downloading – Page 3 – DECISION STATS

Customizing your R software startup

Customizing your R software startup helps you do the following.

Thus it helps you to boot up R faster.

It automatically loads packages that you use regularly (like a R GUI -Deducer, Rattle or R Commander), set a CRAN mirror that you mostly use or is nearest for downloading new packages, and set some optional parameters.

Everytime you start R Instead of doing this , loading same R packages, setting a CRAN mirror,setting some new functions- the user needs to do this just once by customizing the R Profile SITE file.

This is done by editing the $R_HOME/etc/Renviron file for globally setting a default or the .Renviron file that is created in your home directory for a shared system.

There are two special functions you can customize in these files.
.First( ) will be run at the start of the R session and
.Last( ) will be run when the R session is shutting down.

When R starts up, it loads the .Rprofile file in your home directory and executes the .First() function.

Where is the R Profile file?
It is located in the \etc folder of your R folder- folder you installed R in.
In Windows the folder will be of the format -”C:\Program Files\R\R-x.ab.c\etc”
where x.ab.c will be the R version number (like 2.11.1)
Example
.First <- function(){
library(rattle)
rattle()
cat(“\nHello World”, date(), “\n”)
}

will automatically start the Rattle GUI for data mining and print Hello World with the date in your session.

You can also modify the Rcmd_environ file in the same \etc folder if you are particular on your settings

## Default browser
R_BROWSER=${R_BROWSER-‘C:\Documents and Settings\abc\Local Settings\Application Data\Google\Chrome\Application\chrome.exe}## Default editorEDITOR=${EDITOR-${notepad++}}

will change the default Web browser to Chrome and the default editor to Notepad++ which is an enhanced Code Editor.

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

IPSUR – A Free R Textbook

Here is a free R textbook called IPSUR-

http://ipsur.r-forge.r-project.org/book/index.php

IPSUR stands for Introduction to Probability and Statistics Using R, ISBN: 978-0-557-24979-4, which is a textbook written for an undergraduate course in probability and statistics. The approximate prerequisites are two or three semesters of calculus and some linear algebra in a few places. Attendees of the class include mathematics, engineering, and computer science majors.

IPSUR is FREE, in the GNU sense of the word. Hard copies are available for purchase here from Lulu and will be available (coming soon) from the other standard online retailers worldwide. The price of the book is exactly the manufacturing cost plus the retailers’ markup. You may be able to get it even cheaper by downloading an electronic copy and printing it yourself, but if you elect this route then be sure to get the publisher-quality PDF from theDownloads page. And double check the price. It was cheaper for my students to buy a perfect-bound paperback from Lulu and have it shipped to their door than it was to upload the PDF to Fed-Ex Kinkos and Xerox a coil-bound copy (and on top of that go pick it up at the store).

If you are going to buy from anywhere other than Lulu then be sure to check the time-stamp on the copyright page. There is a 6 to 8 week delay from Lulu to Amazon and you may not be getting the absolute latest version available.

Refer to the Installation page for instructions to install an electronic copy of IPSUR on your personal computer. See the Feedback page for guidance about questions or comments you may have about IPSUR.

Also see http://ipsur.r-forge.r-project.org/rcmdrplugin/index.php for the R Cmdr Plugin

This plugin for the R Commander accompanies the text Introduction to Probability and Statistics Using R by G. Jay Kerns. The plugin contributes functions unique to the book as well as specific configuration and functionality to R Commander, the pioneering work by John Fox of McMaster University.

RcmdrPlugin.IPSUR’s primary goal is to provide a user-friendly graphical user interface (GUI) to the open-source and freely available R statistical computing environment. RcmdrPlugin.IPSUR is equipped to handle many of the statistical analyses and graphical displays usually encountered by upper division undergraduate mathematics, statistics, and engineering majors. Available features are comparable to many expensive commercial packages such as Minitab, SPSS, and JMP-IN.

Since the audience of RcmdrPlugin.IPSUR is slightly different than Rcmdr’s, certain functionality has been added and selected error-checks have been disabled to permit the student to explore alternative regions of the statistical landscape. The resulting benefit of increased flexibility is balanced by somewhat increased vulnerability to syntax errors and misuse; the instructor should keep this and the academic audience in mind when usingRcmdrPlugin.IPSUR in the classroom

Cutting Down Office Costs:Downloading by DAP and Bit Torrents

Some of these tips may be familiar.Some may be surprisingly different

Here are ways to 1) search for hard to find softwares 2)download and queue downloads with resume/pause functions

Bit Torrents are the best way to download anything . To quote the Openoffice website ”

BitTorrent is a P2P method where a central ‘tracker’ keeps track of who is downloading and sharing specific files.

When using BitTorrent to download OpenOffice.org, your computer automatically uses spare bandwidth to help share the file with others, and this means that you don’t have to put up with slower downloads during peak download times (such as just after a release), because the more people downloading, the more people sharing.

Also, your download is automatically checked for integrity to make sure that it is identical to the official version.

To use BitTorrent technology, you must have a BitTorrent “client” installed.

uTorrent (Windows)
Official BitTorrent Client (Cross-Platform)
Azureus (Cross-Platform)
ABC (Windows, Linux)
Shareaza (Windows)
Tomato Torrent (Mac OS X)
BitComet (Windows)
aria2 (Linux) “

For normal downloads , use DAP from www.speedbit.com. Thats best suited. Also try compressing stuff before uploading.This does have an impact on office bandwidth usage costs. For cutting down on software costs for your organization, download Ubuntu Linux from http://www.ubuntu.com and OpenOffice from http://www.openoffice.org and use it for top 10 % technically qualified people, or bottom 10 % computers that basically use simple processing tasks like email, office,front desk etc.Then expand or tweak the percentages based on the results and satisfaction from users.

To cut down on intranet costs , you can use simple softwares from www.wordpress.org and host it on a computer for whole office to use it as an intranet. For creating an office newsletter , you can burn the feed at www.feedburner.com and use the email plugin to offer subscription to the email users.

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