Getting started

This very simple case-study is designed to get you up-and-running quickly with statsmodels. Starting from raw data, we will show the steps needed to estimate a statistical model and to draw a diagnostic plot. We will only use functions provided by statsmodels or its pandas and patsy dependencies.

Loading modules and functions

After installing statsmodels and its dependencies, we load a few modules and functions:

In [1]: import statsmodels.api as sm

In [2]: import pandas

In [3]: from patsy import dmatrices

pandas builds on numpy arrays to provide rich data structures and data analysis tools. The pandas.DataFrame function provides labelled arrays of (potentially heterogenous) data, similar to the R “data.frame”. The pandas.read_csv function can be used to convert a comma-separated values file to a DataFrame object.

patsy is a Python library for describing statistical models and building Design Matrices using R-like formulas.

Data

We download the Guerry dataset, a collection of historical data used in support of Andre-Michel Guerry’s 1833 Essay on the Moral Statistics of France. The data set is hosted online in comma-separated values format (CSV) by the Rdatasets repository. We could download the file locally and then load it using read_csv, but pandas takes care of all of this automatically for us:

In [4]: df = sm.datasets.get_rdataset("Guerry", "HistData", cache=True).data
---------------------------------------------------------------------------
gaierror                                  Traceback (most recent call last)
/usr/lib/python3.5/urllib/request.py in do_open(self, http_class, req, **http_conn_args)
   1253             try:
-> 1254                 h.request(req.get_method(), req.selector, req.data, headers)
   1255             except OSError as err: # timeout error

/usr/lib/python3.5/http/client.py in request(self, method, url, body, headers)
   1106         """Send a complete request to the server."""
-> 1107         self._send_request(method, url, body, headers)
   1108 

/usr/lib/python3.5/http/client.py in _send_request(self, method, url, body, headers)
   1151             body = _encode(body, 'body')
-> 1152         self.endheaders(body)
   1153 

/usr/lib/python3.5/http/client.py in endheaders(self, message_body)
   1102             raise CannotSendHeader()
-> 1103         self._send_output(message_body)
   1104 

/usr/lib/python3.5/http/client.py in _send_output(self, message_body)
    933 
--> 934         self.send(msg)
    935         if message_body is not None:

/usr/lib/python3.5/http/client.py in send(self, data)
    876             if self.auto_open:
--> 877                 self.connect()
    878             else:

/usr/lib/python3.5/http/client.py in connect(self)
   1252 
-> 1253             super().connect()
   1254 

/usr/lib/python3.5/http/client.py in connect(self)
    848         self.sock = self._create_connection(
--> 849             (self.host,self.port), self.timeout, self.source_address)
    850         self.sock.setsockopt(socket.IPPROTO_TCP, socket.TCP_NODELAY, 1)

/usr/lib/python3.5/socket.py in create_connection(address, timeout, source_address)
    693     err = None
--> 694     for res in getaddrinfo(host, port, 0, SOCK_STREAM):
    695         af, socktype, proto, canonname, sa = res

/usr/lib/python3.5/socket.py in getaddrinfo(host, port, family, type, proto, flags)
    732     addrlist = []
--> 733     for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
    734         af, socktype, proto, canonname, sa = res

gaierror: [Errno -3] Temporary failure in name resolution

During handling of the above exception, another exception occurred:

URLError                                  Traceback (most recent call last)
<ipython-input-4-8c6e29b11c8f> in <module>()
----> 1 df = sm.datasets.get_rdataset("Guerry", "HistData", cache=True).data

/build/statsmodels-0.8.0/.pybuild/pythonX.Y_3.5/build/statsmodels/datasets/utils.py in get_rdataset(dataname, package, cache)
    288                      "master/doc/"+package+"/rst/")
    289     cache = _get_cache(cache)
--> 290     data, from_cache = _get_data(data_base_url, dataname, cache)
    291     data = read_csv(data, index_col=0)
    292     data = _maybe_reset_index(data)

