BiBTeX and the Canadian Journal of Earth Sciences

While prepping a manuscript for the Canadian Journal of Earth Sciences, I needed a BiBTeX (.bst) style file that I could use to format my references properly if I wanted to use BiBTeX and LaTeX to write the manuscript. CJES does alow you to submit LaTeX (.tex) files, however I couldn’t find a reference style file online. Instead, I used the custom-bib package to create a custom file that matched up with the CJES reference format. In order to hopefully save others from extra work, I’ve posted the resulting file here for anyone to use. Be forewarned though, some of the more awkward types of references may not be exactly as they should be, and for the final submission I think you may need to copy the bibliography and paste it directly in the LaTeX file you submit.

Enjoy.

philosophiae doctor

I have officially received my PhD from McGill University, and can now identify myself as Dr. Vavrek, although I still keep on filling out forms and checking off the ‘Mr.’ box. Along with that, I’ve managed to get hired on at the Royal Ontario Museum as an Assistant Curator, though the contract is only for a year and a half. I’ll be at the ROM helping to set up a big new exhibit that’s set to open in the summer of 2012. Big things happening!

Parallelized functions in R

I have released a new package on CRAN called ‘parfossil‘ where I have been experimenting with a number of parallelized functions. While R is a readily accessible and fast-to-code language when it comes to stats, it can be really slow when it comes to large analyses, especially on non-desktop computers. However, for my research most of the analysis time is spent in repetitive loops, like Monte Carlo or bootstrap analysis. Currently, R runs everything in serial, with each permutation in a resampling analysis done one after another. This was the only way when most machines only had one core, but with the proliferation of multicore chips even on laptops, this means we are only using a portion of our computer’s power when we run an analysis. With multicore chips we can assign different tasks to different cores, but this is often a difficult thing to code for. Luckily Revolution Analytics has made available a simple to use package called ‘foreach‘ with an included function of the same name that makes the process of parallelization much easier. So far, with the functions I have recoded to run in parallel, I am seeing a speed up of 1.5 to 1.8 times just on my dual core laptop. I would imagine that using a quad core chip would see somewhere above a 3 times speedup; that could mean several hours to even days less of waiting in some cases for some really large data sets. And over the next few years most computer chips will have even more cores available to them. The future of R computing is in parallel.

Maastrichtian Dinosaur Provinciality

Hans Larsson and I had our paper published recently in PNAS on the low beta diversity of Maastrichtian dinosaurs in the Western Interior. Hopefully a few people will read the methods and notice that we used the fossil package to do a lot of the stats in it, and others might start using it as well. If you have any questions about the paper or the package, feel free to contact me any time.

Teaching

I have been reading a bunch of articles lately on education, and how to improve it. It’s been making me think a lot about my own education, especially in university. I just want to know if the major universities are ever going to give education more than a fleeting thought. Obviously, research is very important, but at what point should it be to the exclusion of teaching? If you never take the time to teach others what you know, then what? Knowledge not passed along is knowledge lost. I would hate to have toiled away at my research, uncovering new things, but not have shared that with others before I died. And I mean more than what can be passed along in a journal article. Too many journal articles are never read anyhow; if you actually take the time to teach someone what you know, then you know that knowledge will have been passed on. And when I talk about teaching, I mean more than just standing in front of a room and saying words. There was a class in university that I went to less than half the time, and I did better for it because I didn’t get confused by the abysmal teacher reading nothing but equations off a Powerpoint slide. I think that too often, profs forget that the people they are teaching could become some of the most important people in their lives: namely, politicians. If these future politicians (and their constituents) a never taught how exciting or amazing a subject is, that subject might not get as much funding the next year, because nobody cares about it. Teaching can be in your own self interests.

Building a Better Teacher (NYT)

Why We Must Fire Bad Teachers

Fixing US STEM education is possible, but will take money

fossil Package Updated to 0.2.4

I just uploaded a new version of fossil to the CRAN website, with a number of changes. There are some fixes in the way the spp.est() function was handling abundance data, and I’ve added a small species/locality dataset that I used for a number of new examples in the package. I’m also currently working on a new clustering method to include, but it’s still being worked on at the moment. Hopefully it’ll be in the package before too long.

Enjoy!

LaTeX and Palaeontologia Electronica

I’ve been trying to prepare a manuscript for submission to Palaeontologia Electronica (PE), and as my workflow at the moment has been revolving around LaTeX, I took te plunge into creating my own custom bibliography style file in PE format. Luckily for me I could use the great makebst.tex file by Patrick W. Daly which simplified the process to a series of multiple choice questions. I somehow doubt that there is that many other palaeontologists using LaTeX for manuscript submissions, but anyhow here’s the palelec.bst file (I can’t upload .bst files to this site, so just copy and save the text in a text editor as palelec.bst). Hopefully it works, as I’ve been fighting a bit with WordPress to get it to render properly, but if need be, you can always contact me and I can send out a copy of the original .bst file.

UPDATED: This is a link to the original file.