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'sections': [('Overview of first week', 2, None, '___sec0'),
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('Matrices in Python', 2, None, '___sec26'),
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('Meet the Pandas', 2, None, '___sec27'),
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('Friday August 21', 2, None, '___sec28'),
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('Reading Data and fitting', 2, None, '___sec29'),
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<a class="navbar-brand" href="week34-bs.html">Week 34: Introduction to the course, Logistics and Practicalities</a>
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<!-- navigation toc: --> <li><a href="._week34-bs001.html#___sec0" style="font-size: 80%;"><b>Overview of first week</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs002.html#___sec1" style="font-size: 80%;"><b>Thursday August 20</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs007.html#___sec6" style="font-size: 80%;"><b>Recommended textbooks</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs008.html#___sec7" style="font-size: 80%;"><b>Prerequisites</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs009.html#___sec8" style="font-size: 80%;"><b>Learning outcomes</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs010.html#___sec9" style="font-size: 80%;"><b>Topics covered in this course: Statistical analysis and optimization of data</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs011.html#___sec10" style="font-size: 80%;"><b>Topics covered in this course: Machine Learning</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs012.html#___sec11" style="font-size: 80%;"><b>Extremely useful tools, strongly recommended</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs013.html#___sec12" style="font-size: 80%;"><b>Other courses on Data science and Machine Learning at UiO</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs014.html#___sec13" style="font-size: 80%;"><b>Introduction</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs015.html#___sec14" style="font-size: 80%;"><b>What is Machine Learning?</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs016.html#___sec15" style="font-size: 80%;"><b>Types of Machine Learning</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs017.html#___sec16" style="font-size: 80%;"><b>Software and needed installations</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs018.html#___sec17" style="font-size: 80%;"><b>Python installers</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs019.html#___sec18" style="font-size: 80%;"><b>Useful Python libraries</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs020.html#___sec19" style="font-size: 80%;"><b>Installing R, C++, cython or Julia</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs021.html#___sec20" style="font-size: 80%;"><b>Installing R, C++, cython, Numba etc</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs022.html#___sec21" style="font-size: 80%;"><b>Numpy examples and Important Matrix and vector handling packages</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs023.html#___sec22" style="font-size: 80%;"><b>Basic Matrix Features</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs024.html#___sec23" style="font-size: 80%;"> Some famous Matrices</a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs025.html#___sec24" style="font-size: 80%;"> More Basic Matrix Features</a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs026.html#___sec25" style="font-size: 80%;"><b>Numpy and arrays</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs027.html#___sec26" style="font-size: 80%;"><b>Matrices in Python</b></a></li>
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<!-- navigation toc: --> <li><a href="#___sec27" style="font-size: 80%;"><b>Meet the Pandas</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs029.html#___sec28" style="font-size: 80%;"><b>Friday August 21</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs030.html#___sec29" style="font-size: 80%;"><b>Reading Data and fitting</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs031.html#___sec30" style="font-size: 80%;"><b>Friday August 21</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs032.html#___sec31" style="font-size: 80%;"> Simple linear regression model using <b>scikit-learn</b></a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs032.html#___sec32" style="font-size: 80%;"> To our real data: nuclear binding energies. Brief reminder on masses and binding energies</a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs032.html#___sec33" style="font-size: 80%;"> Organizing our data</a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs032.html#___sec34" style="font-size: 80%;"> Seeing the wood for the trees</a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs032.html#___sec35" style="font-size: 80%;"> And what about using neural networks?</a></li>
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<!-- navigation toc: --> <li><a href="._week34-bs032.html#___sec36" style="font-size: 80%;"><b>A first summary</b></a></li>
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<a name="part0028"></a>
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<!-- !split -->
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<h2 id="___sec27" class="anchor">Meet the Pandas </h2>
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<p>
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<br /><br /><center><p><img src="fig/pandas.jpg" align="bottom" width=600></p></center><br /><br />
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<p>
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Another useful Python package is
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<a href="https://pandas.pydata.org/" target="_self">pandas</a>, which is an open source library
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providing high-performance, easy-to-use data structures and data
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analysis tools for Python. <b>pandas</b> stands for panel data, a term borrowed from econometrics and is an efficient library for data analysis with an emphasis on tabular data.
