Comparison with SAS

For potential users coming from SAS this page is meant to demonstrate how different SAS operations would be performed in pandas.

If you’re new to pandas, you might want to first read through 10 Minutes to pandas to familiarize yourself with the library.

As is customary, we import pandas and numpy as follows:

In [1]: import pandas as pd

In [2]: import numpy as np

Note

Throughout this tutorial, the pandas DataFrame will be displayed by calling df.head(), which displays the first N (default 5) rows of the DataFrame. This is often used in interactive work (e.g. Jupyter notebook or terminal) - the equivalent in SAS would be:

proc print data=df(obs=5);
run;

Data Structures

General Terminology Translation

pandas SAS
DataFrame data set
column variable
row observation
groupby BY-group
NaN .

DataFrame / Series

A DataFrame in pandas is analogous to a SAS data set - a two-dimensional data source with labeled columns that can be of different types. As will be shown in this document, almost any operation that can be applied to a data set using SAS’s DATA step, can also be accomplished in pandas.

A Series is the data structure that represents one column of a DataFrame. SAS doesn’t have a separate data structure for a single column, but in general, working with a Series is analogous to referencing a column in the DATA step.

Index

Every DataFrame and Series has an Index - which are labels on the rows of the data. SAS does not have an exactly analogous concept. A data set’s row are essentially unlabeled, other than an implicit integer index that can be accessed during the DATA step (_N_).

In pandas, if no index is specified, an integer index is also used by default (first row = 0, second row = 1, and so on). While using a labeled Index or MultiIndex can enable sophisticated analyses and is ultimately an important part of pandas to understand, for this comparison we will essentially ignore the Index and just treat the DataFrame as a collection of columns. Please see the indexing documentation for much more on how to use an Index effectively.

Data Input / Output

Constructing a DataFrame from Values

A SAS data set can be built from specified values by placing the data after a datalines statement and specifying the column names.

data df;
    input x y;
    datalines;
    1 2
    3 4
    5 6
    ;
run;

A pandas DataFrame can be constructed in many different ways, but for a small number of values, it is often convenient to specify it as a python dictionary, where the keys are the column names and the values are the data.

In [3]: df = pd.DataFrame({
   ...:           'x': [1, 3, 5],
   ...:           'y': [2, 4, 6]})
   ...: 

In [4]: df
Out[4]: 
   x  y
0  1  2
1  3  4
2  5  6

Reading External Data

Like SAS, pandas provides utilities for reading in data from many formats. The tips dataset, found within the pandas tests (csv) will be used in many of the following examples.

SAS provides PROC IMPORT to read csv data into a data set.

proc import datafile='tips.csv' dbms=csv out=tips replace;
    getnames=yes;
run;

The pandas method is read_csv(), which works similarly.

In [5]: url = 'https://raw.github.com/pandas-dev/pandas/master/pandas/tests/data/tips.csv'

In [6]: tips = pd.read_csv(url)

URLErrorTraceback (most recent call last)
<ipython-input-6-eb7031f85b0e> in <module>()
----> 1 tips = pd.read_csv(url)

/build/pandas-7ugdL0/pandas-0.19.2/debian/python-pandas/usr/lib/python2.7/dist-packages/pandas/io/parsers.pyc in parser_f(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, escapechar, comment, encoding, dialect, tupleize_cols, error_bad_lines, warn_bad_lines, skipfooter, skip_footer, doublequote, delim_whitespace, as_recarray, compact_ints, use_unsigned, low_memory, buffer_lines, memory_map, float_precision)
    644                     skip_blank_lines=skip_blank_lines)
    645 
--> 646         return _read(filepath_or_buffer, kwds)
    647 
    648     parser_f.__name__ = name

/build/pandas-7ugdL0/pandas-0.19.2/debian/python-pandas/usr/lib/python2.7/dist-packages/pandas/io/parsers.pyc in _read(filepath_or_buffer, kwds)
    373     filepath_or_buffer, _, compression = get_filepath_or_buffer(
    374         filepath_or_buffer, encoding,
--> 375         compression=kwds.get('compression', None))
    376     kwds['compression'] = (inferred_compression if compression == 'infer'
    377                            else compression)

