Creating 3D Graphs with Data in R

Creating 3D graphs  in a 3d scatterplot is a 2 minute task in R using the woderful R Commander GUI. You can see an example video-

I loaded R,                                                                                                                                               then loaded the GUI,                                                                                                                           inputted data (from an attached package) but you can input data from a csv,           then went to Graphs- 3D ScatterPlot.

Here is the result-

and here is the video.

Not bad for 2 minutes of clicking a GUI.

Here is the auto generated code by R Commander.

> data(iris3, package="datasets")
> iris3 <-
> names(iris3) <- make.names(names(iris3))
> library(rgl, pos=4)
> library(mgcv, pos=4)
> scatter3d(iris3$Petal.W..Setosa, iris3$Petal.L..Setosa, +   iris3$Sepal.L..Setosa, fit="linear", residuals=TRUE, bg="black", +   axis.scales=TRUE, grid=TRUE, ellipsoid=FALSE, xlab="Petal.W..Setosa", +   ylab="Petal.L..Setosa", zlab="Sepal.L..Setosa")
> scatter3d(iris3$Petal.L..Versicolor, iris3$Petal.L..Setosa, +   iris3$Petal.L..Virginica, fit="linear", residuals=TRUE, bg="white", +   axis.scales=TRUE, grid=TRUE, ellipsoid=FALSE, xlab="Petal.L..Versicolor", +   ylab="Petal.L..Setosa", zlab="Petal.L..Virginica")
> rgl.snapshot("C:/Documents and Settings/abc/Desktop/RGLGraph.png")

Better Data Visualization in Stats Stats is the analytical software which helps bloggers on hosted blogs. It recently underwent a revamp in design-

Note a simple change from Line to Histogram charts, and added Tabs can add so much value to data.

However really needs to addin Geo-Coded Stats (Visitors from where) and Some level of Campaign Tracking (similar to Goals in Google Analytics)

Earlier WP Stats

Now WP Stats

Interview Dean Abbott Abbott Analytics

Here is an interview with noted Analytics Consultant and trainer Dean Abbott. Dean is scheduled to take a workshop on Predictive Analytics at PAW (Predictive Analytics World Conference)  Oct 18 , 2010 in Washington D.C

Ajay-  Describe your upcoming hands on workshop at Predictive Analytics World and how it can help people learn more predictive modeling.


Dean- The hands-on workshop is geared toward individuals who know something about predictive analytics but would like to experience the process. It will help people in two regards. First, by going through the data assessment, preparation, modeling and model assessment stages in one day, the attendees will see how predictive analytics works in reality, including some of the pain associated with false starts and mistakes. At the same time, they will experience success with building reasonable models to solve a problem in a single day. I have found that for many, having to actually build the predictive analytics solution if an eye-opener. Seeing demonstrations show the capabilities of a tool, but greater value for an end-user is the development of intuition of what to do at each each stage of the process that makes the theory of predictive analytics real.

Second, they will gain experience using a top-tier predictive analytics software tool, Enterprise Miner (EM). This is especially helpful for those who are considering purchasing EM, but also for those who have used open source tools and have never experienced the additional power and efficiencies that come with a tool that is well thought out from a business solutions standpoint (as opposed to an algorithm workbench).

Ajay-  You are an instructor with software ranging from SPSS, S Plus, SAS Enterprise Miner, Statistica and CART. What features of each software do you like best and are more suited for application in data cases.

Dean- I’ll add Tibco Spotfire Miner, Polyanalyst and Unica’s Predictive Insight to the list of tools I’ve taught “hands-on” courses around, and there are at least a half dozen more I demonstrate in lecture courses (JMP, Matlab, Wizwhy, R, Ggobi, RapidMiner, Orange, Weka, RandomForests and TreeNet to name a few). The development of software is a fascinating undertaking, and each tools has its own strengths and weaknesses.

