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Coding_with_Python_in_Jupyter_Notebooks.html
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Coding_with_Python_in_Jupyter_Notebooks.html
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<!DOCTYPE html>
<html>
<head><meta charset="utf-8" />
<title>Coding_with_Python_in_Jupyter_Notebooks</title>
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<h1 id="Running-Python-in-Notebooks">Running Python in Notebooks<a class="anchor-link" href="#Running-Python-in-Notebooks">¶</a></h1><hr>
<p>Jupyter (previously known as IPython) is a dynamic interaction platform that works with the shell and your browser so that you may code and visualize the results in one environment. The closest analog is an RMarkdown document. An important advantage is that you can step by step build your results and analysis, write your text, and visualize the graphs and results without having to constantly re-render the entire document to see updates. This strength is also a weakness as you may inadvertently introduce errors, load data, or create variables in the wrong order, causing errors when trying to replicate.</p>
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<h2 id="Basics-of-Jupyter-(IPython)-Notebooks">Basics of Jupyter (IPython) Notebooks<a class="anchor-link" href="#Basics-of-Jupyter-(IPython)-Notebooks">¶</a></h2><p>To start up a Jupyter notebook server, simply navigate to the directory where you want the notebooks to be saved and run the command.</p>
<div class="highlight"><pre>jupyter notebook
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<p>A browser should open with a notebook navigator. From here, you can either click to open an existing notebook or click the "New" button and select "Python 3". You may rename any notebook by clicking its title at the top of the page.</p>
<p>Notebooks are sequences of cells. Cells can be markdown, code, or raw text. You can run Markdown or code in cells, similar to RMarkdown.</p>
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<h2 id="Calling-the-Command-Line-from-Jupyter">Calling the Command Line from Jupyter<a class="anchor-link" href="#Calling-the-Command-Line-from-Jupyter">¶</a></h2><h4 id="Note:-you-can-call-the-command-line-from-jupyter-by-using-a-"!"-before-the-command.">Note: you can call the command line from jupyter by using a "!" before the command.<a class="anchor-link" href="#Note:-you-can-call-the-command-line-from-jupyter-by-using-a-"!"-before-the-command.">¶</a></h4><h4 id="For-example,-you-could-use-this-option-to-commit-your-work-on-Git"><em>For example, you could use this option to commit your work on Git</em><a class="anchor-link" href="#For-example,-you-could-use-this-option-to-commit-your-work-on-Git">¶</a></h4>
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<div class=" highlight hl-ipython3"><pre><span class="o">!</span>git status
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<pre>On branch master
Your branch is up-to-date with 'origin/master'.
nothing to commit, working directory clean
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<h1 id="Getting-the-Data">Getting the Data<a class="anchor-link" href="#Getting-the-Data">¶</a></h1>
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<h2 id="Today,-we-will-be-using-data-from-the-NOAA-National-Climatic-Data-Center">Today, we will be using data from the <a href="https://www.ncdc.noaa.gov/oa/climate/ghcn-daily/">NOAA National Climatic Data Center</a><a class="anchor-link" href="#Today,-we-will-be-using-data-from-the-NOAA-National-Climatic-Data-Center">¶</a></h2><p>Further documentation on this data is available here: <a href="http://doi.org/10.7289/V5D21VHZ">http://doi.org/10.7289/V5D21VHZ</a>. A readme file and <a href="http://www1.ncdc.noaa.gov/pub/data/ghcn/daily/readme.txt">codebook for the data</a> is also available.</p>
<p>We will download the daily data, as well as data on the ghcnd stations using <a href="https://curl.haxx.se/docs/manpage.html">curl</a>.</p>
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<div class=" highlight hl-ipython3"><pre><span class="c">#Download the Data Using Curl</span>
<span class="o">!</span>curl -O http://www1.ncdc.noaa.gov/pub/data/ghcn/daily/by_year/2016.csv.gz
<span class="o">!</span>gunzip 2016.csv.gz