/build/pandas-7ugdL0/pandas-0.19.2/debian/python-pandas/usr/lib/python2.7/dist-packages/pandas/io/common.pyc in get_filepath_or_buffer(filepath_or_buffer, encoding, compression)
    236 
    237     if _is_url(filepath_or_buffer):
--> 238         req = _urlopen(str(filepath_or_buffer))
    239         if compression == 'infer':
    240             content_encoding = req.headers.get('Content-Encoding', None)

/usr/lib/python2.7/urllib2.pyc in urlopen(url, data, timeout, cafile, capath, cadefault, context)
    152     else:
    153         opener = _opener
--> 154     return opener.open(url, data, timeout)
    155 
    156 def install_opener(opener):

/usr/lib/python2.7/urllib2.pyc in open(self, fullurl, data, timeout)
    427             req = meth(req)
    428 
--> 429         response = self._open(req, data)
    430 
    431         # post-process response

/usr/lib/python2.7/urllib2.pyc in _open(self, req, data)
    445         protocol = req.get_type()
    446         result = self._call_chain(self.handle_open, protocol, protocol +
--> 447                                   '_open', req)
    448         if result:
    449             return result

/usr/lib/python2.7/urllib2.pyc in _call_chain(self, chain, kind, meth_name, *args)
    405             func = getattr(handler, meth_name)
    406 
--> 407             result = func(*args)
    408             if result is not None:
    409                 return result

/usr/lib/python2.7/urllib2.pyc in https_open(self, req)
   1239         def https_open(self, req):
   1240             return self.do_open(httplib.HTTPSConnection, req,
-> 1241                 context=self._context)
   1242 
   1243         https_request = AbstractHTTPHandler.do_request_

/usr/lib/python2.7/urllib2.pyc in do_open(self, http_class, req, **http_conn_args)
   1196         except socket.error, err: # XXX what error?
   1197             h.close()
-> 1198             raise URLError(err)
   1199         else:
   1200             try:

URLError: <urlopen error [Errno 111] Connection refused>

In [7]: tips.head()

NameErrorTraceback (most recent call last)
<ipython-input-7-9b5f9fb19d63> in <module>()
----> 1 tips.head()

NameError: name 'tips' is not defined

Like PROC IMPORT, read_csv can take a number of parameters to specify how the data should be parsed. For example, if the data was instead tab delimited, and did not have column names, the pandas command would be:

tips = pd.read_csv('tips.csv', sep='\t', header=None)

# alternatively, read_table is an alias to read_csv with tab delimiter
tips = pd.read_table('tips.csv', header=None)

In addition to text/csv, pandas supports a variety of other data formats such as Excel, HDF5, and SQL databases. These are all read via a pd.read_* function. See the IO documentation for more details.

Exporting Data

The inverse of PROC IMPORT in SAS is PROC EXPORT

proc export data=tips outfile='tips2.csv' dbms=csv;
run;

Similarly in pandas, the opposite of read_csv is to_csv(), and other data formats follow a similar api.

tips.to_csv('tips2.csv')

Data Operations

Operations on Columns

In the DATA step, arbitrary math expressions can be used on new or existing columns.

data tips;
    set tips;
    total_bill = total_bill - 2;
    new_bill = total_bill / 2;
run;

pandas provides similar vectorized operations by specifying the individual Series in the DataFrame. New columns can be assigned in the same way.