I personally gravitate toward tools with data flow / icon interface because I think more that way, and I’ve tired of learning more programming languages.

Since the predictive analytics algorithms are roughly the same (backdrop is backdrop no matter which tool you use), the key differentiators are

(1) how data can be loaded in and how tightly integrated can the tool be with the database,

(2) how well big data can be handled,

(3) how extensive are the data manipulation options,

(4) how flexible are the model reporting options, and

(5) how can you get the models and/or predictions out.

There are vast differences in the tools on these matters, so when I recommend tools for customers, I usually interview them quite extensively to understand better how they use data and how the models will be integrated into their business practice.

A final consideration is related to the efficiency of using the tool: how much automation can one introduce so that user-interaction is minimized once the analytics process has been defined. While I don’t like new programming languages, scripting and programming often helps here, though some tools have a way to run the visual programming data diagram itself without converting it to code.

Ajay- What are your views on the increasing trend of consolidation and mergers and acquisitions in the predictive analytics space. Does this increase the need for vendor neutral analysts and consultants as well as conferences.

Dean- When companies buy a predictive analytics software package, it’s a mixed bag. SPSS purchasing of Clementine was ultimately good for the predictive analytics, though it took several years for SPSS to figure out what they wanted to do with it. Darwin ultimately disappeared after being purchased by Oracle, but the newer Oracle data mining tool, ODM, integrates better with the database than Darwin did or even would have been able to.

The biggest trend and pressure for the commercial vendors is the improvements in the Open Source and GNU tools. These are becoming more viable for enterprise-level customers with big data, though from what I’ve seen, they haven’t caught up with the big commercial players yet. There is great value in bringing both commercial and open source tools to the attention of end-users in the context of solutions (rather than sales) in a conference setting, which is I think an advantage that Predictive Analytics World has.

As a vendor-neutral consultant, flux is always a good thing because I have to be proficient in a variety of tools, and it is the breadth that brings value for customers entering into the predictive analytics space. But it is very difficult to keep up with the rapidly-changing market and that is something I am weighing myself: how many tools should I keep in my active toolbox.

Ajay-  Describe your career and how you came into the Predictive Analytics space. What are your views on various MS Analytics offered by Universities.

Dean- After getting a masters degree in Applied Mathematics, my first job was at a small aerospace engineering company in Charlottesville, VA called Barron Associates, Inc. (BAI); it is still in existence and doing quite well! I was working on optimal guidance algorithms for some developmental missile systems, and statistical learning was a key part of the process, so I but my teeth on pattern recognition techniques there, and frankly, that was the most interesting part of the job. In fact, most of us agreed that this was the most interesting part: John Elder (Elder Research) was the first employee at BAI, and was there at that time. Gerry Montgomery and Paul Hess were there as well and left to form a data mining company called AbTech and are still in analytics space.

After working at BAI, I had short stints at Martin Marietta Corp. and PAR Government Systems were I worked on analytics solutions in DoD, primarily radar and sonar applications. It was while at Elder Research in the 90s that began working in the commercial space more in financial and risk modeling, and then in 1999 I began working as an independent consultant.

One thing I love about this field is that the same techniques can be applied broadly, and therefore I can work on CRM, web analytics, tax and financial risk, credit scoring, survey analysis, and many more application, and cross-fertilize ideas from one domain into other domains.

Regarding MS degrees, let me first write that I am very encouraged that data mining and predictive analytics are being taught in specific class and programs rather than as just an add-on to an advanced statistics or business class. That stated, I have mixed feelings about analytics offerings at Universities.

I find that most provide a good theoretical foundation in the algorithms, but are weak in describing the entire process in a business context. For those building predictive models, the model-building stage nearly always takes much less time than getting the data ready for modeling and reporting results. These are cross-discipline tasks, requiring some understanding of the database world and the business world for us to define the target variable(s) properly and clean up the data so that the predictive analytics algorithms to work well.

