Data Frame in Python

Exploring some Python Packages and R packages to move /work with both Python and R without melting your brain or exceeding your project deadline

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If you liked the data.frame structure in R, you have some way to work with them at a faster processing speed in Python.

Here are three packages that enable you to do so-

(1) pydataframe http://code.google.com/p/pydataframe/

An implemention of an almost R like DataFrame object. (install via Pypi/Pip: “pip install pydataframe”)

Usage:

        u = DataFrame( { "Field1": [1, 2, 3],
                        "Field2": ['abc', 'def', 'hgi']},
                        optional:
                         ['Field1', 'Field2']
                         ["rowOne", "rowTwo", "thirdRow"])

A DataFrame is basically a table with rows and columns.

Columns are named, rows are numbered (but can be named) and can be easily selected and calculated upon. Internally, columns are stored as 1d numpy arrays. If you set row names, they’re converted into a dictionary for fast access. There is a rich subselection/slicing API, see help(DataFrame.get_item) (it also works for setting values). Please note that any slice get’s you another DataFrame, to access individual entries use get_row(), get_column(), get_value().

DataFrames also understand basic arithmetic and you can either add (multiply,…) a constant value, or another DataFrame of the same size / with the same column names, like this:

#multiply every value in ColumnA that is smaller than 5 by 6.
my_df[my_df[:,'ColumnA'] < 5, 'ColumnA'] *= 6

#you always need to specify both row and column selectors, use : to mean everything
my_df[:, 'ColumnB'] = my_df[:,'ColumnA'] + my_df[:, 'ColumnC']

#let's take every row that starts with Shu in ColumnA and replace it with a new list (comprehension)
select = my_df.where(lambda row: row['ColumnA'].startswith('Shu'))
my_df[select, 'ColumnA'] = [row['ColumnA'].replace('Shu', 'Sha') for row in my_df[select,:].iter_rows()]

Dataframes talk directly to R via rpy2 (rpy2 is not a prerequiste for the library!)

 

(2) pandas http://pandas.pydata.org/

Library Highlights

  • A fast and efficient DataFrame object for data manipulation with integrated indexing;
  • Tools for reading and writing data between in-memory data structures and different formats: CSV and text files, Microsoft Excel, SQL databases, and the fast HDF5 format;
  • Intelligent data alignment and integrated handling of missing data: gain automatic label-based alignment in computations and easily manipulate messy data into an orderly form;
  • Flexible reshaping and pivoting of data sets;
  • Intelligent label-based slicing, fancy indexing, and subsetting of large data sets;
  • Columns can be inserted and deleted from data structures for size mutability;
  • Aggregating or transforming data with a powerful group by engine allowing split-apply-combine operations on data sets;
  • High performance merging and joining of data sets;
  • Hierarchical axis indexing provides an intuitive way of working with high-dimensional data in a lower-dimensional data structure;
  • Time series-functionality: date range generation and frequency conversion, moving window statistics, moving window linear regressions, date shifting and lagging. Even create domain-specific time offsets and join time series without losing data;
  • The library has been ruthlessly optimized for performance, with critical code paths compiled to C;
  • Python with pandas is in use in a wide variety of academic and commercial domains, including Finance, Neuroscience, Economics, Statistics, Advertising, Web Analytics, and more.

Why not R?

First of all, we love open source R! It is the most widely-used open source environment for statistical modeling and graphics, and it provided some early inspiration for pandas features. R users will be pleased to find this library adopts some of the best concepts of R, like the foundational DataFrame (one user familiar with R has described pandas as “R data.frame on steroids”). But pandas also seeks to solve some frustrations common to R users:

  • R has barebones data alignment and indexing functionality, leaving much work to the user. pandas makes it easy and intuitive to work with messy, irregularly indexed data, like time series data. pandas also provides rich tools, like hierarchical indexing, not found in R;
  • R is not well-suited to general purpose programming and system development. pandas enables you to do large-scale data processing seamlessly when developing your production applications;
  • Hybrid systems connecting R to a low-productivity systems language like Java, C++, or C# suffer from significantly reduced agility and maintainability, and you’re still stuck developing the system components in a low-productivity language;
  • The “copyleft” GPL license of R can create concerns for commercial software vendors who want to distribute R with their software under another license. Python and pandas use more permissive licenses.