In [8]: tips['total_bill'] = tips['total_bill'] - 2

NameErrorTraceback (most recent call last)
<ipython-input-8-99eac591b314> in <module>()
----> 1 tips['total_bill'] = tips['total_bill'] - 2

NameError: name 'tips' is not defined

In [9]: tips['new_bill'] = tips['total_bill'] / 2.0

NameErrorTraceback (most recent call last)
<ipython-input-9-66d9d3f6fc9d> in <module>()
----> 1 tips['new_bill'] = tips['total_bill'] / 2.0

NameError: name 'tips' is not defined

In [10]: tips.head()

NameErrorTraceback (most recent call last)
<ipython-input-10-9b5f9fb19d63> in <module>()
----> 1 tips.head()

NameError: name 'tips' is not defined

Filtering

Filtering in SAS is done with an if or where statement, on one or more columns.

data tips;
    set tips;
    if total_bill > 10;
run;

data tips;
    set tips;
    where total_bill > 10;
    /* equivalent in this case - where happens before the
       DATA step begins and can also be used in PROC statements */
run;

DataFrames can be filtered in multiple ways; the most intuitive of which is using boolean indexing

In [11]: tips[tips['total_bill'] > 10].head()

NameErrorTraceback (most recent call last)
<ipython-input-11-da383754b0cf> in <module>()
----> 1 tips[tips['total_bill'] > 10].head()

NameError: name 'tips' is not defined

If/Then Logic

In SAS, if/then logic can be used to create new columns.

data tips;
    set tips;
    format bucket $4.;

    if total_bill < 10 then bucket = 'low';
    else bucket = 'high';
run;

The same operation in pandas can be accomplished using the where method from numpy.

In [12]: tips['bucket'] = np.where(tips['total_bill'] < 10, 'low', 'high')

NameErrorTraceback (most recent call last)
<ipython-input-12-496f2fc45c1b> in <module>()
----> 1 tips['bucket'] = np.where(tips['total_bill'] < 10, 'low', 'high')

NameError: name 'tips' is not defined

In [13]: tips.head()

NameErrorTraceback (most recent call last)
<ipython-input-13-9b5f9fb19d63> in <module>()
----> 1 tips.head()

NameError: name 'tips' is not defined

Date Functionality

SAS provides a variety of functions to do operations on date/datetime columns.

data tips;
    set tips;
    format date1 date2 date1_plusmonth mmddyy10.;
    date1 = mdy(1, 15, 2013);
    date2 = mdy(2, 15, 2015);
    date1_year = year(date1);
    date2_month = month(date2);
    * shift date to beginning of next interval;
    date1_next = intnx('MONTH', date1, 1);
    * count intervals between dates;
    months_between = intck('MONTH', date1, date2);
run;

The equivalent pandas operations are shown below. In addition to these functions pandas supports other Time Series features not available in Base SAS (such as resampling and and custom offsets) - see the timeseries documentation for more details.

In [14]: tips['date1'] = pd.Timestamp('2013-01-15')

NameErrorTraceback (most recent call last)
<ipython-input-14-b3452c22a4d8> in <module>()
----> 1 tips['date1'] = pd.Timestamp('2013-01-15')

NameError: name 'tips' is not defined

In [15]: tips['date2'] = pd.Timestamp('2015-02-15')

NameErrorTraceback (most recent call last)
<ipython-input-15-7cc1a1a8c40a> in <module>()
----> 1 tips['date2'] = pd.Timestamp('2015-02-15')

NameError: name 'tips' is not defined

In [16]: tips['date1_year'] = tips['date1'].dt.year

NameErrorTraceback (most recent call last)
<ipython-input-16-cfc1ce15858c> in <module>()
----> 1 tips['date1_year'] = tips['date1'].dt.year

NameError: name 'tips' is not defined

In [17]: tips['date2_month'] = tips['date2'].dt.month

NameErrorTraceback (most recent call last)
<ipython-input-17-3f13318c9e1e> in <module>()
----> 1 tips['date2_month'] = tips['date2'].dt.month

NameError: name 'tips' is not defined

In [18]: tips['date1_next'] = tips['date1'] + pd.offsets.MonthBegin()

NameErrorTraceback (most recent call last)
<ipython-input-18-ec7a37674786> in <module>()
----> 1 tips['date1_next'] = tips['date1'] + pd.offsets.MonthBegin()

