Eric’s Enlightenment for Thursday, May 14, 2015

1. Alcohol kills more people worldwide than HIV, AIDS, violence and tuberculosis combined.
2. Some crystals don’t recrystallize after heating and cooling, but form amorphous supercooled liquids.  Modifying the molecular structure of diketopyrrolopyrrole using shear forces can induce this type of behaviour.  Here is a video demonstration.  Here is the original paper.
3. How pyrex was born out of an accident in cooking spongecake 100 years ago.  (Hat Tip: Lauren Wolf)
4. Check out David Campbell’s graduate statistical computing course at SFU.  It dives into some cool topics in his research that are not always covered in statistical computing, like approximate Bayesian computation and many computational Bayesian methods.

Eric’s Enlightenment for Wednesday, May 6, 2015

1. Moldova has mysteriously lost one-eighth of its GDP, possibly to fraudulent loans.
2. Kai Brothers was diagnosed with HIV in 1989, but did not show any symptoms for 25 years.  Does he have a natural defense against HIV?  Now that he is starting to show symptoms, should he start taking anti-retroviral drugs and deny scientists the chance to look for that natural defense in his blood?
3. Use the VVALUE function in SAS to convert formatted values of a variable into new values of a character variable.
4. Alex Reinhart diligently compiled and explained a list of major “egregious statistical fallacies regularly committed in the name of science”.  Check them out on his web site and in his book entitled “Statistics Done Wrong“.  I highly recommend reading the section entitled “The p value and the base rate fallacy“.
   

Useful Functions in R for Manipulating Text Data

Introduction

In my current job, I study HIV at the genetic and biochemical levels.  Thus, I often work with data involving the sequences of nucleotides or amino acids of various patient samples of HIV, and this type of work involves a lot of manipulating text.  (Strictly speaking, I analyze sequences of nucleotides from DNA that are reverse-transcribed from the HIV’s RNA.)  In this post, I describe some common functions in R that I often use for text processing.

Obtaining Basic Information about Character Variables

In R, I often work with text data in the form of character variables.  To check if a variable is a character variable, use the is.character() function.

> year = 2014
> is.character(year)
[1] FALSE

If a variable is not a character variable, you can convert it to a character variable using the as.character() function.

> year.char = as.character(year)
> is.character(year.char)
[1] TRUE

A basic piece of information about a character variable is the number of characters that exist in this string.  Use the nchar() function to obtain this information.

> nchar(year.char)
[1] 4

Fall HIV/Antiretroviral Update: Monday, November 18, 2013 – Sheraton Wall Centre Hotel in Vancouver

Please join me to learn more about recent research in all aspects of HIV and AIDS in this one-day seminar!  More information about this event, including the full list of speakers and the titles of their presentations, can be found here.  Here is the description of the event from the web page:

This is an open educational event sponsored by the BC Centre for Excellence in HIV/AIDS and accredited by the College of Family Physicians of Canada. A light breakfast, lunch and refreshments throughout the day will be provided on site.

Online registration is now closed. If you still wish to register, please send a request to the following e-mail: pwhite@cfenet.ubc.ca

Please note that seating is available for up to 350 people and, therefore, pre-registration is strongly recommended. On-site registration will not be available.

If you will attend this event, please feel free to come up and say “Hello”!

A New Job at the British Columbia Centre for Excellence in HIV/AIDS

Dear Readers of The Chemical Statistician,

You may have noticed that I have blogged less frequently in the past few months; this has been due to a major change in my career: I recently accepted a new job in the Laboratory Program at the British Columbia Centre for Excellence (BC-CFE) in HIV/AIDS in Vancouver!

A bioinformatician who works in this group recommended me for this position to his supervisors during this past summer.  Having lived in Vancouver before, I have heard a lot about the work that the BC-CFE in HIV/AIDS has done for many years to improve the lives of HIV and AIDS patients and prevent HIV transmission.