(3) datamatrix http://pypi.python.org/pypi/datamatrix/0.8

datamatrix 0.8

A Pythonic implementation of R’s data.frame structure.

Latest Version: 0.9

This module allows access to comma- or other delimiter separated files as if they were tables, using a dictionary-like syntax. DataMatrix objects can be manipulated, rows and columns added and removed, or even transposed

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Modeling in Python

Continue reading “Data Frame in Python”

Python with Friends

Wanted to learn Python? Stuck on a desk with no redemption. You have two very lucid options. One is use Google. I mean not the search engine, but their class on learning Python.

The videos are available on Youtube at http://www.youtube.com/user/GoogleDevelopers (starting at http://www.youtube.com/watch?v=tKTZoB2Vjuk&feature=plcp)


http://code.google.com/edu/languages/google-python-class/

The other is new module of Python at code academy. It is truly awesome even if you dont know any programming!

So learn some awesome python today and be an excellent hacker tommorow!

http://www.codecademy.com/tracks/python

#SAS 9.3 and #Rstats 2.13.1 Released

A bit early but the latest editions of both SAS and R were released last week.

SAS 9.3 is clearly a major release with multiple enhancements to make SAS both relevant and pertinent in enterprise software in the age of big data. Also many more R specific, JMP specific and partners like Teradata specific enhancements.

http://support.sas.com/software/93/index.html

Features

Data management

  • Enhanced manageability for improved performance
  • In-database processing (EL-T pushdown)
  • Enhanced performance for loading oracle data
  • New ET-L transforms
  • Data access

Data quality

  • SAS® Data Integration Server includes DataFlux® Data Management Platform for enhanced data quality
  • Master Data Management (DataFlux® qMDM)
    • Provides support for master hub of trusted entity data.

Analytics

  • SAS® Enterprise Miner™
    • New survival analysis predicts when an event will happen, not just if it will happen.
    • New rate making capability for insurance predicts optimal insurance premium for individuals based on attributes known at application time.
    • Time Series Data Mining node (experimental) applies data mining techniques to transactional, time-stamped data.
    • Support Vector Machines node (experimental) provides a supervised machine learning method for prediction and classification.
  • SAS® Forecast Server
    • SAS Forecast Server is integrated with the SAP APO Demand Planning module to provide SAP users with access to a superior forecasting engine and automatic forecasting capabilities.
  • SAS® Model Manager
    • Seamless integration of R models with the ability to register and manage R models in SAS Model Manager.
    • Ability to perform champion/challenger side-by-side comparisons between SAS and R models to see which model performs best for a specific need.
  • SAS/OR® and SAS® Simulation Studio
    • Optimization
    • Simulation
      • Automatic input distribution fitting using JMP with SAS Simulation Studio.

Text analytics

  • SAS® Text Miner
  • SAS® Enterprise Content Categorization
  • SAS® Sentiment Analysis

Scalability and high-performance

  • SAS® Analytics Accelerator for Teradata (new product)
  • SAS® Grid Manager
 and latest from http://www.r-project.org/ I was a bit curious to know why the different licensing for R now (from GPL2 to GPL2- GPL 3)

LICENCE:

No parts of R are now licensed solely under GPL-2. The licences for packages rpart and survival have been changed, which means that the licence terms for R as distributed are GPL-2 | GPL-3.


This is a maintenance release to consolidate various minor fixes to 2.13.0.
CHANGES IN R VERSION 2.13.1:

  NEW FEATURES:

    • iconv() no longer translates NA strings as "NA".

    • persp(box = TRUE) now warns if the surface extends outside the
      box (since occlusion for the box and axes is computed assuming
      the box is a bounding box). (PR#202.)

    • RShowDoc() can now display the licences shipped with R, e.g.
      RShowDoc("GPL-3").

    • New wrapper function showNonASCIIfile() in package tools.