NameError: name 'tips' is not defined

In [19]: tips['months_between'] = (tips['date2'].dt.to_period('M') -
   ....:                           tips['date1'].dt.to_period('M'))
   ....: 

NameErrorTraceback (most recent call last)
<ipython-input-19-fa3eb7557d9c> in <module>()
----> 1 tips['months_between'] = (tips['date2'].dt.to_period('M') -
      2                           tips['date1'].dt.to_period('M'))

NameError: name 'tips' is not defined

In [20]: tips[['date1','date2','date1_year','date2_month',
   ....:       'date1_next','months_between']].head()
   ....: 

NameErrorTraceback (most recent call last)
<ipython-input-20-63ecc82db826> in <module>()
----> 1 tips[['date1','date2','date1_year','date2_month',
      2       'date1_next','months_between']].head()

NameError: name 'tips' is not defined

Selection of Columns

SAS provides keywords in the DATA step to select, drop, and rename columns.

data tips;
    set tips;
    keep sex total_bill tip;
run;

data tips;
    set tips;
    drop sex;
run;

data tips;
    set tips;
    rename total_bill=total_bill_2;
run;

The same operations are expressed in pandas below.

# keep
In [21]: tips[['sex', 'total_bill', 'tip']].head()

NameErrorTraceback (most recent call last)
<ipython-input-21-5d3e68507f85> in <module>()
----> 1 tips[['sex', 'total_bill', 'tip']].head()

NameError: name 'tips' is not defined

# drop
In [22]: tips.drop('sex', axis=1).head()

NameErrorTraceback (most recent call last)
<ipython-input-22-92fb22b07591> in <module>()
----> 1 tips.drop('sex', axis=1).head()

NameError: name 'tips' is not defined

# rename
In [23]: tips.rename(columns={'total_bill':'total_bill_2'}).head()

NameErrorTraceback (most recent call last)
<ipython-input-23-fc43878ab5b8> in <module>()
----> 1 tips.rename(columns={'total_bill':'total_bill_2'}).head()

NameError: name 'tips' is not defined

Sorting by Values

Sorting in SAS is accomplished via PROC SORT

proc sort data=tips;
    by sex total_bill;
run;

pandas objects have a sort_values() method, which takes a list of columns to sort by.

In [24]: tips = tips.sort_values(['sex', 'total_bill'])

NameErrorTraceback (most recent call last)
<ipython-input-24-5de00c1749a0> in <module>()
----> 1 tips = tips.sort_values(['sex', 'total_bill'])

NameError: name 'tips' is not defined

In [25]: tips.head()

NameErrorTraceback (most recent call last)
<ipython-input-25-9b5f9fb19d63> in <module>()
----> 1 tips.head()

NameError: name 'tips' is not defined

Merging

The following tables will be used in the merge examples

In [26]: df1 = pd.DataFrame({'key': ['A', 'B', 'C', 'D'],
   ....:                     'value': np.random.randn(4)})
   ....: 

In [27]: df1
Out[27]: 
  key     value
0   A -0.857326
1   B  1.075416
2   C  0.371727
3   D  1.065735

In [28]: df2 = pd.DataFrame({'key': ['B', 'D', 'D', 'E'],
   ....:                      'value': np.random.randn(4)})
   ....: 

In [29]: df2
Out[29]: 
  key     value
0   B -0.227314
1   D  2.102726
2   D -0.092796
3   E  0.094694

In SAS, data must be explicitly sorted before merging. Different types of joins are accomplished using the in= dummy variables to track whether a match was found in one or both input frames.

proc sort data=df1;
    by key;
run;

proc sort data=df2;
    by key;
run;

data left_join inner_join right_join outer_join;
    merge df1(in=a) df2(in=b);

    if a and b then output inner_join;
    if a then output left_join;
    if b then output right_join;
    if a or b then output outer_join;
run;

pandas DataFrames have a merge() method, which provides similar functionality. Note that the data does not have to be sorted ahead of time, and different join types are accomplished via the how keyword.