The programs that have a practicum of some kind are the most useful, in my opinion. There are some certificate programs out there that have more of a business-oriented framework, and the NC State program builds an internship into the degree itself. These are positive steps in the field that I’m sure will continue as predictive analytics graduates become more in demand.


DEAN ABBOTT is President of Abbott Analytics in San Diego, California. Mr. Abbott has over 21 years of experience applying advanced data mining, data preparation, and data visualization methods in real-world data intensive problems, including fraud detection, response modeling, survey analysis, planned giving, predictive toxicology, signal process, and missile guidance. In addition, he has developed and evaluated algorithms for use in commercial data mining and pattern recognition products, including polynomial networks, neural networks, radial basis functions, and clustering algorithms, and has consulted with data mining software companies to provide critiques and assessments of their current features and future enhancements.

Mr. Abbott is a seasoned instructor, having taught a wide range of data mining tutorials and seminars for a decade to audiences of up to 400, including DAMA, KDD, AAAI, and IEEE conferences. He is the instructor of well-regarded data mining courses, explaining concepts in language readily understood by a wide range of audiences, including analytics novices, data analysts, statisticians, and business professionals. Mr. Abbott also has taught both applied and hands-on data mining courses for major software vendors, including Clementine (SPSS, an IBM Company), Affinium Model (Unica Corporation), Statistica (StatSoft, Inc.), S-Plus and Insightful Miner (Insightful Corporation), Enterprise Miner (SAS), Tibco Spitfire Miner (Tibco), and CART (Salford Systems).

Using JMP 9 and R together

An interesting blog post at!.html on using the new JMP 9 with R, and quite possibly using SAS as well.

Example Code-

Here’s the R integration JSL code used to run the bootstrap

rconn = R Connect();
rconn << Submit(“\[

# Load Boot package

RStatFctn <- function(x,d) {return(mean(x[d]))}

b.basic = matrix(data=NA, nrow=1000, ncol=2)
b.normal = matrix(data=NA, nrow=1000, ncol=2)
b.percent =matrix(data=NA, nrow=1000, ncol=2)
b.bca =matrix(data=NA, nrow=1000, ncol=2)

for(i in 1:1000){
rnormdat = rnorm(30,0,1)
b <- boot(rnormdat, RStatFctn, R = 1000), conf =095,type=c(“basic”,”norm”,”perc”,”bca”)) b.basic[i,] =$basic[,4:5]
b.normal[i,] =$normal[,2:3]
b.percent[i,] =$percent[,4:5]
b.bca[i,] =$bca[,4:5]
b_basic= rconn << Get(b.basic);
b_normal = rconn << Get(b.normal);
b_percent= rconn << Get(b.percent);
b_bca = rconn << Get(b.bca);
rconn << Disconnect();

Using the R Connect() JSL command and assigning it to the object “rconn”, the code sends messages to the JSL scriptable object “rconn” to submit R code via the Submit() command and to retrieve R matrices containing the bootstrap confidence intervals back via the Get() commands.

and I also found interesting what the write has to say about using JMP (for visual analysis) and SAS (bigger datasets handling) and R (for advanced statistics) together

Other standard JMP tools such as the Data Filter can help to explore these results in ways that cannot easily and quickly be done in R


With a little JSL and the statistical and graphics platforms of JMP coupled with the breadth and variety of packages and functions in R, one can build complete easy-to-use applications for statistical analysis.

JMP can also integrate with SAS, which adds the ability to work with large-scale data through the file-based system as well as the depth and advanced capabilities of SAS procedures. With these seamless integrations, JMP can become a hub that enables you to connect with both SAS and R, as well as provide unique statistical features such as the JMP Profiler and interactive graphic features such as Graph Builder

and in the meanwhile here is a data visualization of a frequency analysis of various words bundled together from

Red R 1.8- Pretty GUI

Red R 1.8 has been compiled and is available for download.

