send email by R

For automated report delivery I have often used send email options in BASE SAS. For R, for scheduling tasks and sending me automated mails on completion of tasks I have two R options and 1 Windows OS scheduling option. Note red font denotes the parameters that should be changed. Anything else should NOT be changed.

Option 1-

Use the mail package at

http://cran.r-project.org/web/packages/mail/mail.pdf

> library(mail)

Attaching package: ‘mail’

The following object(s) are masked from ‘package:sendmailR’:

sendmail

>
> sendmail(“ohri2007@gmail.com“, subject=”Notification from R“,message=“Calculation finished!”, password=”rmail”)
[1] “Message was sent to ohri2007@gmail.com! You have 19 messages left.”

Disadvantage- Only 20 email messages by IP address per day. (but thats ok!)

Option 2-

use sendmailR package at http://cran.r-project.org/web/packages/sendmailR/sendmailR.pdf

install.packages()
library(sendmailR)
from <- sprintf(“<sendmailR@%s>”, Sys.info()[4])
to <- “<ohri2007@gmail.com>”
subject <- “Hello from R
body <- list(“It works!”, mime_part(iris))
sendmail(from, to, subject, body,control=list(smtpServer=”ASPMX.L.GOOGLE.COM”))

 

 

BiocInstaller version 1.2.1, ?biocLite for help
> install.packages(“sendmailR”)
Installing package(s) into ‘/home/ubuntu/R/library’
(as ‘lib’ is unspecified)
also installing the dependency ‘base64’

trying URL ‘http://cran.at.r-project.org/src/contrib/base64_1.1.tar.gz&#8217;
Content type ‘application/x-gzip’ length 61109 bytes (59 Kb)
opened URL
==================================================
downloaded 59 Kb

trying URL ‘http://cran.at.r-project.org/src/contrib/sendmailR_1.1-1.tar.gz&#8217;
Content type ‘application/x-gzip’ length 6399 bytes
opened URL
==================================================
downloaded 6399 bytes

BiocInstaller version 1.2.1, ?biocLite for help
* installing *source* package ‘base64’ …
** package ‘base64’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -fpic -g -O2 -c base64.c -o base64.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o base64.so base64.o -L/usr/local/lib64/R/lib -lR
installing to /home/ubuntu/R/library/base64/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices …
** testing if installed package can be loaded
BiocInstaller version 1.2.1, ?biocLite for help

* DONE (base64)
BiocInstaller version 1.2.1, ?biocLite for help
* installing *source* package ‘sendmailR’ …
** package ‘sendmailR’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices …
** testing if installed package can be loaded
BiocInstaller version 1.2.1, ?biocLite for help

* DONE (sendmailR)

The downloaded packages are in
‘/tmp/RtmpsM222s/downloaded_packages’
> library(sendmailR)
Loading required package: base64
> from <- sprintf(“<sendmailR@%s>”, Sys.info()[4])
> to <- “<ohri2007@gmail.com>”
> subject <- “Hello from R”
> body <- list(“It works!”, mime_part(iris))
> sendmail(from, to, subject, body,
+ control=list(smtpServer=”ASPMX.L.GOOGLE.COM”))
$code
[1] “221”

$msg
[1] “2.0.0 closing connection ff2si17226764qab.40”

Disadvantage-This worked when I used the Amazon Cloud using the BioConductor AMI (for free 2 hours) at http://www.bioconductor.org/help/cloud/

It did NOT work when I tried it use it from my Windows 7 Home Premium PC from my Indian ISP (!!) .

It gave me this error

or in wait_for(250) :
SMTP Error: 5.7.1 [180.215.172.252] The IP you’re using to send mail is not authorized

 

PAUSE–

ps Why do this (send email by R)?

Note you can add either of the two programs of the end of the code that you want to be notified automatically. (like daily tasks)

This is mostly done for repeated business analytics tasks (like reports and analysis that need to be run at specific periods of time)

pps- What else can I do with this?

Can be modified to include sms or tweets  or even blog by email by modifying the   “to”  location appropriately.