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<b>pandas</b> has two major classes, the <b>DataFrame</b> class with two-dimensional data objects and tabular data organized in columns and the class <b>Series</b> with a focus on one-dimensional data objects. Both classes allow you to index data easily as we will see in the examples below.
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<b>pandas</b> allows you also to perform mathematical operations on the data, spanning from simple reshapings of vectors and matrices to statistical operations.
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<p>
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The following simple example shows how we can, in an easy way make tables of our data. Here we define a data set which includes names, place of birth and date of birth, and displays the data in an easy to read way. We will see repeated use of <b>pandas</b>, in particular in connection with classification of data.
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<p>
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<!-- code=python (!bc pycod) typeset with pygments style "default" -->
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<div class="highlight" style="background: #f8f8f8"><pre style="line-height: 125%"><span></span><span style="color: #008000; font-weight: bold">import</span> <span style="color: #0000FF; font-weight: bold">pandas</span> <span style="color: #008000; font-weight: bold">as</span> <span style="color: #0000FF; font-weight: bold">pd</span>
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<span style="color: #008000; font-weight: bold">from</span> <span style="color: #0000FF; font-weight: bold">IPython.display</span> <span style="color: #008000; font-weight: bold">import</span> display
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data <span style="color: #666666">=</span> {<span style="color: #BA2121">'First Name'</span>: [<span style="color: #BA2121">"Frodo"</span>, <span style="color: #BA2121">"Bilbo"</span>, <span style="color: #BA2121">"Aragorn II"</span>, <span style="color: #BA2121">"Samwise"</span>],
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<span style="color: #BA2121">'Last Name'</span>: [<span style="color: #BA2121">"Baggins"</span>, <span style="color: #BA2121">"Baggins"</span>,<span style="color: #BA2121">"Elessar"</span>,<span style="color: #BA2121">"Gamgee"</span>],
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<span style="color: #BA2121">'Place of birth'</span>: [<span style="color: #BA2121">"Shire"</span>, <span style="color: #BA2121">"Shire"</span>, <span style="color: #BA2121">"Eriador"</span>, <span style="color: #BA2121">"Shire"</span>],
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<span style="color: #BA2121">'Date of Birth T.A.'</span>: [<span style="color: #666666">2968</span>, <span style="color: #666666">2890</span>, <span style="color: #666666">2931</span>, <span style="color: #666666">2980</span>]
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}
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data_pandas <span style="color: #666666">=</span> pd<span style="color: #666666">.</span>DataFrame(data)
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display(data_pandas)
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</pre></div>
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<p>
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In the above we have imported <b>pandas</b> with the shorthand <b>pd</b>, the latter has become the standard way we import <b>pandas</b>. We make then a list of various variables
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and reorganize the aboves lists into a <b>DataFrame</b> and then print out a neat table with specific column labels as <em>Name</em>, <em>place of birth</em> and <em>date of birth</em>.
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Displaying these results, we see that the indices are given by the default numbers from zero to three.