    • nobs() now has a "mle" method in package stats4.

    • trace() now deals correctly with S4 reference classes and
      corresponding reference methods (e.g., $trace()) have been added.

    • xz has been updated to 5.0.3 (very minor bugfix release).

    • tools::compactPDF() gets more compression (usually a little,
      sometimes a lot) by using the compressed object streams of PDF
      1.5.

    • cairo_ps(onefile = TRUE) generates encapsulated EPS on platforms
      with cairo >= 1.6.

    • Binary reads (e.g. by readChar() and readBin()) are now supported
      on clipboard connections.  (Wish of PR#14593.)

    • as.POSIXlt.factor() now passes ... to the character method
      (suggestion of Joshua Ulrich).  [Intended for R 2.13.0 but
      accidentally removed before release.]

    • vector() and its wrappers such as integer() and double() now warn
      if called with a length argument of more than one element.  This
      helps track down user errors such as calling double(x) instead of
      as.double(x).

  INSTALLATION:

    • Building the vignette PDFs in packages grid and utils is now part
      of running make from an SVN checkout on a Unix-alike: a separate
      make vignettes step is no longer required.

      These vignettes are now made with keep.source = TRUE and hence
      will be laid out differently.

    • make install-strip failed under some configuration options.

    • Packages can customize non-standard installation of compiled code
      via a src/install.libs.R script. This allows packages that have
      architecture-specific binaries (beyond the package's shared
      objects/DLLs) to be installed in a multi-architecture setting.

  SWEAVE & VIGNETTES:

    • Sweave() and Stangle() gain an encoding argument to specify the
      encoding of the vignette sources if the latter do not contain a
      \usepackage[]{inputenc} statement specifying a single input
      encoding.

    • There is a new Sweave option figs.only = TRUE to run each figure
      chunk only for each selected graphics device, and not first using
      the default graphics device.  This will become the default in R
      2.14.0.

    • Sweave custom graphics devices can have a custom function
      foo.off() to shut them down.

    • Warnings are issued when non-portable filenames are found for
      graphics files (and chunks if split = TRUE).  Portable names are
      regarded as alphanumeric plus hyphen, underscore, plus and hash
      (periods cause problems with recognizing file extensions).

    • The Rtangle() driver has a new option show.line.nos which is by
      default false; if true it annotates code chunks with a comment
      giving the line number of the first line in the sources (the
      behaviour of R >= 2.12.0).

    • Package installation tangles the vignette sources: this step now
      converts the vignette sources from the vignette/package encoding
      to the current encoding, and records the encoding (if not ASCII)
      in a comment line at the top of the installed .R file.

  DEPRECATED AND DEFUNCT:

    • The internal functions .readRDS() and .saveRDS() are now
      deprecated in favour of the public functions readRDS() and
      saveRDS() introduced in R 2.13.0.

    • Switching off lazy-loading of code _via_ the LazyLoad field of
      the DESCRIPTION file is now deprecated.  In future all packages
      will be lazy-loaded.

    • The off-line help() types "postscript" and "ps" are deprecated.

  UTILITIES:

    • R CMD check on a multi-architecture installation now skips the
      user's .Renviron file for the architecture-specific tests (which
      do read the architecture-specific Renviron.site files).  This is
      consistent with single-architecture checks, which use
      --no-environ.

    • R CMD build now looks for DESCRIPTION fields BuildResaveData and
      BuildKeepEmpty for per-package overrides.  See ‘Writing R
      Extensions’.

  BUG FIXES:

    • plot.lm(which = 5) was intended to order factor levels in
      increasing order of mean standardized residual.  It ordered the
      factor labels correctly, but could plot the wrong group of
      residuals against the label.  (PR#14545)

    • mosaicplot() could clip the factor labels, and could overlap them
      with the cells if a non-default value of cex.axis was used.
      (Related to PR#14550.)

    • dataframe[[row,col]] now dispatches on [[ methods for the
      selected column (spotted by Bill Dunlap).

    • sort.int() would strip the class of an object, but leave its
      object bit set.  (Reported by Bill Dunlap.)

