May 2013
1 post
3 tags
Reading an R file from GitHub
Lets say that I want to read in this R file from GitHub into R.
The first thing you have to do is locate the raw file. You can do so by clicking on the Raw button in GitHub. In this case it’s https://raw.github.com/lcolladotor/ballgownR-devel/master/ballgownR/R/infoGene.R
One would think that using source() would work, but it doesn’t as shown...
April 2013
6 posts
2 tags
Join and participate in Biostats Social today!
¡Hello everyone!
I hope you had a great time this weekend, at the retreat or elsewhere. Now that the department is hyped up with plenty of new ideas and things to do for the self-study and beyond, I think that it’s a great time to remind everyone about Biostats Social.
At it’s bones, Biostats Social is just a private Google Group. But overall it provides us with a space to share...
6 tags
Using plyr and doMC for quick and easy...
A few weeks back I dedicated a short amount of time to actually read what plyr (Wickham, 2011) is about and I was surprised. The whole idea behind plyr is very simple: expand the apply() family to do things easy. plyr has many functions whose name ends with ply which is short of apply. Then, the functions are identified by two letters before ply which are abbreviations for the input (first letter)...
3 tags
Epi vs Biostat Kickball match Spring 2013
This past Saturday the Epi and Biostat troops met for another fun kickball match. Obviously Biostat beat Epi, yup I know: again! This time the score was 15-8 (according to our bookkeeper and captain John) or 12-8 (according to some in Epi).
There was a hint of a surprise at the beginning when Epi scored two runs in the top of the first inning. However, the tide changed back with a homerun by...
2 tags
Fluid
While I was looking for a Google Tasks app for the Mac, I found the following Quora thread where Dave Thompson suggests trying out Fluid.
It’s free and super simple to use and with it I create apps for some of the sites that I visit frequently like Gmail. One advantage I see is that I can now look on a specific desktop my Gmail (right now I’m using 8) and help me organize my work....
5 tags
Laptop fixed =)
I just want to thank everyone that gave me ideas of what to try and whom to ask for solving the issue I was having with my laptop.
For future reference and to complement my previous post, here’s a list of other things I tried.
I ran a memory test using memtest from here.
I updated my OS-X to 10.8.3 from 10.7.5, and although it froze the first time it was installing, it did pick up from...
5 tags
Need some help fixing my Mac...
2 days ago I was writing some R code for #jhsph753 in an Rmd file. I was careless and didn’t realize that one computation would be very RAM intensive until I was running #knitr (as a ‘silent’ process from TextMate2). My computer started swapping and became unresponsive, without being able to force quit. So I did a hard restart: aka, I shut it down by holding the power button.
...
March 2013
10 posts
4 tags
Have you been 'relative stupid'?
I enjoyed reading “The importance of stupidity in scientific research” by Martin A. Schwartz which I learned existed through @hmason and @simplystats.
I found the point of how it’s normal to feel stupid in academia and specially in Ph.D. programs to be illuminating. But Schwartz clarifies that there are other kinds of stupid:
we don’t do a good enough job of teaching...
2 tags
"Do analytics really tell the whole story?"
“Do analytics really tell the whole story?” by Vic Ketchman explores how analytics is used nowadays in the NFL draft. The entry point is the “Moneyball” movie and Ketchman’s piece is mainly a digested interview to Tony Villiotti from draftmetrics.com
According to him:
What is analytics? It’s the accumulation of meaningful patterns in data, for the purpose of using...
6 tags
Great commentary on sequestration's impact on...
Today Jeffrey T. Leek and Steven L. Salzberg published a paper commentary in Genome Biology today titled “Sequestration: inadvertently killing biomedical research to score political points” (Leek & Salzberg, 2013) which I think is a must read for anyone. Seriously!
I do not mean anyone involved in research, or all scientists. I mean, this commentary should be in the national media. Why?
...
8 tags
New Citi ThankYou ballon TV commercial looks like...
I don’t know about you, but I think that this new “Citi ThankYou Cards” TV commercial is trying to ride the popularity train from the “HELLO KITTY IN SPACE” video.
