective:
1989: Guido van Rossum implements the very first version of Python at the CWI in the Netherlands as a Christmas "hobby" project.
1995: Jim Hugunin creates Numeric—the predecessor to NumPy.
1999: Pearu Peterson wrote f2py as a bridge between Fortran and Python.
2000: Python 2.0 is released.
2001: The SciPy library is released. Also, Numarray, a competing library of Numeric is created. Fernando Perez releases IPython, which starts out as an "afternoon hack". NLTK is released as a research project.
2002: John Hunter creates the Matplotlib library.
2005: NumPy is released by Travis Oliphant. NumPy, initially, is Numeric extended with features inspired by Numarray.
2006: NumPy 1.0 is released. The first version of SQLAlchemy is released.
2007: The scikit-learn project is initiated as a Google Summer of Code project by David Cournapeau. Cython was forked from Pyrex. Cython is later intensively used in pandas and scikit-learn to improve performance.
2008: Wes McKinney starts working on pandas. Python 3.0 is released.
2011: The IPython 0.12 release introduces the IPython notebook. Packt Publishing releases NumPy 1.5 Beginner's Guide.
2012: Packt Publishing releases NumPy Cookbook.
2013: Packt Publishing releases NumPy Beginner's Guide, Second Edition.
2014: Fernando Perez announces Project Jupyter, which aims to make a language-agnostic notebook. Packt Publishing releases Learning NumPy Array and Python Data Analysis.
2015: Packt Publishing releases NumPy Beginner's Guide, Third Edition and NumPy Cookbook, Second Edition.
The future is a bright place, where an incredible amount of data lives in the Cloud and software runs on any imaginable device with an intuitive customizable interface. (I know young people who can't stop talking about how awesome their phone is and how one day we will all be programming on tablets by dragging and dropping). It seems there is a certain angst in the Python community about not being relevant in the future. Of course, the more you have invested in Python, the more it matters.
To figure out what to do, we need to know what makes Python special. A school of thought claims that Python is a glue language gluing C, Fortran, R, Java, and other languages; therefore, we just need better glue. This probably also means "borrowing" features from other languages. Personally, I like the way Python works, its flexible nature, its data structures, and the fact that it has so many libraries and features. I think the future is in more delicious syntactic sugar and just-in-time compilers. Somehow we should be able to continue writing Python code, which automatically is converted for us in concurrent (machine) code. Unseen machinery under the hood manages lower level details and sends data and instructions to CPUs, GPUs, or the Cloud. The code should be able to easily communicate with whatever storage backend we are using. Ideally, all of this magic will be just as convenient as automatic garbage collection. It may sound like an impossible "click of a button" dream, but I think it is worth pursuing.
Chapter 1, Laying the Foundation for Reproducible Data Analysis, is a pretty important chapter, and I recommend that you do not skip it. It explains Anaconda, Docker, unit testing, logging, and other essential elements of reproducible data analysis.
Chapter 2, Creating Attractive Data Visualizations, demonstrates how to visualize data and mentions frequently encountered pitfalls.
Chapter 3, Statistical Data Analysis and Probability, discusses statistical probability distributions and correlation between two variables.
Chapter 4, Dealing with Data and Numerical Issues, is about outliers and other common data issues. Data is almost never perfect, so a large portion of the analysis effort goes into dealing with data imperfections.
Chapter 5, Web Mining, Databases, and Big Data, is light on mathematics, but more focused on technical topics, such as databases, web scraping, and big data.
Chapter 6, Signal Processing and Timeseries, is about time series data, which is abundant and requires special techniques. Usually, we are interested in trends and seasonality or periodicity.
Chapter 7, Selecting Stocks with Financial Data Analysis, focuses on stock investing because stock price data is abundant. This is the only chapter on finance and the content should be at least partially relevant if stocks don't interest you.
Chapter 8, Text Mining and Social Network Analysis, helps you cope with the floods of textual and social media information.
Chapter 9, Ensemble Learning and Dimensionality Reduction, covers ensemble learning, classification and regression algorithms, as well as hierarchical clustering.
Chapter 10, Evaluating Classifiers, Regressors, and Clusters, evaluates the classifiers and regressors from Chapter 9, Ensemble Learning and Dimensionality Reduction, the preceding chapter.