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<b>pandas</b> is extremely flexible and we can easily change the above indices by defining a new type of indexing as
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<p>
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<!-- code=python (!bc pycod) typeset with pygments style "default" -->
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<div class="highlight" style="background: #f8f8f8"><pre style="line-height: 125%"><span></span>data_pandas <span style="color: #666666">=</span> pd<span style="color: #666666">.</span>DataFrame(data,index<span style="color: #666666">=</span>[<span style="color: #BA2121">'Frodo'</span>,<span style="color: #BA2121">'Bilbo'</span>,<span style="color: #BA2121">'Aragorn'</span>,<span style="color: #BA2121">'Sam'</span>])
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display(data_pandas)
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</pre></div>
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<p>
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Thereafter we display the content of the row which begins with the index <b>Aragorn</b>
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<p>
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<!-- code=python (!bc pycod) typeset with pygments style "default" -->
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<div class="highlight" style="background: #f8f8f8"><pre style="line-height: 125%"><span></span>display(data_pandas<span style="color: #666666">.</span>loc[<span style="color: #BA2121">'Aragorn'</span>])
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</pre></div>
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<p>
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We can easily append data to this, for example
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<p>
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<!-- code=python (!bc pycod) typeset with pygments style "default" -->
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<div class="highlight" style="background: #f8f8f8"><pre style="line-height: 125%"><span></span>new_hobbit <span style="color: #666666">=</span> {<span style="color: #BA2121">'First Name'</span>: [<span style="color: #BA2121">"Peregrin"</span>],
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<span style="color: #BA2121">'Last Name'</span>: [<span style="color: #BA2121">"Took"</span>],
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<span style="color: #BA2121">'Place of birth'</span>: [<span style="color: #BA2121">"Shire"</span>],
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<span style="color: #BA2121">'Date of Birth T.A.'</span>: [<span style="color: #666666">2990</span>]
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}
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data_pandas<span style="color: #666666">=</span>data_pandas<span style="color: #666666">.</span>append(pd<span style="color: #666666">.</span>DataFrame(new_hobbit, index<span style="color: #666666">=</span>[<span style="color: #BA2121">'Pippin'</span>]))
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display(data_pandas)
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</pre></div>
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<p>
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Here are other examples where we use the <b>DataFrame</b> functionality to handle arrays, now with more interesting features for us, namely numbers. We set up a matrix
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of dimensionality \( 10\times 5 \) and compute the mean value and standard deviation of each column. Similarly, we can perform mathematial operations like squaring the matrix elements and many other operations.
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<p>
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<!-- code=python (!bc pycod) typeset with pygments style "default" -->
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<div class="highlight" style="background: #f8f8f8"><pre style="line-height: 125%"><span></span><span style="color: #008000; font-weight: bold">import</span> <span style="color: #0000FF; font-weight: bold">numpy</span> <span style="color: #008000; font-weight: bold">as</span> <span style="color: #0000FF; font-weight: bold">np</span>
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<span style="color: #008000; font-weight: bold">import</span> <span style="color: #0000FF; font-weight: bold">pandas</span> <span style="color: #008000; font-weight: bold">as</span> <span style="color: #0000FF; font-weight: bold">pd</span>
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<span style="color: #008000; font-weight: bold">from</span> <span style="color: #0000FF; font-weight: bold">IPython.display</span> <span style="color: #008000; font-weight: bold">import</span> display
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np<span style="color: #666666">.</span>random<span style="color: #666666">.</span>seed(<span style="color: #666666">100</span>)
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<span style="color: #408080; font-style: italic"># setting up a 10 x 5 matrix</span>
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rows <span style="color: #666666">=</span> <span style="color: #666666">10</span>
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cols <span style="color: #666666">=</span> <span style="color: #666666">5</span>
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a <span style="color: #666666">=</span> np<span style="color: #666666">.</span>random<span style="color: #666666">.</span>randn(rows,cols)
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df <span style="color: #666666">=</span> pd<span style="color: #666666">.</span>DataFrame(a)
