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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

—————————————

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

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RevoDeployR and commercial BI using R and R based cloud computing using Open CPU

Revolution Analytics has of course had RevoDeployR, and in a  webinar strive to bring it back to center spotlight.

BI is a good lucrative market, and visualization is a strength in R, so it is matter of time before we have more R based BI solutions. I really liked the two slides below for explaining RevoDeployR better to newbies like me (and many others!)

Integrating R into 3rd party and Web applications using RevoDeployR

Please click here to download the PDF.

Here are some additional links that may be of interest to you:

 

( I still think someone should make a commercial version of Jeroen Oom’s web interfaces and Jeff Horner’s web infrastructure (see below) for making customized Business Intelligence (BI) /Data Visualization solutions , UCLA and Vanderbilt are not exactly Stanford when it comes to deploying great academic solutions in the startup-tech world). I kind of think Google or someone at Revolution  should atleast dekko OpenCPU as a credible cloud solution in R.

I still cant figure out whether Revolution Analytics has a cloud computing strategy and Google seems to be working mysteriously as usual in broadening access to the Google Compute Cloud to the rest of R Community.

Open CPU  provides a free and open platform for statistical computing in the cloud. It is meant as an open, social analysis environment where people can share and run R functions and objects. For more details, visit the websit: www.opencpu.org

and esp see

https://public.opencpu.org/userapps/opencpu/opencpu.demo/runcode/

Jeff Horner’s

http://rapache.net/

Jerooen Oom’s

Talking on Big Data Analytics

I am going  being sponsored to a Government of India sponsored talk on Big Data Analytics at Bangalore on Friday the 13 th of July. If you are in Bangalore, India you may drop in for a dekko. Schedule and Abstracts (i am on page 7 out 9) .

Your tax payer money is hard at work- (hassi majak only if you are a desi. hassi to fassi.)

13 July 2012 (9.30 – 11.00 & 11.30 – 1.00)
Big Data Big Analytics
The talk will showcase using open source technologies in statistical computing for big data, namely the R programming language and its use cases in big data analysis. It will review case studies using the Amazon Cloud, custom packages in R for Big Data, tools like Revolution Analytics RevoScaleR package, as well as the newly launched SAP Hana used with R. We will also review Oracle R Enterprise. In addition we will show some case studies using BigML.com (using Clojure) , and approaches using PiCloud. In addition it will showcase some of Google APIs for Big Data Analysis.

Lastly we will talk on social media analysis ,national security use cases (i.e. cyber war) and privacy hazards of big data analytics.

Schedule

View more presentations from Ajay Ohri.
Abstracts

View more documents from Ajay Ohri.

 

Using Google Analytics with R

Some code to read in data from Google Analytics data. Some modifications include adding the SSL authentication code and modifying (in bold) the table.id parameter to choose correct website from a GA profile with many websites

The Google Analytics Package files can be downloaded from http://code.google.com/p/r-google-analytics/downloads/list

It provides access to Google Analytics data natively from the R Statistical Computing programming language. You can use this library to retrieve an R data.frame with Google Analytics data. Then perform advanced statistical analysis, like time series analysis and regressions.

Supported Features

  • Access to v2 of the Google Analytics Data Export API Data Feed
  • A QueryBuilder class to simplify creating API queries
  • API response is converted directly into R as a data.frame
  • Library returns the aggregates, and confidence intervals of the metrics, dynamically if they exist
  • Auto-pagination to return more than 10,000 rows of information by combining multiple data requests. (Upper Limit 1M rows)
  • Authorization through the ClientLogin routine
  • Access to all the profiles ids for the authorized user
  • Full documentation and unit tests
Code-

> library(XML)

>

> library(RCurl)

Loading required package: bitops

>

> #Change path name in the following to the folder you downloaded the Google Analytics Package

>

> source(“C:/Users/KUs/Desktop/CANADA/R/RGoogleAnalytics/R/RGoogleAnalytics.R”)

>

> source(“C:/Users/KUs/Desktop/CANADA/R/RGoogleAnalytics/R/QueryBuilder.R”)

> # download the file needed for authentication

> download.file(url=”http://curl.haxx.se/ca/cacert.pem&#8221;, destfile=”cacert.pem”)

trying URL ‘http://curl.haxx.se/ca/cacert.pem&#8217; Content type ‘text/plain’ length 215993 bytes (210 Kb) opened

URL downloaded 210 Kb

>

> # set the curl options

> curl <- getCurlHandle()

> options(RCurlOptions = list(capath = system.file(“CurlSSL”, “cacert.pem”,

+ package = “RCurl”),

+ ssl.verifypeer = FALSE))

