rstats – Page 21 – DECISION STATS

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.

Learning Data Visualization From a Data Scientist (justinbozonier.posterous.com)
Red R 1.8- Groovy GUI (r-bloggers.com)
Rapid Miner- R Extension (r-bloggers.com)

PAW Reception and R Meetup

New DC meetup for R Users-

source- http://www.meetup.com/R-users-DC/calendar/14236478/

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.

Agenda:

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

Talks:
“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.

Running a R GUI,and parallel programming on Amazon EC2

Ok here is an update to the post on running R on an Amazon EC2.

https://decisionstats.wordpress.com/2010/09/25/running-r-on-amazon-ec2/

1) Login to Amazon Console using instructions in earlier post

2) Select AMI-Platform Ubuntu-i-5575773f

Basically select the latest 64 bit instance from Ubuntu

3) Proceed as in post before to launch AMI and instance- here I chose large with 4cores

3.1) Before connecting to your session

search Synaptic Package Manager for x11-

I installed the X11 VNC server package –

and now interactive sessions will work (read GUIs)

3.2) Modify the line

ssh -i decisionstats2.pem root@ec2-75-101-182-203.compute-1.amazonaws.com

ssh -i decisionstats2.pem -X ubuntu@ec2-75-101-182-203.compute-1.amazonaws.com

This will connect you.

4) INSTALL R – Cran R is a standard Ubuntu Package

using

sudo apt-get install r-base

then type R

and install.packages(“Rcmdr”)

Note – you should be able to see the grey colored Tcl/Tpk script showing cran locations

in a seperate window if X11 is working

5) doSNOW package works on the Ubuntu 64- The results are below for

check <-function(n) {check <-function(n) {

+ for(i in 1:1000)

+ {

+ sme <- matrix(rnorm(100), 10,10)

+ solve(sme)

+ }

> times <- 100

> system.time(x <- foreach(j=1:times ) %dopar% check(j))
user system elapsed
0.150 0.080 7.303
> system.time(for(j in 1:times ) x <- check(j))
user system elapsed
27.460 2.300 29.757

The time of 7.3 is almost 5.5 times faster than running it locally on a dual core, and still 3 times faster than running foreach locally. Note I used 4 cores this time in snow.

5) The Tcl/Tk interface of R Cmdr takes a long time to load on EC2 than locally. It may be due to the fact I was running Ubuntu using a VM Player (http://www.vmware.com/go/downloadplayer/ ). However there seems to be a general slowing down when viewing graphics.

or simply

sudo apt-get install r-cran-rcmdr

Running R on Amazon EC2

On my second day of bludering about high technology, I came across http://rgrossman.com/2009/05/17/running-r-on-amazons-ec2/ which describes how to run R on Amazon EC2.

I tried it out and have subsequently added some screenshots to this tutorial so as to help you run R. My intention of course was to run a R GUI preferable Revolution Enterprise on the Amazon EC 2- and crunch uhm a lot of data.

Now go through the steps as follows-

0) Logging onto Amazon Console

http://aws.amazon.com/ec2/

Note you need your Amazon Id (even the same id which you use for buying books).

Note we are into Amazon EC2 as shown by the upper tab. Click upper tab to get into the Amazon EC2

2) Choosing the right AMI-

On the left margin, you can click AMI -Images.

Now you can search for the image-

I chose Ubuntu images (linux images are cheaper) and opendata in the search as belows- I get two images.

You can choose whether you want 32 bit or 64 bit image. Thumb rule- 64 bit images are preferable for data intensive tasks.

Click on launch instance in the upper tab ( near the search feature)

2) A pop up comes up, which shows the 5 step process to launch your computing.

Choose the right compute instance- As the screenshot shows- there are various compute instances and they all are at different multiples of prices or compute units.

After choosing the compute instance of your choice (extra large is highlighted)- click on continue-

3) Instance Details-

I did not choose cloudburst monitoring as it has a extra charge- and I am just trying out things.So I simply clicked continue.

4) Add Tag Details- If you are running a lot of instances you need to create your own tags to help you manage them. Advisable if you are running many instances.

Since I am going to run just one- I clicked continue with adding just two things OS and Stats Package.

5) Create a key pair- A key pair is an added layer of encryption. Click on create new pair and name it (note the name will be handy in coming steps)

After clicking and downloading the key pair- you come into security groups. Security groups is just a set of instructions to help keep your data transfer secure. So I created a new security group.