3) Using Windows Task Scheduler to run R codes automatically (either the above)

or just sending an email

got to Start>  All Programs > Accessories >System Tools > Task Scheduler ( or by default C:Windowssystem32taskschd.msc)

Create a basic task

Now you can use this to run your daily/or scheduled R code  or you can send yourself email as well.

and modify the parameters- note the SMTP server (you can use the ones for google in example 2 at ASPMX.L.GOOGLE.COM)

and check if it works!

 

Related

 Geeky Things , Bro

Configuring IIS on your Windows 7 Home Edition-

note path to do this is-

Control Panel>All Control Panel Items> Program and Features>Turn Windows features on or off> Internet Information Services

and

http://stackoverflow.com/questions/709635/sending-mail-from-batch-file

 

Facebook and R

Part 1 How do people at Facebook use R?

tamar Rosenn, Facebook

Itamar conveyed how Facebook’s Data Team used R in 2007 to answer two questions about new users: (i) which data points predict whether a user will stay? and (ii) if they stay, which data points predict how active they’ll be after three months?

For the first question, Itamar’s team used recursive partitioning (via the rpartpackage) to infer that just two data points are significantly predictive of whether a user remains on Facebook: (i) having more than one session as a new user, and (ii) entering basic profile information.

For the second question, they fit the data to a logistic model using a least angle regression approach (via the lars package), and found that activity at three months was predicted by variables related to three classes of behavior: (i) how often a user was reached out to by others, (ii) frequency of third party application use, and (iii) what Itamar termed “receptiveness” — related to how forthcoming a user was on the site.

source-http://www.dataspora.com/2009/02/predictive-analytics-using-r/

and cute graphs like the famous

https://www.facebook.com/notes/facebook-engineering/visualizing-friendships/469716398919

 

and

studying baseball on facebook

https://www.facebook.com/notes/facebook-data-team/baseball-on-facebook/10150142265858859

by counting the number of posts that occurred the day after a team lost divided by the total number of wins, since losses for great teams are remarkable and since winning teams’ fans just post more.

 

But mostly at

https://www.facebook.com/data?sk=notes and https://www.facebook.com/data?v=app_4949752878

 

and creating new packages

1. jjplot (not much action here!)

https://r-forge.r-project.org/scm/viewvc.php/?root=jjplot

though

I liked the promise of JJplot at

http://pleasescoopme.com/2010/03/31/using-jjplot-to-explore-tipping-behavior/

2. ising models

https://github.com/slycoder/Rflim

https://www.facebook.com/note.php?note_id=10150359708746212

3. R pipe

https://github.com/slycoder/Rpipe

 

even the FB interns are cool

http://brenocon.com/blog/2009/02/comparison-of-data-analysis-packages-r-matlab-scipy-excel-sas-spss-stata/

 

Part 2 How do people with R use Facebook?

Using the API at https://developers.facebook.com/tools/explorer

and code mashes from

 

http://romainfrancois.blog.free.fr/index.php?post/2012/01/15/Crawling-facebook-with-R

http://applyr.blogspot.in/2012/01/mining-facebook-data-most-liked-status.html

but the wonderful troubleshooting code from http://www.brocktibert.com/blog/2012/01/19/358/

which needs to be added to the code first

 

and using network package

>access_token=”XXXXXXXXXXXX”

Annoyingly the Facebook token can expire after some time, this can lead to huge wait and NULL results with Oauth errors

If that happens you need to regenerate the token

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

Roman’s Famous Facebook Function (altered)

> facebook <- function( path = “me”, access_token , options){
+ if( !missing(options) ){
+ options <- sprintf( “?%s”, paste( names(options), “=”, unlist(options), collapse = “&”, sep = “” ) )
+ } else {
+ options <- “”
+ }
+ data <- getURL( sprintf( “https://graph.facebook.com/%s%s&access_token=%s&#8221;, path, options, access_token ), cainfo=”cacert.pem” )
+ fromJSON( data )
+ }

 

Now getting the friends list
> friends <- facebook( path=”me/friends” , access_token=access_token)
> # extract Facebook IDs
> friends.id <- sapply(friends$data, function(x) x$id)
> # extract names
> friends.name <- sapply(friends$data, function(x) iconv(x$name,”UTF-8″,”ASCII//TRANSLIT”))
> # short names to initials
> initials <- function(x) paste(substr(x,1,1), collapse=””)
> friends.initial <- sapply(strsplit(friends.name,” “), initials)