> curlSetOpt(.opts = list(proxy = ‘proxyserver:port’), curl = curl)

An object of class “CURLHandle” Slot “ref”: <pointer: 0000000006AA2B70>

>

> # 1. Create a new Google Analytics API object

>

> ga <- RGoogleAnalytics()

>

> # 2. Authorize the object with your Google Analytics Account Credentials

>

> ga$SetCredentials(“USERNAME”, “PASSWORD”)

>

> # 3. Get the list of different profiles, to help build the query

>

> profiles <- ga$GetProfileData()

>

> profiles #Error Check to See if we get the right website

$profile AccountName ProfileName TableId

1 dudeofdata.com dudeofdata.com ga:44926237

2 knol.google.com knol.google.com ga:45564890

3 decisionstats.com decisionstats.com ga:46751946

$total.results

total.results

1 3

>

> # 4. Build the Data Export API query

>

> #Modify the start.date and end.date parameters based on data requirements

>

> #Modify the table.id at table.id = paste(profiles$profile[X,3]) to get the X th website in your profile

> # 4. Build the Data Export API query

> query <- QueryBuilder() > query$Init(start.date = “2012-01-09″, + end.date = “2012-03-20″, + dimensions = “ga:date”,

+ metrics = “ga:visitors”,

+ sort = “ga:date”,

+ table.id = paste(profiles$profile[3,3]))

>

>

> #5. Make a request to get the data from the API

>

> ga.data <- ga$GetReportData(query)

[1] “Executing query: https://www.google.com/analytics/feeds/data?start-date=2012%2D01%2D09&end-date=2012%2D03%2D20&dimensions=ga%3Adate&metrics=ga%3Avisitors&sort=ga%3Adate&ids=ga%3A46751946&#8243;

>

> #6. Look at the returned data

>

> str(ga.data)

List of 3

$ data :’data.frame’: 72 obs. of 2 variables: ..

$ ga:date : chr [1:72] “20120109″ “20120110″ “20120111″ “20120112″ … ..

$ ga:visitors: num [1:72] 394 405 381 390 323 47 169 67 94 89 …

$ aggr.totals :’data.frame’: 1 obs. of 1 variable: ..

$ aggregate.totals: num 28348

$ total.results: num 72

>

> head(ga.data$data)

ga:date ga:visitors

1 20120109 394

2 20120110 405

3 20120111 381

4 20120112 390

5 20120113 323

6 20120114 47 >

> #Plotting the Traffic >

> plot(ga.data$data[,2],type=”l”)

Update- Some errors come from pasting Latex directly to WordPress. Here is some code , made pretty-r in case you want to play with the GA api

library(XML)

library(RCurl)

#Change path name in the following to the folder you downloaded the Google Analytics Package 

source("C:/Users/KUs/Desktop/CANADA/R/RGoogleAnalytics/R/RGoogleAnalytics.R")

source("C:/Users/KUs/Desktop/CANADA/R/RGoogleAnalytics/R/QueryBuilder.R")
# download the file needed for authentication
download.file(url="http://curl.haxx.se/ca/cacert.pem", destfile="cacert.pem")

# set the curl options
curl <- getCurlHandle()
options(RCurlOptions = list(capath = system.file("CurlSSL", "cacert.pem",
package = "RCurl"),
ssl.verifypeer = FALSE))
curlSetOpt(.opts = list(proxy = 'proxyserver:port'), curl = curl)

# 1. Create a new Google Analytics API object 

ga <- RGoogleAnalytics()

# 2. Authorize the object with your Google Analytics Account Credentials 

ga$SetCredentials("ohri2007@gmail.com", "XXXXXXX")

# 3. Get the list of different profiles, to help build the query

profiles <- ga$GetProfileData()

profiles #Error Check to See if we get the right website

# 4. Build the Data Export API query 

#Modify the start.date and end.date parameters based on data requirements 

#Modify the table.id at table.id = paste(profiles$profile[X,3]) to get the X th website in your profile 
# 4. Build the Data Export API query
query <- QueryBuilder()
query$Init(start.date = "2012-01-09",
                   end.date = "2012-03-20",
                   dimensions = "ga:date",
                   metrics = "ga:visitors",
                   sort = "ga:date",
                   table.id = paste(profiles$profile[3,3]))

#5. Make a request to get the data from the API 

ga.data <- ga$GetReportData(query)

#6. Look at the returned data 

str(ga.data)

head(ga.data$data)

#Plotting the Traffic 

plot(ga.data$data[,2],type="l")

Created by Pretty R at inside-R.org

Teradata Analytics

A recent announcement showing Teradata partnering with KXEN and Revolution Analytics for Teradata Analytics.

http://www.teradata.com/News-Releases/2012/Teradata-Expands-Integrated-Analytics-Portfolio/

The Latest in Open Source Emerging Software Technologies
Teradata provides customers with two additional open source technologies – “R” technology from Revolution Analytics for analytics and GeoServer technology for spatial data offered by the OpenGeo organization – both of which are able to leverage the power of Teradata in-database processing for faster, smarter answers to business questions.