If you have seen Red R, well it resembles software like Enterprise Miner or Rapid Miner in the visual sense as it basically has a work-flow style of showing and setting up data analysis.

I played a bit with it, and this version is a definite improvement over the last ones.- Here is one more really groovy GUI for R- and it’s quite professionally done.

And a Youtube tutorial as well

Take a bow- Kyle and Anup- nice coding indeed.

PAW Reception and R Meetup

New DC meetup for R Users-


October’s R meet-up will be co-located with the Predictive Analytics World Conference (http://www.predictive…) taking place in Washington DC October 19-20. PAW is the premiere business-focused event for predictive analytics professionals, managers and commercial practitioners.


6:30 – 7:30 PAW Reception (open to meet-up attendees)
7:30 – 9:00 DC-R Meetup

“How to speak ggplot2 like a native”
Harlan D. Harris, PhD @HarlanH

“Saving the world with R”
Michael Milton @michaelmilton

Important Registration Instructions:
You are welcome to RSVP here at meetup. The PAW organizers have requested that we register in the PAW site for the R meetup so they can provide badges to members which will give you access to the reception. There is no charge to register using the PAW site. Please click here to register.

Speaker Bios

Harlan D. Harris, PhD, is a statistical data scientist working for Kaplan Test Prep and Admissions in New York City. He has degrees from the University of Wisconsin-Madison and the University of Illinois at Urbana-Champaign. Prior to turning to the private sector, he worked as a researcher and lecturer in various areas of Artificial Intelligence and Cognitive Science at the University of Illinois, Columbia University, the University of Connecticut, and New York University.

Harlan’s talk is titled “How to speak ggplot2 like a native.”. One of the most innovative ideas in data visualization in recent years is that graphical images can be described using a grammar. Just as a fluent speaker of a language can talk more precisely and clearly than someone using a tourist phrasebook, graphics based on a grammar can yield more insights than graphics based on a limited set of templates (bar chart, pie graph, etc.). There are at least two implementations of the Grammar of Graphics idea in R, of which the most popular is the ggplot2 package written by Prof. Hadley Wickham. Just as with natural languages, ggplot2 has a surface structure made up of R vocabulary elements, as well as a deep structure that mediates the link between the vocabulary and the “semantic” representation of the data shown on a computer screen. In this introductory presentation, the links among these levels of representation are demonstrated, so that new ggplot2 users can build the mental models necessary for fluent and creative visualization of their data.

Michael Milton is a Client Manager at Blue State Digital. When he’s not saving the world by designing interactive marketing strategies that connect passionate users with causes and organizations, he writes about data and analytics. For O’Reilly Media, he wrote Head First Data Analysis and Head First Excel and has created the videos Great R: Level 1 and Getting the Most Out of Google Apps for Business.

Michael’s talk is called “How to Save the World Using R.” In this wide-ranging discussion, Michael will highlight individuals and organizations who are using R to help others as well as ways in which R can be used to promote good statistical thinking.

E-Webinar by PAW

Here is a webinar by Predictive Analytics World conference, sponsored by Netezza.

Introducing the first PAW Hosted eWebinar

The New Age of Analytical Marketing
– October 13 2010 at 2pm (EST)

The volume and variety of online customer data is growing exponentially as consumers continue to shift shopping, communication, social interaction, media consumption and more onto the web. This new customer information, coupled with new marketing channels such as social media and mobile, present marketers with a tremendous opportunity to create richer, more personalized experiences for customers while also increased sales and ROI.

  • Translate new online customer data and marketing channels into improved business results.
  • Make better use of customer analytics.
  • Explore the opportunities and challenges associated with today’s customer analytics best practices.
Moderator Special Guest Speakers:

Eric Siegel, Ph.D.
Predictive Analytics World

Vineet Singh
Director Innovation, Analytics and Engineering

Krishnan Parasuraman
CTI/ Chief Architect