<span class="o">!</span>curl -O http://www1.ncdc.noaa.gov/pub/data/ghcn/daily/ghcnd-stations.txt
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<pre> % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 146M 100 146M 0 0 7363k 0 0:00:20 0:00:20 --:--:-- 8656k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 8461k 100 8461k 0 0 2487k 0 0:00:03 0:00:03 --:--:-- 2487k
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<h1 id="Exploratory-Data-Analysis-with-Pandas">Exploratory Data Analysis with Pandas<a class="anchor-link" href="#Exploratory-Data-Analysis-with-Pandas">¶</a></h1><p><a href="http://pandas.pydata.org/">Pandas</a> is a library created by <a href="http://blog.wesmckinney.com/">Wes McKinney</a> that introduces the R-like dataframe object to Python and makes working with data in Python a lot easier. It's also a lot more efficient than the R dataframe and pretty much makes Python superior to R in every imaginable way (except for ggplot 2).</p>
<p>We start by importing the libraries we're going to use: <code>pandas</code> and <code>matplotlib</code>.</p>
<p>For R users, importing a package is equivalent to <code>library(package_name)</code>.</p>
<p>Note that packages are often loaded in Python using an alias, as shown below. In this way, when we later call a pandas function, we can refer to it as <code>pd.function_name</code> instead of <code>pandas.function_name</code>.</p>
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<div class=" highlight hl-ipython3"><pre><span class="c"># Import Statements</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="c">#Turn of Notebook Package Warnings</span>
<span class="kn">import</span> <span class="nn">warnings</span>
<span class="n">warnings</span><span class="o">.</span><span class="n">filterwarnings</span><span class="p">(</span><span class="s">'ignore'</span><span class="p">)</span>
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<p>In Jupyter notebooks, some utilities can be imported with <a href="https://ipython.org/ipython-doc/3/interactive/magics.html">magic statements</a> indicated by a <code>%</code>, not to be confused with the python operator <code>%</code>. Magic commands only apply to the Jupyter notebook and begin a line.</p>
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<div class=" highlight hl-ipython3"><pre><span class="c">#Magic Statement</span>
<span class="o">%</span><span class="k">matplotlib</span> inline
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<p>We will also set the file location used. If you cloned the repository and ran the steps sequentially, then the relative directory location should be correct.</p>
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<div class=" highlight hl-ipython3"><pre><span class="c"># File Locations</span>
<span class="c"># Change these on your machine (if needed)</span>
<span class="n">datadir</span> <span class="o">=</span> <span class="s">""</span>
<span class="n">weather_data_raw</span> <span class="o">=</span> <span class="n">datadir</span> <span class="o">+</span> <span class="s">"2016.csv"</span>
<span class="n">station_data_raw</span> <span class="o">=</span> <span class="n">datadir</span> <span class="o">+</span> <span class="s">"ghcnd-stations.txt"</span>
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<h2 id="Loading-Data-into-a-Pandas-DataFrame">Loading Data into a Pandas DataFrame<a class="anchor-link" href="#Loading-Data-into-a-Pandas-DataFrame">¶</a></h2><p>So far we've been working with raw text files. That's one way to store and interact with data, but there are only a limited set of functions that can take as input raw text. Python has an amazing array of data structures to work with that give you a lot of extra power in working with data.</p>
<p>Build in Data Structures</p>
<ul>
<li>strings ""</li>
<li>lists []</li>
<li>tuples ()</li>
<li>sets {}</li>
<li>dictionaries {'key':value}</li>
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<p>Additional Essential Data Structures</p>
<ul>
<li>numpy arrys ([])</li>
<li>pandas Series</li>
<li>pandas DataFrame</li>
<li>tensorflow Tensors</li>
</ul>
<p>Today we'll primarily be working with the pandas DataFrame. The pandas DataFrame is a two-dimensional size-mutable, potentially heterogeneous tabular data structure with labeled axes. It's basically a spreadsheet you can program and it's an incredibly useful Python object for data analysis.</p>
