Category Archives: Uncategorized

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.

Reproducible Results: Not Likely

A PLoS article this week puts some numbers (small, though they may be) on how truly free and open scientists are in sharing their data. For the article, the authors sent information requests for data previously published on in PLoS journals. The thing about these journals is that they have an explicit data sharing policy, which makes it clear that the raw data sets they use in their analyses must be made available to other researchers.

Just a little history about the PLoS journals: they were originally set up with the ideal of Open Access as a founding tenet. This included not only sharing your data but making the journal itself freely accessible to anyone, free of subscription.

But back to the article itself. THe authors found that out of 10 requests for data, they recieved only one dataset. In fact, some of the data holders seemed rather indignant in the thought that someone might actually want to look at THEIR data, as I’m sure they thought the only reason why would be for the requesters to scoop the next big story to come out of these datasets.

In the end, this study only really serves to emphasize the fact that science is still a very closed (and I would say, closeminded) place to work in.

Evolution Essentials

A great summary on Ars Technica about 5 essential things that most people don’t understand about evolution. It’s a good read even if you do think you know a lot about evolution, as it emphasizes some points that I think are often muddled in a lot of scientific discussions (subobtimal solutions being better than no solution, for example).

Patented Phylogenetics

Ars Technica has a story about how Microsoft tried to patent clustering phylogenetic methods. If the patent would have gone through, it could have meant that anyone who wanted to use a phylogenetics clustering program (PAUP, Mesquite, etc) would have suddenly found themselves unable to do so, at least not without paying Microsoft first the associated fees for licensing their patent (or else by pirating the software, which seems to be a common theme in cash strapped labs). Luckily, there is plenty of prior art (meaning, Microsoft was obviously not the first person to do it), so they won’t be granted the patent in the end. Something like this makes an (arguably) good case for scientists to release any code and programs they produce under an Open Source license, which in effect would preserve their work in the public domain for future scientists to use.

Creationism 2.0

If you happen to take William Dembski’s course on ‘Intellient Design’ at Southwestern Baptist Theological Seminary, you will be pleased to know that you can get an easy 20% of your mark from simply posting replies defending creationism ‘Intelligent Design’  on ‘hostile’ websites (presumably, that means ANY scientific website). Richard Dawkins (who is very intelligent while simultaneously arrogant,  or at least so he seemed from the talk I saw) mentions this as well as plucking out some other gems from the course, such as a question from the Christian Faith and Science module which reads:

Trace the connections between Darwinian evolution, eugenics, abortion, infanticide, and euthanasia. Why are materialists so ready to embrace these as a package deal? What view of humanity and reality is required to resist them?

Remember kids: don’t evolve.

Zombie Defense: Strike Hard, Strike Often

Most people should remember from elementary school how we were supposed to create a fire escape plan for our house and practise it with our families, but what about other equally dangerous and deadly situations? I always found my school lacking in it’s zombie plague contingency plans; luckily we now have a better idea of a plan of action. Four students from Carleton and University of Ottawa have run different outbreak and response models (PDF) for zombie infection. Unfortunately, the news is not great. Only one scenario works in favour of non-zombies, that of a strike hard and strike often approach. Even at that, the authors are not entirely convinced the plan would be successful, especially as coordinating attacks during a time of turmoil would be very difficult. So remember to be on the lookout for zombies at all times, as the earlier the infection is caught, the more likely the human race may survive.

Death of the Dead Tree Journal

Ars Technica has a story on the American Chemical Society and their plans for switching most of their journals over to electronic format only. In some ways, the news may seem surprising, but at the same time, it does seem somewhat inevitable. I know that personally I do virtually all of my research online in some fashion. Anymore, if the article isn’t online and isn’t that vital to the work I’m doing, I’m not going to waste my time tracking it down when there are likely other papers that will work as well and are online, and I think this kind of attitude is (for better or worse) fairly common among my generation in the sciences. The days of the printed article are likely numbered. This is not to say that books will stop being published, but I see books (and by this I mean something I read for enjoyment) and journals (something I read for my job) as two different things. Journal articles are more useful to me if they are electronic, as then I can have them instantly in front of me without having to search through a filing cabinet, I don’t have the clutter of papers that I print of to skim once and never use again, and I can search with various tools to find what I want even if I can’t remember the specific paper. Books, on the other hand, I want to be able to enjoy slower and away from the distractions of a computer. I don’t need to search the text of a book and I like taking them to places where I have no power source, such as the park or camping. Books are more useful to me in dead tree format, and I will continue to buy them in that format. But I can honestly say that so long as I can access journals on line in high quality PDF format, that I won’t miss the fact that they’re no longer being printed. In fact, not printing them means lower costs for me in a couple of ways: research libraries no longer need to spend money building larger and larger buildings to hold journal collections that are rarely looked at; and (hopefully) journal subscription costs come down because of the savings of not having to pay for printing. Let the future begin.