    • pbirthday() and qbirthday() did not implement the algorithm
      exactly as given in their reference and so were unnecessarily
      inaccurate.

      pbirthday() now solves the approximate formula analytically
      rather than using uniroot() on a discontinuous function.

      The description of the problem was inaccurate: the probability is
      a tail probablity (‘2 _or more_ people share a birthday’)

    • Complex arithmetic sometimes warned incorrectly about producing
      NAs when there were NaNs in the input.

    • seek(origin = "current") incorrectly reported it was not
      implemented for a gzfile() connection.

    • c(), unlist(), cbind() and rbind() could silently overflow the
      maximum vector length and cause a segfault.  (PR#14571)

    • The fonts argument to X11(type = "Xlib") was being ignored.

    • Reading (e.g. with readBin()) from a raw connection was not
      advancing the pointer, so successive reads would read the same
      value.  (Spotted by Bill Dunlap.)

    • Parsed text containing embedded newlines was printed incorrectly
      by as.character.srcref().  (Reported by Hadley Wickham.)

    • decompose() used with a series of a non-integer number of periods
      returned a seasonal component shorter than the original series.
      (Reported by Rob Hyndman.)

    • fields = list() failed for setRefClass().  (Reported by Michael
      Lawrence.)

    • Reference classes could not redefine an inherited field which had
      class "ANY". (Reported by Janko Thyson.)

    • Methods that override previously loaded versions will now be
      installed and called.  (Reported by Iago Mosqueira.)

    • addmargins() called numeric(apos) rather than
      numeric(length(apos)).

    • The HTML help search sometimes produced bad links.  (PR#14608)

    • Command completion will no longer be broken if tail.default() is
      redefined by the user. (Problem reported by Henrik Bengtsson.)

    • LaTeX rendering of markup in titles of help pages has been
      improved; in particular, \eqn{} may be used there.

    • isClass() used its own namespace as the default of the where
      argument inadvertently.

    • Rd conversion to latex mis-handled multi-line titles (including
      cases where there was a blank line in the \title section).
Also see this interesting blog
Examples of tasks replicated in SAS and R

Protected: Using SAS and C/C++ together

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PySpread Magic

Python logo
Image via Wikipedia

Just working with PySpread- and worked on a 1 million by 1 million spreadsheet- Python sure looks promising for the way ahead for stat computing ( you need to

sudo apt-get install python-numpy python-rpy python-scipy python-gmpy wxpython*,

cd to the untarred bz2 file from http://pyspread.sourceforge.net/download.html,  (like

:~/Downloads$ cd pyspread-0.1.2

:~/Downloads/pyspread-0.1.2

sudo python setup.py install

)

http://pyspread.sourceforge.net/

by Martin Manns

 

about Pyspread is a cross-platform Python spreadsheet application. It is based on and written in the programming language Python.

Instead of spreadsheet formulas, Python expressions are entered into the spreadsheet cells. Each expression returns a Python object that can be accessed from other cells. These objects can represent anything including lists or matrices.

Pyspread screenshot
features
  • Three dimensional grid with up to 85,899,345 rows and 14,316,555 columns (64 bit systems, depends on row height and column width). Note that a million cells require about 500 MB of memory.
  • Complex data types such as lists, trees or matrices within a single cell.
  • Macros for functionalities that are too complex for a single Python expression.
  • Python module access from each cell, which allows:
    • Arbitrary size rational numbers (via gmpy),
    • Fixed point decimal numbers for business calculations, (via the decimal module from the standard library)
    • Advanced statistics including plotting functions (via RPy)
    • Much more via <your favourite module>.
  • CSV import and export
  • Clipboard access
Pyspread screenshot

warning The concept of pyspread allows doing everything from each cell that a Python script can do. This powerful feature has its drawbacks. A spreadsheet may very well delete your hard drive or send your data via the Internet. Of course this is a non-issue if you sandbox properly or if you only use self developed spreadsheets.

Since this is not the case for everyone (see discussion at lwn.net), a GPG signature based trust model for spreadsheet files has been introduced. It ensures that only your own trusted files are executed on loading. Untrusted files are displayed in safe mode. You can approve a file manually. Inspect carefully.