/build/statsmodels-0.8.0/.pybuild/pythonX.Y_3.5/build/statsmodels/datasets/utils.py in _get_data(base_url, dataname, cache, extension)
    219     url = base_url + (dataname + ".%s") % extension
    220     try:
--> 221         data, from_cache = _urlopen_cached(url, cache)
    222     except HTTPError as err:
    223         if '404' in str(err):

/build/statsmodels-0.8.0/.pybuild/pythonX.Y_3.5/build/statsmodels/datasets/utils.py in _urlopen_cached(url, cache)
    210     # not using the cache or didn't find it in cache
    211     if not from_cache:
--> 212         data = urlopen(url).read()
    213         if cache is not None:  # then put it in the cache
    214             _cache_it(data, cache_path)

/usr/lib/python3.5/urllib/request.py in urlopen(url, data, timeout, cafile, capath, cadefault, context)
    161     else:
    162         opener = _opener
--> 163     return opener.open(url, data, timeout)
    164 
    165 def install_opener(opener):

/usr/lib/python3.5/urllib/request.py in open(self, fullurl, data, timeout)
    464             req = meth(req)
    465 
--> 466         response = self._open(req, data)
    467 
    468         # post-process response

/usr/lib/python3.5/urllib/request.py in _open(self, req, data)
    482         protocol = req.type
    483         result = self._call_chain(self.handle_open, protocol, protocol +
--> 484                                   '_open', req)
    485         if result:
    486             return result

/usr/lib/python3.5/urllib/request.py in _call_chain(self, chain, kind, meth_name, *args)
    442         for handler in handlers:
    443             func = getattr(handler, meth_name)
--> 444             result = func(*args)
    445             if result is not None:
    446                 return result

/usr/lib/python3.5/urllib/request.py in https_open(self, req)
   1295         def https_open(self, req):
   1296             return self.do_open(http.client.HTTPSConnection, req,
-> 1297                 context=self._context, check_hostname=self._check_hostname)
   1298 
   1299         https_request = AbstractHTTPHandler.do_request_

/usr/lib/python3.5/urllib/request.py in do_open(self, http_class, req, **http_conn_args)
   1254                 h.request(req.get_method(), req.selector, req.data, headers)
   1255             except OSError as err: # timeout error
-> 1256                 raise URLError(err)
   1257             r = h.getresponse()
   1258         except:

URLError: <urlopen error [Errno -3] Temporary failure in name resolution>

The Input/Output doc page shows how to import from various other formats.

We select the variables of interest and look at the bottom 5 rows:

In [5]: vars = ['Department', 'Lottery', 'Literacy', 'Wealth', 'Region']

In [6]: df = df[vars]
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-6-97b909d2ba47> in <module>()
----> 1 df = df[vars]

NameError: name 'df' is not defined

In [7]: df[-5:]
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-7-387a2dedaa82> in <module>()
----> 1 df[-5:]

NameError: name 'df' is not defined

Notice that there is one missing observation in the Region column. We eliminate it using a DataFrame method provided by pandas:

In [8]: df = df.dropna()
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-8-c783d194b823> in <module>()
----> 1 df = df.dropna()

NameError: name 'df' is not defined

In [9]: df[-5:]
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-9-387a2dedaa82> in <module>()
----> 1 df[-5:]

NameError: name 'df' is not defined

Substantive motivation and model

We want to know whether literacy rates in the 86 French departments are associated with per capita wagers on the Royal Lottery in the 1820s. We need to control for the level of wealth in each department, and we also want to include a series of dummy variables on the right-hand side of our regression equation to control for unobserved heterogeneity due to regional effects. The model is estimated using ordinary least squares regression (OLS).

