Uninstalling old version of R in Ubuntu 12.04.4 for R 3.1.1

After many frustrated attempts at installing the newer version of R aka R version 3.1.1 (2014-07-10) I finally figured out what was perhaps happening.

I had done the glorious and famous step 0 of:
sudo apt-get update
sudo apt-get remove r-base
sudo apt-get remove r-base-core

up to no avail! R.2 something always managed to run and execute itself.

"Sock it to Me"

What finally worked was an interesting combinations of various suggestions on internet that some how worked together - like a miracle!

The long and short of the procedure of installing R. 3.1.1  after successfully effacing the older version of R is:

Uninstalling the older version
Step 1: Do the Step 0 (the above mentioned glorious and famous step 0) of removing r-base and r-base-core

Step2: See what still remains:
 dpkg --get-selections | grep "^r\-"'

Step 3: Individually purge the files that belong to 'r-' family. I used sudo apt-get purge (name of R related file)

Installing the R 3.1.1 (2014-07-10) -- "Sock it to Me" 
Step 4: Followed suggestions as mentioned here: (http://askubuntu.com/a/352438) Please note that when I typed in the command for seeing r packages
apt-cache showpkg r-base I saw different packages than the ones mentioned in the comments. This is explainable as packages keep updating with newer ones showing up. I had the following show up:

Package: r-base
Versions:
3.1.1-1precise0 (/var/lib/apt/lists/cran.rstudio.com_bin_linux_ubuntu_precise_Packages) (/var/lib/dpkg/status)
 Description Language:
                 File: /var/lib/apt/lists/cran.rstudio.com_bin_linux_ubuntu_precise_Packages
                  MD5: 5787ca79ed716232c4cc2087ed9b425b
so I did
sudo apt-get install -f r-base=3.1.1-1precise0

Step 5: Typed in R and bingo!!

Enjoy R folks!

Research warns that Frozen Boogers are linked to Sure Death

Bleaksburg, VA.  Following reports of the area woman, who got frozen boogers during her stroll in single digit temperatures yesterday, researchers are now warning that frozen boogers are directly related to sure death.
Virginia Tech researcher P. See was heard screaming in campus hallway, "Stay away from frozen boogers! They are (like) death bombs!"

Research done at the local University in Bleaksburg, suggests that there is a strong correlation between death and frozen boogers. Dr. See was further heard saying, "Almost everyone, who had frozen boogers is now dead. Those who are still alive will die one day. I repeat- Stay away from frozen boogers!!", he shouted emphatically.

He added quickly, "If one actually succeeds in avoiding frozen boogers, one is not guaranteed not to die. However it is still very important that frozen boogers are completely avoided. The numbers of death related to frozen boogers are very important and can not be ignored." 

Earlier today officials at UBF issued a warning notice to all their poorly paid labourers and advised them to avoid deadly frozen boogers. 

University warned its denizens to not pick up frozen boogers off the grass or the snow. Students were advised to not scratch underneath desks during class as the bullies can easily plant frozen boogers there.

According to an area woman, her boogers froze during her casual stroll to work yesterday. The secret sources informed that she attempted to snort boogers off her nasal cavity when they froze mid air. The detailed news can be found here.

Area woman misses work as she frantically searches for Onion Reporters to report frozen booger

Bleaksburg, VA: Area woman is reported to be on a look out for Onion Reporters. Locals reported that she is missing work that she is actually paid to do, as she is looking around for Onion reporters frantically. It is reported that today morning the area woman attempted to snort her nose boogers out on the snow as she walked to work, and her nose boogers froze, leaving her helplessly looking for Onion reporters. 

An area man unable to comprehend her passion to get news of her frozen boogers out was heard saying,"She is so frantically running around searching for Onion reporters. I mean, man! It is just frozen booger! She is acting like like it is frozen brain or innards or intestines or so!"

Her colleagues at work on the other hand, totally echo the need for attention and media hype of her frozen boogers. One of her colleague was heard saying about her frozen boogers, "This is perhaps the most interesting scientific observation to have come out of our work group! Like ever ever!"