And I added some ways in security group to connect (like SSH using Port 22)

7) Last step- Review Details and Click Launch

8) On the Left margin click on instances ( you were in Images.>AMI earlier)

It will take some 3-5 minutes to launch an instance. You can see status as pending till then.

9) Pending instance as shown by yellow light-

10) Once the instance is running -it is shown by a green light.

Click on the check box, and on upper tab go to instance actions. Click on connect-

you see a popup with instructions like these-

Open the SSH client of your choice (e.g., PuTTY, terminal).

Locate your private key file, decisionstats2.pem

Use chmod to make sure your key file isn’t publicly viewable, ssh won’t work otherwise:
chmod 400 decisionstats.pem

Connect to your instance using instance’s public DNS [ec2-75-101-182-203.compute-1.amazonaws.com].

Example

Enter the following command line:

ssh -i decisionstats2.pem root@ec2-75-101-182-203.compute-1.amazonaws.com

IMPORTANT-

If you are choosing Ubuntu Terminal to connect- you need to change the word root from above to Ubuntu above.

12) To launch R, just type R at the terminal

If all goes well you should be able to see this-

choose to install any custom packages (like

install.packages(‘doSNOW’)

work on R using command line

13) IMPORTANT- After doing your R work, please CLOSE your instance (

Go to LEFT Margin-Instances-Check the check box of instance you are running- on upper tab- Instance Actions- Click Terminate.

Submitted By:	Eduardo L Leoni
US East AMI ID:	ami-1b9b7c72
AMI Manifest:	PolMethImages/imageR64.manifest.xml
License:	Public
Operating System:	Linux/Uni

Note there are other Amazon Machine Images as well which have R- I found this as well-

Amazon EC2 Ubuntu 8.10 intrepid AMI built by Eric Hammond; Eduardo Leoni added R, many R packages, JAGS, mysql-client and subversion.

Submitted By: Eduardo L Leoni

US East AMI ID: ami-1b9b7c72

AMI Manifest: PolMethImages/imageR64.manifest.xml

License: Public

Operating System: Linux/Uni

2) You can install Revolution R on 32 bit Ubuntu using sudo apt install revolution-r

Various versions of Revolution R are supported on different versions of Linux

see http://www.revolutionanalytics.com/why-revolution-r/which-r-is-right-for-me.php

I may be willing to try Red Hat Enterprise Linux on the ec2 with 64 bit AND Revolution Enterprise to see the maximum juice I can get. or you can try it using an image below- It would be interesting if there could be an Amazon Machine Image for that (paid-public and private-academic)

AMI ID: ami-8ba347e2
Name:–
Description:–
Source:redhat-cloud/RHEL-5-Server/5.2/x86_64/Beta-2.6.18-92.1.1/RHEL5.2-Server-x86_64-Beta-2.6.18-92.1.1.manifest.xml
Owner:432018295444	Visibility:Public	Product Code:54DBF944
State:available	Kernel ID:aki-89a347e0	RAM Disk ID:ari-88a347e1
Image Type:machine	Architecture:x86_64	Platform:Red Hat
Root Device Type:instance-store	Root Device:–	Image Size:0 bytes
Block Devices:N/A – Instance Store
Virtualization:paravirtual

3) My ultimate goal is to run a parallel session using all cores on an EC2 instance and a R GUI (like R Commander or Rattle)

4) For sake of running a test- I re did the parallel test I did on my 2 core laptop

but using 68.4 gb Memory and 8 cores (26 Compute Units brrr)

> check <-function(n) {

+ for(i in 1:1000)

+ {

+ sme <- matrix(rnorm(100), 10,10)

+ solve(sme)

+ }

> times <- 100

> system.time(for(j in 1:times ) x <- check(j))

user system elapsed

20.51 0.00 20.66

Note I still got a faster response than using parallel processors (on a 2 core 3 gb memory) BUT the gain was not as much had I tried to use foreach for running each of the 8 cores parallely. Or running multicore package as in http://www.cerebralmastication.com/2010/02/using-the-r-multicore-package-in-linux-with-wild-and-passionate-abandon/

5) For some reason on Ubuntu 64 bit Amazon image -I cant get Revolution R (even after using sudo apt) , and I am still learning how I can try and get Enterprise Edition fired up on a 64 bit Red Hat Enterprise Linux Amazon AMI (and maybe create an all new Machine Image 😉

6) I was also unable to use the -X command desite having x 11 as in http://rgrossman.com/2009/05/17/running-r-on-amazons-ec2/ so was not able to see graphics,