In [30]: inner_join = df1.merge(df2, on=['key'], how='inner')

In [31]: inner_join
Out[31]: 
  key   value_x   value_y
0   B  1.075416 -0.227314
1   D  1.065735  2.102726
2   D  1.065735 -0.092796

In [32]: left_join = df1.merge(df2, on=['key'], how='left')

In [33]: left_join
Out[33]: 
  key   value_x   value_y
0   A -0.857326       NaN
1   B  1.075416 -0.227314
2   C  0.371727       NaN
3   D  1.065735  2.102726
4   D  1.065735 -0.092796

In [34]: right_join = df1.merge(df2, on=['key'], how='right')

In [35]: right_join
Out[35]: 
  key   value_x   value_y
0   B  1.075416 -0.227314
1   D  1.065735  2.102726
2   D  1.065735 -0.092796
3   E       NaN  0.094694

In [36]: outer_join = df1.merge(df2, on=['key'], how='outer')

In [37]: outer_join
Out[37]: 
  key   value_x   value_y
0   A -0.857326       NaN
1   B  1.075416 -0.227314
2   C  0.371727       NaN
3   D  1.065735  2.102726
4   D  1.065735 -0.092796
5   E       NaN  0.094694

Missing Data

Like SAS, pandas has a representation for missing data - which is the special float value NaN (not a number). Many of the semantics are the same, for example missing data propagates through numeric operations, and is ignored by default for aggregations.

In [38]: outer_join
Out[38]: 
  key   value_x   value_y
0   A -0.857326       NaN
1   B  1.075416 -0.227314
2   C  0.371727       NaN
3   D  1.065735  2.102726
4   D  1.065735 -0.092796
5   E       NaN  0.094694

In [39]: outer_join['value_x'] + outer_join['value_y']
Out[39]: 
0         NaN
1    0.848102
2         NaN
3    3.168461
4    0.972939
5         NaN
dtype: float64

In [40]: outer_join['value_x'].sum()
Out[40]: 2.7212865354426201

One difference is that missing data cannot be compared to its sentinel value. For example, in SAS you could do this to filter missing values.

data outer_join_nulls;
    set outer_join;
    if value_x = .;
run;

data outer_join_no_nulls;
    set outer_join;
    if value_x ^= .;
run;

Which doesn’t work in in pandas. Instead, the pd.isnull or pd.notnull functions should be used for comparisons.

In [41]: outer_join[pd.isnull(outer_join['value_x'])]
Out[41]: 
  key  value_x   value_y
5   E      NaN  0.094694

In [42]: outer_join[pd.notnull(outer_join['value_x'])]
Out[42]: 
  key   value_x   value_y
0   A -0.857326       NaN
1   B  1.075416 -0.227314
2   C  0.371727       NaN
3   D  1.065735  2.102726
4   D  1.065735 -0.092796

pandas also provides a variety of methods to work with missing data - some of which would be challenging to express in SAS. For example, there are methods to drop all rows with any missing values, replacing missing values with a specified value, like the mean, or forward filling from previous rows. See the missing data documentation for more.

In [43]: outer_join.dropna()
Out[43]: 
  key   value_x   value_y
1   B  1.075416 -0.227314
3   D  1.065735  2.102726
4   D  1.065735 -0.092796

In [44]: outer_join.fillna(method='ffill')
Out[44]: 
  key   value_x   value_y
0   A -0.857326       NaN
1   B  1.075416 -0.227314
2   C  0.371727 -0.227314
3   D  1.065735  2.102726
4   D  1.065735 -0.092796
5   E  1.065735  0.094694

In [45]: outer_join['value_x'].fillna(outer_join['value_x'].mean())
Out[45]: 
0   -0.857326
1    1.075416
2    0.371727
3    1.065735
4    1.065735
5    0.544257
Name: value_x, dtype: float64

GroupBy

Aggregation

SAS’s PROC SUMMARY can be used to group by one or more key variables and compute aggregations on numeric columns.

proc summary data=tips nway;
    class sex smoker;
    var total_bill tip;
    output out=tips_summed sum=;
run;

pandas provides a flexible groupby mechanism that allows similar aggregations. See the groupby documentation for more details and examples.