That I may serve~

Being a faculty in a university for me rhymes with the single concept of Service.

Service:

And, in service I uphold the service to students, university and to the community:

To students: As a faculty member, one embraces the choice to serve the students through inclusive, interested, and engaged pedagogy and involved mentoring. A faculty member is in a unique position to directly influence the future of our world and I uphold the service of allowing, encouraging, and helping growth of students as being the fundamental duty of any faculty member. 

To University: The university environment provides fertile ground for advancement of society and as a faculty member the service definitely includes service to university and its smooth functioning. As I have learnt with my interactions with Graduate Student Assembly at Virginia Tech, luncheons with Board of Visitors and interaction with Dean of Graduate School Dr. DePauw, the university officials and their motivation are quintessential for the university to thrive and create a learning environment. A faculty is obliged to serve the institution that serves, allows, and mentors the faculty itself.

To Community: Community through its million direct and indirect means affects and causes the university environment to exist and thrive. Service to presently existing community is as much as a faculty duty as is preparing the future community. Through her outreach efforts, her modeling of ideals that she upholds and respecting that she also represents the university, the faculty member is responsible for contributing to the society, from which the future springs,  and in where the present resides.

The three virtues that I would strive for as a faculty member wannabe are:

Advancement: 

When I ascribe the duty and expectations on (me as) a faculty member to help prepare a sustainable tomorrow, as she serves the present, I fully comprehend the need of the faculty member to be at the leading edge of the latest developments in her field of expertise and interest. And, with this comes the responsibility of staying abreast and aware of latest research, advancement, tools, technologies, and ideas that can help her serve the students, university, and the community better. 

To me faculty member is a lot more than a long standing product and part of a legacy rich institution. She is in charge of being aware of the change, embracing and finding opportunities in change, instead of choosing the state of denial.

Inclusion:

To me a faculty member epitomizes the term 'global citizen' and is a person who embraces, values, and respects diversity in all its forms. In doing so she actively models inclusive practices.  In an increasingly globalized economy and with increasing hopes of a truly globalized world, inclusion is an ideal worth striving for. 

Dissemination:

A chief difference between an expert, scientist and a faculty member, in my mind, is that latter has strong intentions to disseminate knowledge and understanding. Outreach efforts, engaged pedagogy and mentoring are few very powerful tools through which a faculty member reaches out and participates in dissemination. Being a faculty member to me implies embracing that all sciences and human understanding is our collective property and whenever appropriate, it is faculty duty to disseminate the information and understanding. 

I believe that our society always has had the potential to live outside the very confined walls of awareness and understanding, best described by Nobel Laureate Rabindranath Tagore in following lines:

"Where the world has not been broken up into fragments by narrow domestic walls;

Where words come out from the depth of truth;
Where tireless striving stretches its arms towards perfection;
Where the clear stream of reason has not lost its way into the dreary desert sand of dead habit;
Where the mind is led forward ... into ever-widening thought and action" 

As a faculty member wannabe, I want to participate in building a world that the Rabindranath Tagore's lines above describe.
When I recognize a potential for good, I want to allow the potential bloom. And, this does include guiding it and nurturing it. And, when I see a change that is either inevitable or has potential for good of planet, I will allow the change to be, nurture it and help it be aware of its own value and potential.

Spinning 3D MDS plot in R

I did the classical MDS on my data and drew 3D spinning MDS plot and here is the code:
(Note that this code uses vegan, MASS, and rgl packages and the plot below was made in R 2.15.3)

And here is the plot:



Yay!

And yes now here is the data format:
In first column are names of different samples and in next columns abundance of different classes of bacteria. 

Sample A   sp1   sp2   sp3   sp4 ...
Sample B   sp1   sp2   sp3   sp4 ...
Sample C   sp1   sp2   sp3   sp4 ...
.
.