Hm… it looks like a ripoff, smells like a ripoff, tastes like a ripoff… is it a ripoff?
Maybe it’s just flattery, maybe it’s imitation, or maybe it’s...
6 tags
Predicting who will win a NFL match at half time
It was great to have a little break, Spring break, although the weather didn’t feel like spring at all! During the early part of the break I worked on my final project for Jeff Leek’s data analysis class, which we call 140.753 here. Continuing my previous posts on the topic, this time I’ll share the results of my final project.
At the beginning of the course, we had to submit a...
1 tag
"I am a writer" exercise
I do not have a clear memory of when I started to write or in which language it was. My first written words might have been in English since I lived in Boston (USA) three years during my early childhood. By age five I was back in Mexico and that is where I am sure I wrote my first full homeworks. During elementary school, I changed languages once more—this time to French. By middle school, I...
2 tags
And so begins English Composition I
This week started the English Composition I: Achieving Expertise course (Comer, 2013) that I have been looking forward to.
I am not sure yet how long I will last, but I hope to enjoy it as much as I can. Plus, it should help me with my posting and other writing areas. While I last in the course, I plan to publish my writings in the blog too. So you will hopefully see me be more active here.
As...
1 tag
FBit: GitHub repo for posts with R code for this...
This is a test post since I want to improve upon Jeffrey Horner’s strategy for posting R code in Tumblr. The only minor improvement I wanted to try out is hosting the images directly on the web. I mean, right now the images won’t show in RSS readers. I’m not doing anything new at all, just using the imgur_upload function in knitr.
This is part of my plan to write paper posts. I...
2 tags
Commenting scientific papers
I’ve been thinking about commenting papers in blog posts. I did a few some long time ago, but now I’m thinking of doing this activity more systematically. There are several reasons why I’m thinking of doing this, say for 1 paper a week. It has the obvious advantage of forcing me to read a paper in depth per week. At the same time, I want to learn more from others. See what I like...
4 tags
Analyzing SimplyStatistics visits info
Recently we had to analyze the data of the number of visits per day to SimplyStatistics.org. There were two goals:
Estimate the fraction of visitors retained after a spike in the number of visitors
Identify (if any) any factors that influence the fraction estimated in 1.
For me it was a fun project in part because I like SimplyStatistics but also because I think that finding the answers to the...
February 2013
5 posts
1 tag
Alfred: a must for any Mac user
At the beginning of the semester, I decided to go hunting for Mac apps that would help me be more organizing and/or enjoy my Mac even more. After all, I was using the basics –with multiple spaces– and had only customized my favorite editors.
It turns out that Alfred is an excellent app. The free version can get you a lot of mileage and save you lots of time by typing alt + space, then entering...
3 tags
1 tag
Liking "Inbox Zero for Life"
I’ve been using the “Inbox Zero for Life” strategy for a few weeks, and I think that it’s been payed off for me in this short span.
As it’s stated in that long guide, one of the major concerns you might have is that it could end up as just changing a current problem for another one. I think that so far, that hasn’t been the case for me. Sure, my starred emails...
1 tag
After using bit.ly a month or so
I think that I like the idea of moving to bit.ly Well, moving might be an understatement. So far, I’ve been using the regular bookmarks and bookmark folders in Firefox and Google Chrome. But I’m beginning to see the advantage of using bit.ly Sure, getting numbers on who accesses you public bit.ly’s can be interesting. But whether you keep them private or public, I think that the...
4 tags
Sharing my work for "Advanced Methods III"
This semester I’m taking the live version of the Data Analysis class by Jeff Leek. His more popular version of the course is available through Coursera.
One of the things that Jeff promotes is reproducibility and sharing code. I share that tendency and thus created a Git repository for my homework and code for the class: lcollado753. I’m hosting it with GitHub to try it out since I...
December 2012
3 posts
2 tags
Cubby: does it have a niche?
So today I got an invitation to install Cubby in my computer. It looks like another Dropbox service, but what really attracted my attention is the “make a folder a cubby” feature. This allows you to select any folder and get it synched into your devices through the cloud. At least for me, this gives Cubby an important niche. I don’t know about you, but well, there are some things...