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display(df)
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<span style="color: #008000; font-weight: bold">print</span>(df<span style="color: #666666">.</span>mean())
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<span style="color: #008000; font-weight: bold">print</span>(df<span style="color: #666666">.</span>std())
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display(df<span style="color: #666666">**2</span>)
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</pre></div>
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<p>
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Thereafter we can select specific columns only and plot final results
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<p>
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<!-- code=python (!bc pycod) typeset with pygments style "default" -->
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<div class="highlight" style="background: #f8f8f8"><pre style="line-height: 125%"><span></span>df<span style="color: #666666">.</span>columns <span style="color: #666666">=</span> [<span style="color: #BA2121">'First'</span>, <span style="color: #BA2121">'Second'</span>, <span style="color: #BA2121">'Third'</span>, <span style="color: #BA2121">'Fourth'</span>, <span style="color: #BA2121">'Fifth'</span>]
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df<span style="color: #666666">.</span>index <span style="color: #666666">=</span> np<span style="color: #666666">.</span>arange(<span style="color: #666666">10</span>)
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display(df)
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<span style="color: #008000; font-weight: bold">print</span>(df[<span style="color: #BA2121">'Second'</span>]<span style="color: #666666">.</span>mean() )
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<span style="color: #008000; font-weight: bold">print</span>(df<span style="color: #666666">.</span>info())
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<span style="color: #008000; font-weight: bold">print</span>(df<span style="color: #666666">.</span>describe())
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<span style="color: #008000; font-weight: bold">from</span> <span style="color: #0000FF; font-weight: bold">pylab</span> <span style="color: #008000; font-weight: bold">import</span> plt, mpl
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plt<span style="color: #666666">.</span>style<span style="color: #666666">.</span>use(<span style="color: #BA2121">'seaborn'</span>)
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mpl<span style="color: #666666">.</span>rcParams[<span style="color: #BA2121">'font.family'</span>] <span style="color: #666666">=</span> <span style="color: #BA2121">'serif'</span>
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df<span style="color: #666666">.</span>cumsum()<span style="color: #666666">.</span>plot(lw<span style="color: #666666">=2.0</span>, figsize<span style="color: #666666">=</span>(<span style="color: #666666">10</span>,<span style="color: #666666">6</span>))
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plt<span style="color: #666666">.</span>show()
|
|
|
|
|
|
df<span style="color: #666666">.</span>plot<span style="color: #666666">.</span>bar(figsize<span style="color: #666666">=</span>(<span style="color: #666666">10</span>,<span style="color: #666666">6</span>), rot<span style="color: #666666">=15</span>)
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plt<span style="color: #666666">.</span>show()
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</pre></div>
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<p>
|
|
We can produce a \( 4\times 4 \) matrix
|
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<p>
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|
|
|
<!-- code=python (!bc pycod) typeset with pygments style "default" -->
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|
<div class="highlight" style="background: #f8f8f8"><pre style="line-height: 125%"><span></span>b <span style="color: #666666">=</span> np<span style="color: #666666">.</span>arange(<span style="color: #666666">16</span>)<span style="color: #666666">.</span>reshape((<span style="color: #666666">4</span>,<span style="color: #666666">4</span>))
|
|
<span style="color: #008000; font-weight: bold">print</span>(b)
|
|
df1 <span style="color: #666666">=</span> pd<span style="color: #666666">.</span>DataFrame(b)
|
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<span style="color: #008000; font-weight: bold">print</span>(df1)
|
|
</pre></div>
|
|
<p>
|
|
and many other operations.
|
|
|
|
<p>
|
|
The <b>Series</b> class is another important class included in
|
|
<b>pandas</b>. You can view it as a specialization of <b>DataFrame</b> but where
|
|
we have just a single column of data. It shares many of the same features as _DataFrame. As with <b>DataFrame</b>,
|
|
most operations are vectorized, achieving thereby a high performance when dealing with computations of arrays, in particular labeled arrays.
|
|
As we will see below it leads also to a very concice code close to the mathematical operations we may be interested in.
|
|
For multidimensional arrays, we recommend strongly <a href="http://xarray.pydata.org/en/stable/" target="_self">xarray</a>. <b>xarray</b> has much of the same flexibility as <b>pandas</b>, but allows for the extension to higher dimensions than two. We will see examples later of the usage of both <b>pandas</b> and <b>xarray</b>.
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<p>
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<p>
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