In addition to the existing world-class analytic partners, Teradata supports the use of the evolving “R” technology, an open source language for statistical computing and graphics. “R” technology is gaining popularity with data scientists who are exploiting its new and innovative capabilities, which are not readily available. The enhanced “R add-on for Teradata” has a 50 percent performance improvement, it is easier to use, and its capabilities support large data analytics. Users can quickly profile, explore, and analyze larger quantities of data directly in the Teradata Database to deliver faster answers by leveraging embedded analytics.

Teradata has partnered with Revolution Analytics, the leading commercial provider of “R” technology, because of customer interest in high-performing R applications that deliver superior performance for large-scale data. “Our innovative customers understand that big data analytics takes a smart approach to the entire infrastructure and we will enable them to differentiate their business in a cost-effective way,” said David Rich, chief executive officer, Revolution Analytics. “We are excited to partner with Teradata, because we see great affinity between Teradata and Revolution Analytics – we embrace parallel computing and the high performance offered by multi-core and multi-processor hardware.”

and

The Teradata Data Lab empowers business users and leading analytic partners to start building new analytics in less than five minutes, as compared to waiting several weeks for the IT department’s assistance.

“The Data Lab within the Teradata database provides the perfect foundation to enable self-service predictive analytics with KXEN InfiniteInsight,” said John Ball, chief executive officer, KXEN. “Teradata technologies, combined with KXEN’s automated modeling capabilities and in-database scoring, put the power of predictive analytics and data mining directly into the hands of business users. This powerful combination helps our joint customers accelerate insight by delivering top-quality models in orders of magnitude faster than traditional approaches.”

Read more at

http://www.sacbee.com/2012/03/06/4315500/teradata-expands-integrated-analytics.html

Interview JJ Allaire Founder, RStudio

Here is an interview with JJ Allaire, founder of RStudio. RStudio is the IDE that has overtaken other IDE within the R Community in terms of ease of usage. On the eve of their latest product launch, JJ talks to DecisionStats on RStudio and more.

Ajay-  So what is new in the latest version of RStudio and how exactly is it useful for people?

JJ- The initial release of RStudio as well as the two follow-up releases we did last year were focused on the core elements of using R: editing and running code, getting help, and managing files, history, workspaces, plots, and packages. In the meantime users have also been asking for some bigger features that would improve the overall work-flow of doing analysis with R. In this release (v0.95) we focused on three of these features:

Projects. R developers tend to have several (and often dozens) of working contexts associated with different clients, analyses, data sets, etc. RStudio projects make it easy to keep these contexts well separated (with distinct R sessions, working directories, environments, command histories, and active source documents), switch quickly between project contexts, and even work with multiple projects at once (using multiple running versions of RStudio).

Version Control. The benefits of using version control for collaboration are well known, but we also believe that solo data analysis can achieve significant productivity gains by using version control (this discussion on Stack Overflow talks about why). In this release we introduced integrated support for the two most popular open-source version control systems: Git and Subversion. This includes changelist management, file diffing, and browsing of project history, all right from within RStudio.

Code Navigation. When you look at how programmers work a surprisingly large amount of time is spent simply navigating from one context to another. Modern programming environments for general purpose languages like C++ and Java solve this problem using various forms of code navigation, and in this release we’ve brought these capabilities to R. The two main features here are the ability to type the name of any file or function in your project and go immediately to it; and the ability to navigate to the definition of any function under your cursor (including the definition of functions within packages) using a keystroke (F2) or mouse gesture (Ctrl+Click).

Ajay- What’s the product road map for RStudio? When can we expect the IDE to turn into a full fledged GUI?

JJ- Linus Torvalds has said that “Linux is evolution, not intelligent design.” RStudio tries to operate on a similar principle—the world of statistical computing is too deep, diverse, and ever-changing for any one person or vendor to map out in advance what is most important. So, our internal process is to ship a new release every few months, listen to what people are doing with the product (and hope to do with it), and then start from scratch again making the improvements that are considered most important.