This matrix can take a long time to build, so you can change the value of N to say 40 to test your network. I needed to press the escape button to cut short the plotting of all 400 friends of mine.
> # friendship relation matrix
> N <- length(friends.id)
> friendship.matrix <- matrix(0,N,N)
> for (i in 1:N) {
+ tmp <- facebook( path=paste(“me/mutualfriends”, friends.id[i], sep=”/”) , access_token=access_token)
+ mutualfriends <- sapply(tmp$data, function(x) x$id)
+ friendship.matrix[i,friends.id %in% mutualfriends] <- 1
+ }

 

Plotting using Network package in R (with help from the  comments at http://applyr.blogspot.in/2012/01/mining-facebook-data-most-liked-status.html)

> require(network)

>net1<- as.network(friendship.matrix)

> plot(net1, label=friends.initial, arrowhead.cex=0)

(Rgraphviz is tough if you are on Windows 7 like me)

but there is an alternative igraph solution at https://github.com/sciruela/facebookFriends/blob/master/facebook.r

 

After all that-..talk.. a graph..of my Facebook Network with friends initials as labels..

 

Opinion piece-

I hope plans to make the Facebook R package get fulfilled (just as the twitteR  package led to many interesting analysis)

and also Linkedin has an API at http://developer.linkedin.com/apis

I think it would be interesting to plot professional relationships across social networks as well. But I hope to see a LinkedIn package (or blog code) soon.

As for jjplot, I had hoped ggplot and jjplot merged or atleast had some kind of inclusion in the Deducer GUI. Maybe a Google Summer of Code project if people are busy!!

Also the geeks at Facebook.com can think of giving something back to the R community, as Google generously does with funding packages like RUnit, Deducer and Summer of Code, besides sponsoring meet ups etc.

 

(note – this is part of the research for the upcoming book ” R for Business Analytics”)

 

ps-

but didnt get time to download all my posts using R code at

https://gist.github.com/1634662#

or do specific Facebook Page analysis using R at

http://tonybreyal.wordpress.com/2012/01/06/r-web-scraping-r-bloggers-facebook-page-to-gain-further-information-about-an-authors-r-blog-posts-e-g-number-of-likes-comments-shares-etc/

Updated-

 #access token from https://developers.facebook.com/tools/explorer
access_token="AAuFgaOcVaUZAssCvL9dPbZCjghTEwwhNxZAwpLdZCbw6xw7gARYoWnPHxihO1DcJgSSahd67LgZDZD"
require(RCurl)
 require(rjson)
# download the file needed for authentication http://www.brocktibert.com/blog/2012/01/19/358/
download.file(url="http://curl.haxx.se/ca/cacert.pem", destfile="cacert.pem")
# http://romainfrancois.blog.free.fr/index.php?post/2012/01/15/Crawling-facebook-with-R
facebook <- function( path = "me", access_token = token, options){
if( !missing(options) ){
options <- sprintf( "?%s", paste( names(options), "=", unlist(options), collapse = "&", sep = "" ) )
} else {
options <- ""
}
data <- getURL( sprintf( "https://graph.facebook.com/%s%s&access_token=%s", path, options, access_token ), cainfo="cacert.pem" )
fromJSON( data )
}

 # see http://applyr.blogspot.in/2012/01/mining-facebook-data-most-liked-status.html

# scrape the list of friends
friends <- facebook( path="me/friends" , access_token=access_token)
# extract Facebook IDs
friends.id <- sapply(friends$data, function(x) x$id)
# extract names 
friends.name <- sapply(friends$data, function(x)  iconv(x$name,"UTF-8","ASCII//TRANSLIT"))
# short names to initials 
initials <- function(x) paste(substr(x,1,1), collapse="")
friends.initial <- sapply(strsplit(friends.name," "), initials)