 

Here comes PySpread- 85,899,345 rows and 14,316,555 columns

A Bold GNU Head
Image via Wikipedia

Whats new/ One more open source analytics package. Built like a spreadsheet with an ability to import a million cells-

From http://pyspread.sourceforge.net/index.html

about Pyspread is a cross-platform Python spreadsheet application. It is based on and written in the programming language Python.

Instead of spreadsheet formulas, Python expressions are entered into the spreadsheet cells. Each expression returns a Python object that can be accessed from other cells. These objects can represent anything including lists or matrices.

Pyspread screenshot
features In pyspread, cells expect Python expressions and return Python objects. Therefore, complex data types such as lists, trees or matrices can be handled within a single cell. Macros can be used for functions that are too complex for a single expression.

Since Python modules can be easily used without external scripts, arbitrary size rational numbers (via gmpy), fixed point decimal numbers for business calculations, (via the decimal module from the standard library) and advanced statistics including plotting functions (via RPy) can be used in the spreadsheet. Everything is directly available from each cell. Just use the grid

Data can be imported and exported using csv files or the clipboard. Other forms of data exchange is possible using external Python modules.

In  order to simplify sparse matrix editing, pyspread features a three dimensional grid that can be sized up to 85,899,345 rows and 14,316,555 columns (64 bit-systems, depends on row height and column width). Note that importing a million cells requires about 500 MB of memory.

The concept of pyspread allows doing everything from each cell that a Python script can do. This may very well include deleting your hard drive or sending your data via the Internet. Of course this is a non-issue if you sandbox properly or if you only use self developed spreadsheets. Since this is not the case for everyone (see the discussion at lwn.net), a GPG signature based trust model for spreadsheet files has been introduced. It ensures that only your own trusted files are executed on loading. Untrusted files are displayed in safe mode. You can trust a file manually. Inspect carefully.

Pyspread screenshot

requirements Pyspread runs on Linux, Windows and *nix platforms with GTK+ support. There are reports that it works with MacOS X as well. If you would like to contribute by testing on OS X please contact me.

Dependencies

Highly recommended for full functionality

  • PyMe >=0.8.1, Note for Windows™ users: If you want to use signatures without compiling PyMe try out Gpg4win.
  • gmpy >=1.1.0 and
  • rpy >=1.0.3.
maturity Pyspread is in early Beta release. This means that the core functionality is fully implemented but the program needs testing and polish.

and from the wiki

http://sourceforge.net/apps/mediawiki/pyspread/index.php?title=Main_Page

a spreadsheet with more powerful functions and data structures that are accessible inside each cell. Something like Python that empowers you to do things quickly. And yes, it should be free and it should run on Linux as well as on Windows. I looked around and found nothing that suited me. Therefore, I started pyspread.

Concept

  • Each cell accepts any input that works in a Python command line.
  • The inputs are parsed and evaluated by Python’s eval command.
  • The result objects are accessible via a 3D numpy object array.
  • String representations of the result objects are displayed in the cells.

Benefits

  • Each cell returns a Python object. This object can be anything including arrays and third party library objects.
  • Generator expressions can be used efficiently for data manipulation.
  • Efficient numpy slicing is used.
  • numpy methods are accessible for the data.

Installation

  1. Download the pyspread tarball or zip and unzip at a convenient place
  2. In case you do not have it already get and install Python, wxpython and numpy
If you want the examples to work, install gmpy, R and rpy
Really do check the version requirements that are mentioned on http://pyspread.sf.net
  1. Get install privileges (e.g. become root)
  2. Change into the directory and type
python setup.py install
Windows: Replace “python” with your Python interpreter (absolute path)
  1. Become normal user again
  2. Start pyspread by typing
pyspread
  1. Enjoy

Links

Next on Spreadsheet wishlist-

a MSI bundle /Windows Self Installer which has all dependencies bundled in it-linking to PostGresSQL 😉 etc

way to go Mr Martin Manns

mmanns < at > gmx < dot > net