Design matrices (endog & exog)

To fit most of the models covered by statsmodels, you will need to create two design matrices. The first is a matrix of endogenous variable(s) (i.e. dependent, response, regressand, etc.). The second is a matrix of exogenous variable(s) (i.e. independent, predictor, regressor, etc.). The OLS coefficient estimates are calculated as usual:

\hat{\beta} = (X'X)^{-1} X'y

where y is an N \times 1 column of data on lottery wagers per capita (Lottery). X is N \times 7 with an intercept, the Literacy and Wealth variables, and 4 region binary variables.

The patsy module provides a convenient function to prepare design matrices using R-like formulas. You can find more information here: http://patsy.readthedocs.org

We use patsy’s dmatrices function to create design matrices:

In [10]: y, X = dmatrices('Lottery ~ Literacy + Wealth + Region', data=df, return_type='dataframe')
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-10-b205df6907aa> in <module>()
----> 1 y, X = dmatrices('Lottery ~ Literacy + Wealth + Region', data=df, return_type='dataframe')

NameError: name 'df' is not defined

The resulting matrices/data frames look like this:

In [11]: y[:3]
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-11-319cfe32a629> in <module>()
----> 1 y[:3]

NameError: name 'y' is not defined

In [12]: X[:3]
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-12-a0b703194835> in <module>()
----> 1 X[:3]

NameError: name 'X' is not defined

Notice that dmatrices has

  • split the categorical Region variable into a set of indicator variables.
  • added a constant to the exogenous regressors matrix.
  • returned pandas DataFrames instead of simple numpy arrays. This is useful because DataFrames allow statsmodels to carry-over meta-data (e.g. variable names) when reporting results.

The above behavior can of course be altered. See the patsy doc pages.

Model fit and summary

Fitting a model in statsmodels typically involves 3 easy steps:

  1. Use the model class to describe the model
  2. Fit the model using a class method
  3. Inspect the results using a summary method

For OLS, this is achieved by:

In [13]: mod = sm.OLS(y, X)    # Describe model
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-13-c6e56946df97> in <module>()
----> 1 mod = sm.OLS(y, X)    # Describe model

NameError: name 'y' is not defined

In [14]: res = mod.fit()       # Fit model
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-14-6ff53364a7be> in <module>()
----> 1 res = mod.fit()       # Fit model

NameError: name 'mod' is not defined

In [15]: print res.summary()   # Summarize model
  File "<ipython-input-15-6ef19fe76b73>", line 1
    print res.summary()   # Summarize model
            ^
SyntaxError: invalid syntax

The res object has many useful attributes. For example, we can extract parameter estimates and r-squared by typing:

In [16]: res.params
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-16-cdb8a4b8734e> in <module>()
----> 1 res.params

NameError: name 'res' is not defined

In [17]: res.rsquared
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-17-375327da2eb6> in <module>()
----> 1 res.rsquared

NameError: name 'res' is not defined

Type dir(res) for a full list of attributes.

For more information and examples, see the Regression doc page

Diagnostics and specification tests

statsmodels allows you to conduct a range of useful regression diagnostics and specification tests. For instance, apply the Rainbow test for linearity (the null hypothesis is that the relationship is properly modelled as linear):

In [18]: sm.stats.linear_rainbow(res)
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-18-d01346ddcfd4> in <module>()
----> 1 sm.stats.linear_rainbow(res)

NameError: name 'res' is not defined

Admittedly, the output produced above is not very verbose, but we know from reading the docstring (also, print sm.stats.linear_rainbow.__doc__) that the first number is an F-statistic and that the second is the p-value.

statsmodels also provides graphics functions. For example, we can draw a plot of partial regression for a set of regressors by:

In [19]: sm.graphics.plot_partregress('Lottery', 'Wealth', ['Region', 'Literacy'],
   ....:                              data=df, obs_labels=False)
   ....: 
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-19-e6a287f2a415> in <module>()
      1 sm.graphics.plot_partregress('Lottery', 'Wealth', ['Region', 'Literacy'],
----> 2                              data=df, obs_labels=False)

NameError: name 'df' is not defined
_images/gettingstarted_0.png

More

Congratulations! You’re ready to move on to other topics in the Table of Contents