# friendship relation matrix
#N <- length(friends.id)
N <- 200
friendship.matrix <- matrix(0,N,N)
for (i in 1:N) {
  tmp <- facebook( path=paste("me/mutualfriends", friends.id[i], sep="/") , access_token=access_token)
  mutualfriends <- sapply(tmp$data, function(x) x$id)
  friendship.matrix[i,friends.id %in% mutualfriends] <- 1
}
require(network)
net1<- as.network(friendship.matrix)
plot(net1, label=friends.initial, arrowhead.cex=0)

Created by Pretty R at inside-R.org

Moving data between Windows and Ubuntu VMWare partition

I use Windows 7 on my laptop (it came pre-installed) and Ubuntu using the VMWare Player. What are the advantages of using VM Player instead of creating a dual-boot system? Well I can quickly shift from Ubuntu to Windows and bakc again without restarting my computer everytime. Using this approach allows me to utilize software that run only on Windows and run software like Rattle, the R data mining GUI, that are much easier installed on Linux.

However if your statistical software is on your Virtual Disk , and your data is on your Windows disk, you need a way to move data from Windows to Ubuntu.

The solution to this as per Ubuntu forums is –http://communities.vmware.com/thread/55242

Open My Computer, browse to the folder you want to share.  Right-click on the folder, select Properties.  Sharing tab.  Select the radio button to “Share this Folder”.  Change the default generated name if you wish; add a description if you wish.  Click the Permissions button to modify the security settings of what users can read/write to the share.

On the Linux side, it depends on the distro, the shell, and the window manager.

Well Ubuntu makes it really easy to configure the Linux steps to move data within Windows and Linux partitions.

 

NEW UPDATE-

VMmare makes it easy to share between your Windows (host) and Linux (guest) OS

 

Step 1

and step 2

Do this

 

and

Start the Wizard

when you finish the wizard and share a drive or folder- hey where do I see my shared ones-

 

see this folder in Linux- /mnt/hgfs (bingo!)

Hacker HW – Make this folder //mnt/hgfs a shortcut in Places your Ubuntu startup

Hacker Hw 2-

Upload using an anon email your VM dark data to Ubuntu one

Delete VM

Purge using software XX

Reinstall VM and bring back backup

 

Note time to do this

 

 

 

-General Sharing in Windows

 

 

Just open the Network tab in Ubuntu- see screenshots below-

Windows will now ask your Ubuntu user for login-

Once Logged in Windows from within Ubuntu Vmware, this is what happens

You see a tab called “users on “windows username”- pc appear on your Ubuntu Desktop  (see top right of the screenshot)

If you double click it- you see your windows path

You can now just click and drag data between your windows and linux partitions , just the way you do it in Windows .

So based on this- if you want to build  decision trees, artifical neural networks, regression models, and even time series models for zero capital expenditure- you can use both Ubuntu/R without compromising on your IT policy of Windows only in your organization (there is a shortage of Ubuntu trained IT administrators in the enterprise world)

Revised Installation Procedure for utilizing both Ubuntu /R/Rattle data mining on your Windows PC.

Using VMWare to build a free data mining system in R, as well as isolate your analytics system (thus using both Linux and Windows without overburdening your machine)

First Time

  1. http://downloads.vmware.com/d/info/desktop_end_user_computing/vmware_player/4_0Download and Install
  2. http://www.ubuntu.com/download/ubuntu/downloadDownload Only
  3. Create New Virtual Image in VM Ware Player
  4. Applications—–Terminal——sudo apt get-install R (to download and install)
  5.                                          sudo R (to open R)
  6. Once R is opened type this  —-install.packages(rattle)—– This will install rattle
  7. library(rattle) will load Rattle—–
  8. rattle() will open the GUI—-
Getting Data from Host to Guest VM
Next Time
  1. Go to VM Player
  2. Open the VM
  3. sudo R in terminal to bring up R
  4. library(rattle) within R
  5. rattle()
At this point even if you dont know any Linux and dont know any R, you can create data mining models using the Rattle GUI (and time series model using E pack in the R Commander GUI) – What can Rattle do in data mining? See this slideshow-http://www.decisionstats.com/data-mining-with-r-gui-rattle-rstats/
If Google Docs is banned as per your enterprise organizational IT policy of having Windows Explorer only- well you can see these screenshots http://rattle.togaware.com/rattle-screenshots.html

Using Two Operating Systems for RATTLE, #Rstats Data Mining GUI

Using a virtual partition is slightly better than using a dual boot system. That is because you can keep the specialized operating system (usually Linux) within the main operating system (usually Windows), browse and alternate between the two operating system just using a simple command, and can utilize the advantages of both operating system.