 

The Power of Teaching~

Reflecting back on the entire semester of GEDI and PFP classes at VT, I sense that my intention and attitude towards teaching have elevated from the desire to help others (students) find beauty in engineering in a way that I have found, to something even higher. And, that something higher is ineffable enough for me not find a noun suitable for it. I can try adding adjectives to what teaching means to me right now: a purpose for my awareness in this lifetime, something more akin to worship and the journey to higher self.

In My Past-Life

(Pre GEDI and PFP life): I have been a self-studying self-built person for most of my life. Most teachers in my undergraduate education to me were like the priest in a temple/church/mosque/anything-else to whom I pay respect and pretend to listen. My real spiritual development happened outside the holy-moly walls of the pious shrine/building. 

That is how most classes were for me- I attended them (mostly).  I tried not to sleep. I pretended to listen when awake. I tried not to read something else. (Facebook etc were not the thing yet.) I freaking tried all of that above. My real learning happened when I pored into books in my hostel room, in library, in the park, in our athletics stadium.

And, that is exactly the reason why for a long time I have held teaching as a pious profession. My belief has over time reinforced itself with the plethora of note-reading, no-eye-contact-please teachers that I have had. The more my teachers  performed  sadly in their theatrics and interest in teaching, the more convinced I became. 

The reason for this reverse reinforcement was this: It appalled me that the beauty I find in subjects is something that most of my class will probably never experience, because most of them need teachers to show them the beauty. 

So, I would take time and teach my classmates. And, the fire (and the zeal) built on itself.

This Life:

Now I am almost towards the end of this wonderful GEDI and PFP experience. My intention for teaching has risen over the desire to share the beauty as I perceive it to instead waking the genius in my students (and not transferring to them my genius image of the subject.)

I am thrilled. I am inspired. The power of teacher is not only in showing students what the subject is and how freaking exciting and beautiful it can be, but also in awakening the genius in our students. It is in helping them be more self-aware. To help them come vis-a-vis to their self-potential and self-inspirations.

Teachers are powerful. They have this magic wand that they can use to make the future stronger. They instill seeds in their students. (Seeds of what, everyone in the class chooses.) They sit in positions where they can make great service to society as they try to live with high ideals (/model them.) Think Henry L.I.V. Derozio.

Teach, Prey, Love:

In most Indian systems of philosophy the teacher (Guru) is often referred to as a blessing or someone above God. In fact there is a beautiful couplet translated as:

"Guru and God both are here, to whom should I first bow
All glory be unto the guru, path to God who did bestow"

Oh my gawdliness! I can not wait to get the chance for waving my wand in a formal setting! 

PBL: Open ended and close ended~

Having done the PBL and watched the presentations of other groups, I am Thrilled!

Wow! What amazing topics! How amazing ethical, social, financial dilemmas! How very unique structure of the PBLs and layout for assessments. Congrats fellow GEDIs! I am impressed and hopeful that we will all go ahead to become truly the teachers of our students, for our students, and by our students.

Open-ended and Not so open ended PBLs:

I want to broach the topic of PBLs being open ended or close ended. Which is better? Probably this in itself is an open ended question :)

So, I will just focus on what I understood from our presentations (not including the readings) on advantages of both kinds of PBL.

Advantages of Close-ended PBL:

Subjects that need to train students in at least in part finding the right answers can benefit from close-ended PBL. We ofcourse dont want bridges and airplanes with faulty designs. In disciplines where right answer does exist, close ended PBL serve the dual purpose of engaging students through its story and thereby guiding students to arrive at the right answer.

Advantages of Open-ended PBL: 

Oh! And yes when I want to fire students' creative thinking, and imagination, and I want to encourage them to 'push the envelope', of course I will choose an open-ended PBL. Because sorry ma'am and sir, there is no correct answer! It is a continuum with no ends. It is often conflict of interests, ethics, engineering challenges, public welfare, and arts! 

It is beautiful! And we certainly need more of such PBLs in our class rooms!

And, I want to end this blog with the picture below that reinforces the abilities of our students and our future! Great job GEDIs! It was a pleasure to be in same class as you all!