4 tags
Adding youtube videos in pdfs, html reports and...
I got a question today on how to add a video to a beamer pdf presentation. Well, I had never done it, but I got curious enough to google around for a bit and here is the end product.
One way of doing it is using the media9 tex package. For this to work you need to have the latest version of texlive (or miktex). Then, it’s quite straight forward to include the video. The issue is that you...
3 tags
Epi and Biostat go ice skating
In preparation for our Spring kickball match, Epi and Biostat went ice skating this past weekend. A large chunk of us then continued to mingle at a local bar ^^. Enjoy the pictures!
From EpiBiostatIceSkating
November 2012
7 posts
2 tags
Re-purposing Fellgernon Bit
I have decided that it’s in my best interests to separate my academic posts from my personal ones. Thus, I have moved the posts I considered to be personal to my new blog, Fellger Byte. I like the name since it goes along with Fellgernon Bit, plus it involves mostly cooking posts.
Fellgernon Bit will continue to have it’s posts linked on twitter and on the Fellgernon Bit facebook...
2 tags
Testing R code in Tumblr
Using Jeffrey Horner’s guide to include R code in Tumblr posts.
Title
This is an R Markdown document. Markdown is a simple formatting syntax for authoring web pages (click the MD toolbar button for help on Markdown).
When you click the Knit HTML button a web page will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can...
5 tags
Introduction to R and Biostatistics (2012...
To follow my Introducing R and Biostatistics to first year LCG students (2012 version) post, you can now find the presentation online from my site either in presentation format, in a single webpage format, or the raw Rmd file. To prove the point that publishing to RPubs is super easy, you can also find the single webpage format over there. I also like how you can comment and share in RPubs.
One...
2 tags
me: Bad rm, don't delete stuff I didn't want to...
When Sandy was in town at some point I started doing some of my research work, but I shouldn’t have. I basically did a silly mistake and erased files that take a long time to compute.
Prior to being here, I had an alias in my bash profile like this:
alias rm=’rm -i’
But when I setup my bash profile here I googled a bit to find what was the best common solution to avoid...
1 tag
Understanding (not so sure) measurability (S8)
The result of discussing a problem for my Probability Theory class (Exercise 13.3 in Billingsley if you know what I’m talking about) with fellow classmates.
That was the fifth homework. I wonder what is coming!
2 tags
Being the "good" TA is impossible (S7)
During our teaching assistant (TA) training session (which was great), we enumerated the qualities that make a TA be good, bad or were neutral.
The list of things a “good” TA has to do got huge very fast. I claim that anyone doing half of them is a great TA!
2 tags
Logistic regression and interactions (S6)
This was a great image made by my companions for the 2012 masters comprehensive exam. It’s about logistic regression. Anyhow, I thought I should throw it out there without much further explanation.
[Edit: fixed some grammar]
October 2012
13 posts
3 tags
Got acknowledged in a paper ^^ (S4)
During the weekend while I was talking with a friend and former colleague, I realized that my name was mentioned in the acknowledgements section of a paper :) I haven’t been much in touch with what’s been happening back home, so this was a nice surprise.
The paper is: Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia...
4 tags
Introducing R and Biostatistics to first year LCG...
On Friday November 9th I’ll be giving a talk to the first year students from the Undergraduate Program on Genomic Sciences (LCG in Spanish) during their “Seminar 1: Introduction to Bioinformatics” course. It’s just like I did a year ago as I documented in my post Introducing Biostatistics to first year LCG students.
Well, this time I’ll change things a bit. I’m...
2 tags
A peek at our origins (S3)
A good month ago we started the latest pin map in our department. I say latest because it has been done before and at some point that no one knows, the pins will disappear. Anyhow, I was playing around with it and trying to color code the pins according to the flags. In the case of the US I also tried the common blue/red representation for democratic and republican states.
I love the two green...
1 tag
Super basic Illustrator: event invitation
Amanda and I are organizing a cultural student mixer for students in our department. One of the things we needed to do was invite everyone to attend. I like using computers, but graphic design is not something that I’m too excited about, but I still wanted to try something out.