Also you can create project specific discs for enhanced security.

In my (limited ) Mac experience, the comparisons of each operating system are-

1) Mac-  Both robust and aesthetically designed OS, the higher price and hardware-lockin for Mac remains a disadvantage. Also many stats and analytical software just wont work on the Mac

2) Windows- It is cheaper than Mac and easier to use than Linux. Also has the most compatibility with applications (usually when not crashing)

3) Linux- The lightest and most customized software in the OS class, free to use, and has many lite versions for newbies. Not compatible with mainstream corporate IT infrastructure as of 2011.

I personally use VMWare Player for creating the virtual disk (as much more convenient than the wubi.exe method)  from http://www.vmware.com/support/product-support/player/  (and downloadable from http://downloads.vmware.com/d/info/desktop_downloads/vmware_player/3_0)

That enables me to use Ubuntu on the alternative OS- keeping my Windows 7 for some Windows specific applications . For software like Rattle, the R data mining GUI , it helps to use two operating systems, in view of difficulties in GTK+.

Installing Rattle on Windows 7 is a major pain thanks to backward compatibility issues and version issues of GTK, but it installs on Ubuntu like a breeze- and it is very very convenient to switch between the two operating systems

Download Rattle from http://rattle.togaware.com/ and test it on the dual OS arrangement to see yourself.

 

 

 

 

 

Workflows and MyExperiment.org

Here is a great website for sharing workflows – it is called MyExperiment.org and it can also include Work flows from many software.

myExperiment currently has 4742 members270 groups1842 workflows423 files and 173 packs

Could it also include workflow from Red-R from #rstats or Enterprise Miner

Continue reading “Workflows and MyExperiment.org”

LibreOffice News and Google Musings

Tux, the Linux penguin
Image via Wikipedia

Official Bloggers on LibreOffice- http://planet.documentfoundation.org/

Note- for some strange reason I continue to be on top ranked LibreOffice blogs- maybe because I write more on the software itself than on Oracle politics or coffee spillovers.

LibreOffice Beta 2  is ready and I just installed it on Windows 7 – works nice- and I somehow think open Office and Google needs an  example to stop being so scary on cautioning—— hey,hey it’s a  beta – (do you see Oracle saying this release is a beta or Windows saying hey this Windows Vista is a beta for Windows 7- No right?)-

see screenshot of solver in  LibreOffice spreadsheet -works just fine.

We cant wait for Chromium OS and LibreOffice integration (or Google Docs-LibreOffice integration)  so Google starts thinking on those lines (of course

Google also needs to ramp up Google Storage and Google Predict API– but dude are you sure you wanna take on Amazon, Oracle and MS and Yahoo and Apple at the same time. Dear Herr Schmidt- Last German Guy who did that ,  ended up in a bunker in Berlin. (Ever since I had to pay 50 euros as Airline Transit fee -yes Indian passport holders have to do that in Germany- I am kind of non objective on that issue)

Google Management is busy nowadays thinking of trying to beat Facebook -hint -hint-

-buy out the biggest app makers of Facebook apps and create an api for Facebook info download and upload into Orkut –maybe invest like an angel in that startup called Diaspora http://www.joindiaspora.com/) see-

Back to the topic (and there are enough people blogging on Google should or shouldnt do)

-LibreOffice aesthetically rocks! It has a cool feel.

More news- The Wiki is up and awaits you at http://wiki.documentfoundation.org/Documentation

And there is a general pow-wow scheduled at http://www.oookwv.de/ for the Open Office Congress (Kongress)

As you can see I used the Chrome Extension for Google Translate for an instant translation from German into English (though it still needs some work,  Herr Translator)

Back to actually working on LibreOffice- if Word and Powerpoint is all you do- save some money for Christmas and download it today from