<p>You can load data into a dataframe using Pandas' excellent <code>read_*</code> functions.</p>
<p>Today, we will use <code>read_table</code></p>
<p><strong>Tips on Documentation</strong>:</p>
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<li>TAB COMPLETION </li>
<li>Jupyter will pull of the doc string for a command just by asking it a question.</li>
<li>Jupyter will give you the allowable arguments if you it <code>shift + tab</code></li>
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<div class=" highlight hl-ipython3"><pre><span class="c">#Try Getting Help (Esc to Exit)</span>
<span class="n">pd</span><span class="o">.</span><span class="n">read_table</span><span class="o">?</span>
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<h2 id="Load-the-Data-with-Pandas">Load the Data with Pandas<a class="anchor-link" href="#Load-the-Data-with-Pandas">¶</a></h2>
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<div class=" highlight hl-ipython3"><pre><span class="n">weather</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_table</span><span class="p">(</span><span class="n">weather_data_raw</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s">","</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="k">None</span><span class="p">)</span>
<span class="n">stations</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_table</span><span class="p">(</span><span class="n">station_data_raw</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="k">None</span><span class="p">)</span>
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<h2 id="View-the-Data-in-Pandas">View the Data in Pandas<a class="anchor-link" href="#View-the-Data-in-Pandas">¶</a></h2><p>There are lots of options for viewing data in pandas. Just like we did in the command line, you can use <code>head</code> and <code>tail</code> to get a quick view of our data.</p>
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<div class=" highlight hl-ipython3"><pre><span class="n">weather</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
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<td>NOE00133566</td>
<td>20160101</td>
<td>TMAX</td>
<td>95</td>
<td>NaN</td>
<td>NaN</td>
<td>E</td>
<td>NaN</td>
</tr>
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<th>2</th>
<td>NOE00133566</td>
<td>20160101</td>
<td>TMIN</td>
<td>23</td>
<td>NaN</td>
<td>NaN</td>
<td>E</td>
<td>NaN</td>
</tr>
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<th>3</th>
<td>NOE00133566</td>
<td>20160101</td>
<td>PRCP</td>
<td>37</td>
<td>NaN</td>
<td>NaN</td>
<td>E</td>
<td>NaN</td>
</tr>
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<th>4</th>
<td>USC00141761</td>
<td>20160101</td>
<td>TMAX</td>
<td>22</td>
<td>NaN</td>
<td>NaN</td>
<td>7</td>
<td>700.0</td>
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<div class=" highlight hl-ipython3"><pre><span class="n">weather</span><span class="o">.</span><span class="n">tail</span><span class="p">()</span>
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<th>0</th>
<th>1</th>
<th>2</th>
<th>3</th>
<th>4</th>
<th>5</th>
<th>6</th>
<th>7</th>
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<th>25992850</th>
<td>USR0000CSCN</td>
<td>20161019</td>
<td>TMIN</td>
<td>28</td>
<td>H</td>
<td>NaN</td>
<td>U</td>
<td>NaN</td>
</tr>
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<th>25992851</th>
<td>USR0000CSCN</td>
<td>20161019</td>
<td>TAVG</td>
<td>98</td>
<td>NaN</td>
<td>NaN</td>
<td>U</td>
<td>NaN</td>
</tr>
<tr>
<th>25992852</th>
<td>USR0000ABAN</td>
<td>20161019</td>
<td>TMAX</td>
<td>317</td>
<td>H</td>
<td>NaN</td>
<td>U</td>
<td>NaN</td>
</tr>
<tr>
<th>25992853</th>
<td>USR0000ABAN</td>
<td>20161019</td>
<td>TMIN</td>
<td>172</td>
<td>H</td>
<td>NaN</td>
<td>U</td>
<td>NaN</td>
</tr>
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<th>25992854</th>
<td>USR0000ABAN</td>
<td>20161019</td>
<td>TAVG</td>
<td>241</td>
<td>NaN</td>
<td>NaN</td>
<td>U</td>
<td>NaN</td>
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<div class=" highlight hl-ipython3"><pre><span class="c">#Dimensions of the DataFrame</span>
<span class="n">weather</span><span class="o">.</span><span class="n">shape</span>
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<pre>(25992855, 8)</pre>