My goal was to show an image of a bowling lane where the Earth (as the ball) knocks down “statistical...
2 tags
Visualizing colors()
The other day I learnt about the existance of the colors() vector in R which specifies all the character-based colors like “light blue”, “black”, etc. So I made a simple plot to visualize them all. Here’s the code:
mat <- matrix(1:length(colors()), ncol = 9, byrow= TRUE)
df <- data.frame(col = colors(),
x = as.integer(cut(1:length(colors()), 9)),
y =...
3 tags
Bitbucket revamped
Bitbucket announced their new “look” today. The goal is to make it more team friendly but I guess that they also wanted to make it look fresh.
For example, the overview page now has a quick summary:
That can be useful coupled with the simpler navigation tabs. But I think that the best of the new tools is the ability to comment at a given commit at any line change.
This gives a...
4 tags
Why aren't all of our graphs interactive?
During the last pre-happy hour seminar, Karl Broman talked about Why aren’t all of our graphs interactive? I didn’t know, but a few years ago Karl worked in the department and clearly promoted beer-drinking and is the heart of the department. I’m a fan of our pre-happy hour seminars since you have a get to listen to good/fun talks over a beer or two.
But I’m also a fan of...
2 tags
An Online Bioinformatics Curriculum
Last week I talked about online courses in my JHSPH-Biostat through Coursera post. Now I’m back to comment on An Online Bioinformatics Curriculum by David B. Searls. Sur Herrera pointed out this paper to me, and I have to say that if you are considering learning bioinformatics online it will be very useful to you. David Searls first goes through a history recap of online (free) courses....
1 tag
‘Arsenic-life’ bacterium prefers phosphorous after...
‘Arsenic-life’ bacterium prefers phosphorous after all by Daniel Cressey summarizes a recent paper where it’s shown that GFAJ-1 will use phosphorous over arsenate even when phosphorous is very rare in relation to arsenic.
GFAJ-1 is the weird bug I talked about in Genome of Controversial Arsenic Bacterium Sequenced at the end of 2011. The whole story is interesting from the point of view of...
1 tag
tRRaffic
Great for learning how to calculate a relative risk (RR) …
2 tags
02/27/12 PHD comic: 'Inspired by true events' →
Totally what happened to me on Monday night! (whenever I saved this post as a draft :P, but it’s happening again now)
2 tags
Check all your accounts for emails at once in...
Do you use Gmail as your primary email account? Primary, what? Well, I’m sure that you have your personal account somewhere and your work or university account too. You can either log into each email interface or you can integrate them to a single one.
Gmail makes this easy as you can go to the “Settings -> Accounts and Import” to set up Gmail to pull all of your email into...
3 tags
JHSPH-Biostat through Coursera
Have you heard of online education? If you are in the US or Mexico I’m sure that you have seen some ads about online universities. Well, that’s not the type of education I’m talking about. I’m talking about free high-quality education.
For some years, the top option has been the Open Courseware (OCW) organized under the Open Courseware Consortium (OCWC). Back in 2009 I...
September 2012
5 posts
5 tags
Learning about social networks through an...
During this week’s journal club meeting Hilary Parker (homepage, blog) led the session on “Identifying influential and susceptible members of social networks”. Were there some speakers or why did she “lead the session”? By this I mean that Hilary tried a very different (and interesting) format this time. Instead of giving a talk, not a formal one like at seminars, she...
4 tags
Quid @Biostat-JHSPH
Just like most scientific departments, we have a seminar (weekly over here) where very bright people come to us to talk about their work. Being a Biostatistics department, we mostly get faculty from other Biostatistics departments from universities to talk to us. This week was quite different. Amy Heineike from Quid gave us a talk describing their product, which fits perfectly in what is now...
2 tags
4 tags
Introducing Git while making your academic webpage
Last week I gave a presentation during our computing club on how to use git (a version control system). I used as a motivating example the first steps of creating your own academic webpage. The goal was to make it interesting to both new students (who might have been more interested on the webpage part) and older students (for whom version control should be a must). The slides and all the material...
3 tags