Also it prevents me from loogin onto as root, and asks me to login as ubuntu@amazon…. I also wanted to try logging into using my Windows session but kept shuttling between my VM Player Ubuntu session and Windows

7) Hope this was useful. I am thankful to tips from Revolution Blog, R Grossman’s Blog, Creators of the Open Data AMI, Tal’s R Statistics Blog and Cerebral Mastication blog on this

IBM Buys Netezza

IBM just bought Netezza (maker of Twin Fin appliance) for handling big data.

http://dealbook.blogs.nytimes.com/2010/09/20/i-b-m-to-buy-analytics-firm-for-1-7-billion/?hpw

The deal values Netezza at $27 a share, a 9.8 percent premium to its closing price on Friday.

Since Netezza was an existing SAS partner, probably it would impact it more if at all, since IBM-SPSS acquisition. Also Netezza was one of the foremost BI companies for both using and expounding R-

See- Using Netezza and R http://www.biecek.pl/WZUR2009/LukaszBartnik2009c.pdf

and http://www.netezza.com/userconference/pce.html#rmftfic

Below a paper on using R on Netezza-

> library(nzr)

> nzconnect(“user”, “password”, “host”, “database”)

> library(rpart)

> data(kyphosis)

# this creates a table out of kyphosis data.frame

# and sends its data to TwinFin

> invisible(as.nz.data.frame(kyphosis))

> nzQuery(“SELECT * FROM kyphosis”)

KYPHOSIS AGE NUMBER START

1 absent 71 3 5

2 absent 158 3 14

3 present 128 4 5

[ cut ]

# now create a nz.data.frame

> k <- nz.data.frame(“kyphosis”)

> as.data.frame(k)

KYPHOSIS AGE NUMBER START

1 absent 71 3 5

2 absent 158 3 14

3 present 128 4 5

[ cut ]

> nzQuery(“SELECT * FROM kyphosis”)

COUNT

1 81

Rattle Re-Introduced

Latest version of Rattle just went online-

Here is the change log- Dr Graham Williams is also coming out with a book on using Rattle- the R GUI devoted to data mining.

Source-http://cran.r-project.org/web/packages/rattle/index.html

rattle (2.5.42) unstable; urgency=low

  * Update rattle.info() to recursively identify all dependencies,
 report
    their version number and any updates available from CRAN and generate
    command to update packages that have updates available. See
    ?rattle.info for the options.

  * Fix bug causing R Dataset option of the Evaluate window to always
    revert to the first named dataset.

  * Fix bug in transforms where weights were not being handled in
    refreshing of the Data tab.

  * Fix a bug in box plots when trying to label outliers when there aren't
    any.

 -- Graham Williams <Graham.Williams@togaware.com>  Sun, 
19 Sep 2010 05:01:51 +1000

rattle (2.5.41) unstable; urgency=low

  * Use GtkBuilder for Export dialog.

  * Test use of glade vs GtkBuilder on multiple platforms.

  * Rename rattle.info to rattle.version.

  * Add weight column to data tab.

  * Support weights for nnet, multinom, survival.

  * Add weights information to PMML as a PMML Extension.

  * Ensure GtkFrame is available as a data type whilst waiting for 
updated
    RGtk2.

  * Bug fix to packageIsAvailable not reruning any result.

  * Replace destroy with withdraw for plot window as the former has
    started crashing R.

  * Improve Log formatting for various model build commands.

  * Be sure to include the car package for Anova for multinom models.

  * Release pmml 1.2.24: Bug fix glm binomial regression - note as
    classification model.

 -- Graham Williams <Graham.Williams@togaware.com>  Wed, 15 Sep 2010 
14:56:09 +1000
And a video I did of exploring various Rattle options using Camtasia,
 a very useful software for screen capture and video tutorials
from http://www.techsmith.com/download/camtasiatrial.asp
Updated- my video skils being quite bad- I replaced it with another video. 
However Camtasia is the best screen capture video tool

Also , an update Analyticdroid is on hold for now.
see- for more details http://rattle.togaware.com/

Graphics Presentations

Here are some Wow Presentations on Design and User Interfaces and Graphics (including R)- you may have seen some before.

From Dataspora-

A Survey of R Graphics

R Graphics using GGPlot

King of all R graphics-Hadley Wickham

and a rather clever Graphics User Interface presentation

Dark Patterns to Trick People

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