Chapter 11, Analyzing Images, uses the OpenCV library quite a lot to analyze images.
Chapter 12, Parallelism and Performance, is about software performance and I discuss various options to improve performance, including caching and just-in-time compilers.
Appendix A, Glossary, is a brief glossary of technical concepts used throughout the book. The goal is to have a reference that is easy to look up.
Appendix B, Function Reference, is a short reference of functions meant as an extra aid in case you are temporarily unable to look up documentation.
Appendix C, Online Resources, lists resources including presentations, links to documentation, and freely available IPython notebooks and data. This appendix is available as an online chapter.
Appendix D, Tips and Tricks for Command-Line and Miscellaneous Tools, in this book we use various tools such as the IPython notebook, Docker, and Unix shell commands. I give a short list of tips that is not meant to be exhaustive. This appendix is also available as online chapter.
First, you need a Python 3 distribution. I recommend the full Anaconda distribution as it comes with the majority of the software we need. I tested the code with Python 3.4 and the following packages:
joblib 0.8.4
IPython 3.2.1
NetworkX 1.9.1
NLTK 3.0.2
Numexpr 2.3.1
pandas 0.16.2
SciPy 0.16.0
seaborn 0.6.0
sqlalchemy 0.9.9
statsmodels 0.6.1
matplotlib 1.5.0
NumPy 1.10.1
scikit-learn 0.17
dautil 0.0.1a29
For some recipes, you need to install extra software, but this is explained whenever the software is required.
This book is hands-on and low on theory. You should have better than beginner Python knowledge and have some knowledge of linear algebra, calculus, machine learning and statistics. Ideally, you would have read Python Data Analysis, but this is not a requirement. I also recommend the following books:
Building Machine Learning Systems with Python by Willi Richert and Luis Pedro Coelho, 2013
Learning NumPy Array by Ivan Idris, 2014
Learning scikit-learn: Machine Learning in Python by Guillermo Moncecchi, 2013
Learning SciPy for Numerical and Scientific Computing by Francisco J. Blanco-Silva, 2013
Matplotlib for Python Developers by Sandro Tosi, 2009
NumPy Beginner's Guide - Third Edition by Ivan Idris, 2015
NumPy Cookbook – Second Edition by Ivan Idris, 2015
Parallel Programming with Python by Jan Palach, 2014
Python Data Visualization Cookbook by Igor Milovanović, 2013
Python for Finance by Yuxing Yan, 2014
Python Text Processing with NLTK 2.0 Cookbook by Jacob Perkins, 2010
In this book, you will find several headings that appear frequently (Getting ready, How to do it, How it works, There's more, and See also).
To give clear instructions on how to complete a recipe, we use these sections as follows:
This section tells you what to expect in the recipe, and describes how to set up any software or any preliminary settings required for the recipe.
This section usually consists of a detailed explanation of what happened in the previous section.
This section consists of additional information about the recipe in order to make the reader more knowledgeable about the recipe.
In this book, you will find a number of text styles that distinguish between different kinds of information. Here are some examples of these styles and an explanation of their meaning.
Code words in text, database table names, folder names, filenames, file extensions, pathnames, dummy URLs, user input, and Twitter handles are shown as follows: "Plot the data and corresponding linear fits with the Seaborn lmplot()
function."
A block of code is set as follows:
population = dawb.download(indicator=[dawb.get_name('pop_grow'), dawb.get_name('gdp_pcap'), dawb.get_name('primary_education')], country=countries['iso2c'], start=2014, end=2014) population = dawb.rename_columns(population)
When we wish to draw your attention to a particular part of a code block, the relevant lines or items are set in bold:
plt.figure() plt.title('Rainy Weather vs Wind Speed') categorical = df categorical['RAIN'] = categorical['RAIN'] > 0 ax = sns.violinplot(x="RAIN", y="WIND_SPEED", data=categorical)
Any command-line input or output is written as follows:
$ conda install -c scitools cartopy
New terms and important words are shown in bold. Words that you see on the screen, for example, in menus or dialog boxes, appear in the text like this: "In the next screenshot, the Day of year 31 text comes from the tooltip:"
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