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<div class=" highlight hl-ipython3"><pre><span class="c">#Types of Data</span>
<span class="n">weather</span><span class="o">.</span><span class="n">dtypes</span>
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<pre>0 object
1 int64
2 object
3 int64
4 object
5 object
6 object
7 float64
dtype: object</pre>
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<p>Note: You'll notice that some commands have looked like pd.something(), some like data.something(), and some like data.something without (). The difference is a pandas function or class versus methods versus attributes. Methods are actions you take on a dataframe or series, while attributes are descriptors or the dataframe or series.</p>
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<h2 id="Modifying-your-DataFrame">Modifying your DataFrame<a class="anchor-link" href="#Modifying-your-DataFrame">¶</a></h2><p>Notice that we don't have column names and some columns are full of null values. Let's fix that by learning how to name and delete columns.</p>
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<div class=" highlight hl-ipython3"><pre><span class="c">#Current Data Columns</span>
<span class="n">weather</span><span class="o">.</span><span class="n">columns</span>
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<pre>Int64Index([0, 1, 2, 3, 4, 5, 6, 7], dtype='int64')</pre>
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<div class=" highlight hl-ipython3"><pre><span class="c">#Drop columns 4, 5, 6, & 7</span>
<span class="n">weather</span><span class="o">.</span><span class="n">drop</span><span class="p">([</span><span class="mi">4</span><span class="p">,</span><span class="mi">5</span><span class="p">,</span><span class="mi">6</span><span class="p">,</span><span class="mi">7</span><span class="p">],</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="k">True</span><span class="p">)</span>
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<div class=" highlight hl-ipython3"><pre><span class="n">weather</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
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<th>1</th>
<td>NOE00133566</td>
<td>20160101</td>
<td>TMAX</td>
<td>95</td>
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<th>2</th>
<td>NOE00133566</td>
<td>20160101</td>
<td>TMIN</td>
<td>23</td>
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<th>3</th>
<td>NOE00133566</td>
<td>20160101</td>
<td>PRCP</td>
<td>37</td>
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<th>4</th>
<td>USC00141761</td>
<td>20160101</td>
<td>TMAX</td>
<td>22</td>
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<p>Note that the header of the data frame has no column names, only numbers. We can assign column names by creating a list and setting the data frame columns equal to the list.</p>
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<div class=" highlight hl-ipython3"><pre><span class="c">#Assign Column Names Using a List</span>
<span class="n">weather_cols</span> <span class="o">=</span> <span class="p">[</span><span class="s">'station_id'</span><span class="p">,</span><span class="s">'date'</span><span class="p">,</span><span class="s">'measurement'</span><span class="p">,</span><span class="s">'value'</span><span class="p">]</span>
<span class="n">weather</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">weather_cols</span>
<span class="n">weather</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
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<td>NOE00133566</td>
<td>20160101</td>
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<td>37</td>
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<td>USC00141761</td>
<td>20160101</td>
<td>TMAX</td>
<td>22</td>
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<h2 id="Describing-the-Entire-DataFrame">Describing the Entire DataFrame<a class="anchor-link" href="#Describing-the-Entire-DataFrame">¶</a></h2><p>Now that we have columns, we want to get a better global view of our data. There are several ways</p>
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<div class=" highlight hl-ipython3"><pre><span class="n">weather</span><span class="o">.</span><span class="n">describe</span><span class="p">()</span>
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