Georeferencing a Palaeogeographic Map

There a a number of resources on the web and in the literature when it comes to palaeogeographic reconstructions. Two of the most commonly used sites for images are Chris Scotese’s PALEOMAP project and Ron Blakey’s home page. While the images that you can find on them are great, the format the images are in are a bit of a problem when it comes to loading them into a GIS program, as they aren’t in a typical GIS format. For example, the common GeoTIFF format that many GIS images are distributed as contains information about the image’s location, allowing it to be easily opened in GIS program. This makes it easier when trying to combine multiple georeferenced files, as the program will automatically place them in the proper location (and projection) relative to one another.  For my research, this is a very useful tool as it allows me to quickly place and update fossil localities on a map, without having to do everything by hand. Luckily, there are several easy ways to georeference an image.

The first method involves using a cross-platform GIS program called Quantum GIS. Once you have the program installed, open it up and the first thing you will do is enable the Georeferencer plugin. To do this, go to  Plugins > Manage Plugins on the top menu bar. Scroll down and select the Georeferencer plugin, and hit OK. Now, go to Plugins > Georeferencer > Georeferencer to open up the plugin. You will bepresented with two windows. Go to the window titled Georeferencer and navigate to the location of your image that you want to georeference and select it. Once you’ve done this, your image will pop up in the other window. In this window, you will select points on the map for which you know the location, and these points will allow the GIS program to position your image accordingly. To select a point, choose the button with the three red dots and then click on the image. It will ask for the X (typically longitude) and Y (typically latitude) of the point, which you need to enter. You can use the zoom options (top left) to zoom in and out to be more precise when choosing points as well. Once you’re done, you can hit Create to save or Create and Load Layer to save and load it in the program. Your original image should be unaltered, but there will now be a world file with a similar name (but slightly different ending) that contains the coordinates for the image, which the GIS can then use.

While the first method may seem easiest, as it just involves clicking pictures, I prefer a second method. I have installed a command line program (well really, a library and associated utilities) called the Geospatial Data Abstraction Library or GDAL for short. Here again, there are packages for all platforms available for download. Within GDAL, there is a utility called gdal_translate which allows you to georeference an image. To try it out once you have GDAL installed, fire up a terminal (or console, or whatever you like to call your command-line interface). From here, a single line of text can georeference your image. For example, if I have a full world map that is 375 pixels high and 750 pixels wide (as are all of Blakey’s palaeogeographic maps), and I know that the corners of the map are at -180 and 180 degrees longitude and -90 and 90 degrees latitude (as are Blakey’s), I can use the line:

gdal_translate -of GTiff -gcp 0 0 -180 90  -gcp 0 375 -180 -90  -gcp 750 0 180 90  -gcp 750 375 180 -90 90mya.jpg 90.tif

To break down the line a bit, gdal_translate calls the function, -of GTiff tells it I want a GeoTIFF as the output format, and the -gcp 0 0 -180 90 etc. each refer to a corner of the image and it’s longitude (or X) and latitude (or Y) (ie the top left corner or 0 0 is at -180 degrees longitude and 90 degrees latitude). Finally, the last two parts refer to the original image name (90mya.jpg) and output image name (90.tif). While this may seem a little more complex at first, it is far more precise than trying to click exact points on maps, and is much faster to use, especially with multiple images of the same size and position.

Either way, in the end you should have a much more useful image that you can do lots of other things which, like changing to a new projection, which I’ll talk about a bit more in a little while.

Palaeogeography in Google Earth

google_paleoearthWhile playing with some palaeogeographic maps from Ron Blakey’s website recently I was trying to come up with some way of manipulating the maps in a fun, and really visual, manner. I found somewhere about instructions on overlaying images on the globe in Google Earth, probably meant more as a way to place smaller regional maps on the globe. However, I realised that you can overlay a new image across the entire globe as well. What this means is that I could take a palaeogeographic reconstruction and manipulate it in 3D much as I would the modern geography in Google Earth. The picture on the left gives you an idea of what it looks like.

The whole process is pretty simple too. Download an image for whichever time period you like (make sure the map is straight up lat/long, and not a Mollweide projection). Then, open up Google Earth and select Add > Image Overlay and select the image you just downloaded. You probably need to tweak the placement a bit though, so under the Location tab in the Image Overlay window, be sure that you set the boundaries to 90 degrees North and South and 180 degrees East and West, and hit OK. Once you’ve done that, you can spin the globe around and take a look at how the Earth once appeared. One neat thing too is that you can adjust the transparency of the image overlay by using the slider just above the Layers on the left hand side. Have fun!