In [46]: tips_summed = tips.groupby(['sex', 'smoker'])['total_bill', 'tip'].sum()

NameErrorTraceback (most recent call last)
<ipython-input-46-28c41a97a164> in <module>()
----> 1 tips_summed = tips.groupby(['sex', 'smoker'])['total_bill', 'tip'].sum()

NameError: name 'tips' is not defined

In [47]: tips_summed.head()

NameErrorTraceback (most recent call last)
<ipython-input-47-ea803183022e> in <module>()
----> 1 tips_summed.head()

NameError: name 'tips_summed' is not defined

Transformation

In SAS, if the group aggregations need to be used with the original frame, it must be merged back together. For example, to subtract the mean for each observation by smoker group.

proc summary data=tips missing nway;
    class smoker;
    var total_bill;
    output out=smoker_means mean(total_bill)=group_bill;
run;

proc sort data=tips;
    by smoker;
run;

data tips;
    merge tips(in=a) smoker_means(in=b);
    by smoker;
    adj_total_bill = total_bill - group_bill;
    if a and b;
run;

pandas groubpy provides a transform mechanism that allows these type of operations to be succinctly expressed in one operation.

In [48]: gb = tips.groupby('smoker')['total_bill']

NameErrorTraceback (most recent call last)
<ipython-input-48-edc8dc704df9> in <module>()
----> 1 gb = tips.groupby('smoker')['total_bill']

NameError: name 'tips' is not defined

In [49]: tips['adj_total_bill'] = tips['total_bill'] - gb.transform('mean')

NameErrorTraceback (most recent call last)
<ipython-input-49-a4e612bdef86> in <module>()
----> 1 tips['adj_total_bill'] = tips['total_bill'] - gb.transform('mean')

NameError: name 'tips' is not defined

In [50]: tips.head()

NameErrorTraceback (most recent call last)
<ipython-input-50-9b5f9fb19d63> in <module>()
----> 1 tips.head()

NameError: name 'tips' is not defined

By Group Processing

In addition to aggregation, pandas groupby can be used to replicate most other by group processing from SAS. For example, this DATA step reads the data by sex/smoker group and filters to the first entry for each.

proc sort data=tips;
   by sex smoker;
run;

data tips_first;
    set tips;
    by sex smoker;
    if FIRST.sex or FIRST.smoker then output;
run;

In pandas this would be written as:

In [51]: tips.groupby(['sex','smoker']).first()

NameErrorTraceback (most recent call last)
<ipython-input-51-ec794b6abf5a> in <module>()
----> 1 tips.groupby(['sex','smoker']).first()

NameError: name 'tips' is not defined

Other Considerations

Disk vs Memory

pandas operates exclusively in memory, where a SAS data set exists on disk. This means that the size of data able to be loaded in pandas is limited by your machine’s memory, but also that the operations on that data may be faster.

If out of core processing is needed, one possibility is the dask.dataframe library (currently in development) which provides a subset of pandas functionality for an on-disk DataFrame

Data Interop

pandas provides a read_sas() method that can read SAS data saved in the XPORT format. The ability to read SAS’s binary format is planned for a future release.

libname xportout xport 'transport-file.xpt';
data xportout.tips;
    set tips(rename=(total_bill=tbill));
    * xport variable names limited to 6 characters;
run;
df = pd.read_sas('transport-file.xpt')

XPORT is a relatively limited format and the parsing of it is not as optimized as some of the other pandas readers. An alternative way to interop data between SAS and pandas is to serialize to csv.

# version 0.17, 10M rows

In [8]: %time df = pd.read_sas('big.xpt')
Wall time: 14.6 s

In [9]: %time df = pd.read_csv('big.csv')
Wall time: 4.86 s
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