Oh dear...

Just put my last post through this site and, oh dear...

I write like
Dan Brown

I Write Like by Mémoires, Mac journal software. Analyze your writing!

Open source: doing my bit

Although I can hardly claim to be a prolific blogger I do visit this page regularly to look for updates of other people's blogs (see list at left). One of these (The Open Source Paleontologist) is concerned with the public availability of both data and primary literature. Needless to say I agree with much of what is written there. As many of my readers wll know I also maintain my own site: http://www.graemetlloyd.com, where I try and do my bit. As is often the way with these things my ambition for what should be there goes well beyond my actual motivation to produce it. However, there is some stuff that people apparently do find useful and prompted by some recent comments I thought I'd take an opportunity to advertise what is there for those that haven't visited.

1. Dinosaur supertree bonus material

First off there is extra data from my dinosaur supertree paper, produced with my colleagues over at Raptor's Nest and Museological Meanderings. This includes the MRP matrices (as NEXUS files), the original tree and XML files, as well as R source code for the subsampling analyses. Apparently somebody has used this code so it was worthwhile!

2. Dinosaur matrix list

In conjunction with the above I have been collating a list of published cladistic analyses of dinosaurs. Many of these come from the supertree project, but I have kept an eye out for more recent things and just yesterday updated my list, so presently it is current. I also include NEXUS files of the matrices plus MPTs where I've had time to produce them. Again, this list has been used by at least a few people, but I have no doubt there are publications I've missed so for those keen enough to point them out I would be glad of the info. My eventual aim is to produce a proper relational database that allows automated creation of MRP files and hence an "instant" up-to-date formal supertree of the group.

3. Tree dating code

I wrote a post a while back about the problem of dating phylogenetic trees of fossil taxa. I subsequently wrote code to do it in R and know a lot of people already use it. There are plans to include this with some other functions in a full-fledged library - watch this space.

4. Palaeo-polygon area

I have also written some code to measure the area of the polygon described by the convex hull of a bunch of palaeolatitude and longitudes (now available as a downloadable field in the PaleoDB). Again, this was prompted by an old post. However, it should be noted that there are issues with this function. I now have it working better, but have yet to update the page (email me if you're desperately interested and I'll give you the latest one).

5. Red Queen PDF

On a trip to Chicago where I interviewed for their PhD program I was able to get my hands on Leigh Van Valen's ridiculously well cited, but poorly read Red Queen paper. As I got asked for this a lot I ended up scanning it in and making an OCR'd PDF and have made this available (with permission).

6. Endnote libraries for edited volumes

Being of a macroevolutionary bent I have a large personal library and spent a good chunk of my PhD entering everything into Endnote. Services like WoK were great for entering my journal runs of Palaeontology and JVP (I could just download everything from between a starting year to present), but no such electronic resource exists for my several edited books. These I had to enter manually, at no little effort. It seemed prudent then, to make these freely available once I was done and so you can browse and download copies from this page. I ended up using BibTeX for my thesis in the end and so hope to one day add this format too. I have also added links to these volumes on Amazon (if you buy via this link I get money!) and a bookfinder search (which will usually be cheaper, probably why I haven't made any yet).

Well, that's it for now. Hopefully some of you find at least one of these things useful. It is gratifying to me to know people are using it so please let me know if you like it or if there is anything else you'd like to have. After all, blogs are supposed to be interactive, right?

Iron Sky Trailer

Looks set to be the best Nazi sci-fi comedy of all time....:

A meme of one's own

Memes have to start somewhere, so I though I'd have a go at one. The image above is a tag cloud of the song titles in my iTunes library. Of course a meme only works if other people follow suit, so here's how I did it:

1. Fire up your iTunes (or equivalent) and select all your songs and hit Ctrl+C.
2. Open up Excel (or equivalent) and hit Ctrl+V. On most OS's this should just paste your library in text form, with separate columns for song title, artist etc.
3. Select just the song title column and hit Ctrl+C.
4. Point your browser at Tag Crowd and paste into the "Paste text to be visualized" box.
5. Click "Visualize!"
6. Screenshot the results and post them to your blog.

Stuff I'm totally going to do in 2010

I'm not much into New Years resolutions, but there are a few things I hope to do this year, apart from the usual publishing papers and writing grants. In essence these are about digitisation and downsizing.

1) Digitising my DVD collection
Towards the end of last year I purchased a nifty 1-terabyte external hard disk and I've since been ripping my DVD collection onto it using the excellent Handbrake. Most other rippers are actually two programs, but this is really easy to use and does the whole thing for you (with plenty of options for customising the output). I've even set up a separate iTunes library just for this purpose so I can have all the nice DVD covers and everything, but my music remains on my laptop. (There is a trick on the Mac when you load iTunes by holding down alt first that allows you to pick which library you load.) Currently I'm about half way through the ripping, but there are still lots of covers to scan.