Right now some of the things which seem to be top of mind for users are improved support for authoring and reproducible research, various editor enhancements including code folding, and debugging tools.

What you’ll see is us do in a given release is to work on a combination of frequently requested features, smaller improvements to usability and work-flow, bug fixes, and finally architectural changes required to support current or future feature requirements.

While we do try to base what we work on as closely as possible on direct user-feedback, we also adhere to some core principles concerning the overall philosophy and direction of the product. So for example the answer to the question about the IDE turning into a full-fledged GUI is: never. We believe that textual representations of computations provide fundamental advantages in transparency, reproducibility, collaboration, and re-usability. We believe that writing code is simply the right way to do complex technical work, so we’ll always look for ways to make coding better, faster, and easier rather than try to eliminate coding altogether.

Ajay -Describe your journey in science from a high school student to your present work in R. I noticed you have been very successful in making software products that have been mostly proprietary products or sold to companies.

Why did you get into open source products with RStudio? What are your plans for monetizing RStudio further down the line?

JJ- In high school and college my principal areas of study were Political Science and Economics. I also had a very strong parallel interest in both computing and quantitative analysis. My first job out of college was as a financial analyst at a government agency. The tools I used in that job were SAS and Excel. I had a dim notion that there must be a better way to marry computation and data analysis than those tools, but of course no concept of what this would look like.

From there I went more in the direction of general purpose computing, starting a couple of companies where I worked principally on programming languages and authoring tools for the Web. These companies produced proprietary software, which at the time (between 1995 and 2005) was a workable model because it allowed us to build the revenue required to fund development and to promote and distribute the software to a wider audience.

By 2005 it was however becoming clear that proprietary software would ultimately be overtaken by open source software in nearly all domains. The cost of development had shrunken dramatically thanks to both the availability of high-quality open source languages and tools as well as the scale of global collaboration possible on open source projects. The cost of promoting and distributing software had also collapsed thanks to efficiency of both distribution and information diffusion on the Web.

When I heard about R and learned more about it, I become very excited and inspired by what the project had accomplished. A group of extremely talented and dedicated users had created the software they needed for their work and then shared the fruits of that work with everyone. R was a platform that everyone could rally around because it worked so well, was extensible in all the right ways, and most importantly was free (as in speech) so users could depend upon it as a long-term foundation for their work.

So I started RStudio with the aim of making useful contributions to the R community. We started with building an IDE because it seemed like a first-rate development environment for R that was both powerful and easy to use was an unmet need. Being aware that many other companies had built successful businesses around open-source software, we were also convinced that we could make RStudio available under a free and open-source license (the AGPLv3) while still creating a viable business. At this point RStudio is exclusively focused on creating the best IDE for R that we can. As the core product gets where it needs to be over the next couple of years we’ll then also begin to sell other products and services related to R and RStudio.

About-

http://rstudio.org/docs/about

Jjallaire

JJ Allaire

JJ Allaire is a software engineer and entrepreneur who has created a wide variety of products including ColdFusion,Windows Live WriterLose It!, and RStudio.

From http://en.wikipedia.org/wiki/Joseph_J._Allaire
In 1995 Joseph J. (JJ) Allaire co-founded Allaire Corporation with his brother Jeremy Allaire, creating the web development tool ColdFusion.[1] In March 2001, Allaire was sold to Macromedia where ColdFusion was integrated into the Macromedia MX product line. Macromedia was subsequently acquired by Adobe Systems, which continues to develop and market ColdFusion.
After the sale of his company, Allaire became frustrated at the difficulty of keeping track of research he was doing using Google. To address this problem, he co-founded Onfolio in 2004 with Adam Berrey, former Allaire co-founder and VP of Marketing at Macromedia.
On March 8, 2006, Onfolio was acquired by Microsoft where many of the features of the original product are being incorporated into the Windows Live Toolbar. On August 13, 2006, Microsoft released the public beta of a new desktop blogging client called Windows Live Writer that was created by Allaire’s team at Microsoft.
Starting in 2009, Allaire has been developing a web-based interface to the widely used R technical computing environment. A beta version of RStudio was publicly released on February 28, 2011.
JJ Allaire received his B.A. from Macalester College (St. Paul, MN) in 1991.
RStudio-

RStudio is an integrated development environment (IDE) for R which works with the standard version of R available from CRAN. Like R, RStudio is available under a free software license. RStudio is designed to be as straightforward and intuitive as possible to provide a friendly environment for new and experienced R users alike. RStudio is also a company, and they plan to sell services (support, training, consulting, hosting) related to the open-source software they distribute.

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