2) The great paper reduction
My second, much bigger project, is to try and digitise my entire academic library so that I can take more stuff with me on my (fingers crossed) next post-doc. Being a macroevolutionary type my library is quite large and runs to several feet of books and tens of boxfiles. Again, I have already started this, purchasing a nice Epson multi-purpose device that includes a paper feed scanner allowing automated scanning of multiple pages, so less work in creating the initial digital files for the ones I can't just download a PDF for. I then tend to clean these up in Photoshop, usually by ramping up the contrast so OCR is easier, as well as rotating them so the text is nice and straight and cropping any black edges. Initially each file (usually one or two pages) is saved as it's actual page number(s) in the paper (so I can quickly see if any are missing) and each paper is a separate folder. I then combine them into a nice PDF using Acrobat Pro, OCR it for text recognition and then optimise it for a smaller file size. I have PDFs for several boxfiles already, but what I really want to do is link these up to my Endnote library before discarding the original, in a recycling bin of course. Not sure I'll complete this in a year, but hopefully I will be able to clear some space from under my desk where I keep the boxfiles that I have no shelf space for.

3) Selling stuff
During my years at Bristol I managed to acquire far too much stuff - I took one carload to Bristol and two van loads out. I have had to downsize to some degree already in my move to London, but there is still a lot of superfluous stuff in my room that I really need to get rid of, either by selling or giving it away. I haven't been ruthless enough in my life so far in getting rid of things I don't use anymore, but hopefully I can finish 2010 with just the things I really need or love.

4) Getting back into running
Just before my PhD I ran the Bristol half marathon and enjoyed it. Since then I haven't really done any running at all, but I now really need the exercise and for a while now I have been thinking of doing the New York marathon, although this will likely have to wait until 2011 due to a clash with this year's GSA. The only way I'm going to get back into it though is if I sign up for another half marathon as I need the incentive to get training again and it looks like I might be going in for the Budapest half marathon in September.

5) Bookmark liberation
In my end of year review I mentioned that I am now getting into reading in a big way, but there are still several books on my shelves that I started reading, but for whatever reason stopped. It is my hope that I can finish these off over the space of the next 12 months, and indeed more generally reach a point where I have actually read all the books I own (with the exception of things like reference books and the like).

My 2009

Because I'm so awesome I'm sure you'll all be fascinated to read a recap of stuff I did in 2009.

1) Leaving Bristol
I moved to Bristol in September 2002 and lived there until March 2009, a huge chunk of my adult life. During that time I completed my Masters and my PhD, but most of all it was where I made pretty much all of the closest friends I've ever had and it was certainly a bit of a wrench to leave.

2) Moving to Nodnol
The reason for my leaving was to take up my first post-doctoral position as a research assistant at the Natural History Museum. I was initially hesitant about returning to London, the city where I spent my (much less happy) undergraduate years, but I found somewhere quiet and pleasant to live and the project I'm working on is really great and ought to lead to lots of quality publications.

3) US Road Trip
Although one of the joys of palaeontology has to be the traveling I hadn't been on what I would consider a "proper" holiday since before my PhD so I spent most of the year looking forward to a US road trip with John and Phil. Our starting point was NAPC 2009 in Cincinnati, Ohio, our goal: Seattle, Washington. A good 2,500 miles away. I certainly enjoyed myself and as we never came to blows hopefully my traveling companions did too. We managed to take in Ashfalls, The Badlands, Deadwood, Rushmore, Dinosaur Park, Custer State Park, The Bighorn Mountains, Yellowstone and even Cicely, Alaska clocking up some 3,000 miles along the way. We got to Seattle in under 8 days, just in time for the Independence day fireworks and a whistle stop tour of the city. It was slightly depressing to then fly back across the same expanse in just a few hours.

4) Reading
This was the year I discovered the trick to getting through books more quickly: spend more time reading. This was prompted by a couple of things. Firstly I am now a commuter again after four and a half years of walking to work I now get the tube and hence can read on the way to and from work. Secondly I finally read Harry Potter after seeing the sixth film convinced me it would be worth it. I ordered the paperback box set and plowed my way through them in enough time to go and see the film again before it came off release. I certainly enjoyed them and the process got me back into reading novels and I now read more than ever. A quick scan of my book shelf shows that I managed to finish a minimum of 24 books this year, pretty good for me!

5) Lego advent calendar
December has been all about my Lego advent calendar and I've decided I just don't care anymore if they are supposed to be for kids. Lego is awesome, end of.

6) Footy
Although Liverpool turned out not to claim the Premiership I did manage to make it back-to-back wins in the fantasy football. However this season isn't going well on either front. I did manage to see another live game, but this turned out to contain the now infamous beachball incident. I didn't even get to see this goal as the queue to get in meant I couldn't see the pitch until about 10 minutes in. I'm going off football...

Even more distilled procrastination - animal links

Some more links for your delectation.

It seems that dog torture is doubly popular, as is that traditional pastime of cat-waking. (Although I prefer cat buckaroo.) If you want a guaranteed smile then I recommend this. I have no idea what could have inspired this, but it is just a little bit brilliant.

I recently finished this book about the sadly extinct Thylacine and was directed towards this collection of the only surviving footage of the animal in life. I really liked this gorilla photo and found this bird's appearance amusing.

This appealed to my sense of humour, reminds me a bit of the "Matt Damon" bit in Team America. Finally, didn't someone once say you can judge a nation by the way they treat their animals?