data

Friday excitement: Panoramic data inspection

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I teach Tuesdays and Thursdays this year, leaving Fridays welcomely wide open for non-teaching related productivity. Today’s task is arguably the most exhilarating aspect of doing Science – inspecting raw data to make sure there are no major errors or problems in the dataset, so I can then analyze it and change the world. The excitement is truly hard to contain.

Delectable dog food is the dataset; I’m the dog.

No, it’s not the funnest, but it’s an important part of doing Science. To make your life easier, you should inspect data daily as you collect them. This way, you can identify mistakes and make notes about outliers early on, so that you are not stupefied and stalemated by what you see when you sit down to begin analysis.

You (corgi) are getting ready to analyze and you find an anomalous observation (door stop) you didn’t notice when you were collecting data.

Today I’m looking at measurements I took from ape mandibles housed in an English museum last summer; I inspected data before I left the UK for KZ, so today should be a breeze. But no matter how meticulous you are in the field/museum, you still need to inspect your data before analyzing them, just to be safe. If you’re as disorganized as I am, there will be lots of programs each with lots of windows. Here’s a tip: plug into multiple monitors (or at least one big ass monitor), so you can easily espy all open windows and programs in prodigious panorama.

Using two monitors helps when checking data for errors and patterns

Using two monitors helps when checking data for errors and patterns. On my left screen I’m using R to visualize and examine the raw data open in Excel on the right screen. If something seems off on the left screen, I can quickly consult the original spreadsheet on the right.

Barely visible in the above screenshot, these are chimpanzee (red) and gorilla (black) mandible measurements plotted against a measure of body size, preliminarily described in this post from last August. I’m looking at whether any mandibular measurements track body size across the subadult growth period, in hopes that bodily growth can be studied in fossil species samples dominated by kid jaws. As you can (barely) see, some jaw measurements correlate with body size better than others, and sometimes the apes follow similar patterns but other times they don’t.

The data look good, so now I can go on to examine relationships between mandible and body size in more detail. Stay tuned for results!

More FREE badass bioanthro science resources!

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Hark! There’s been quite a long silence here, as I’ve been busy preparing manuscripts related to this post and this post. Also teaching; my new Intro to Biological Anthropology students are writing posts over at nazarbioanthro.blogspot.com – check them out!

Anyway, some more FREE DATA have come to my attention that I figured people may find useful (I’ve posted links to other great resources here and here).

First, my buddy and advisor Milford Wolpoff has helped compile an open online dental dataset. This consists of length and breadth measurements for teeth from humans, fossil humans and non-human apes. And promises of more to come! You can read about the data, and online data-sharing more generally, in this paper at the Paleoanthropology Society website.

Secondably, Herman Pontzer has put together a website, Australopithecus, with lots of great information about human evolution for teachers and students, as well as a datamine of links and metrics and pictures of fossil hominins and apes. Pretty boss.

Third, announced in the American Journal of Physical Anthropology just yesterday is a database of cranial non-metric data, pioneered by Nancy Ossenberg. This is a very comprehensive dataset, with info about up to 84 non-metric traits on over 8,000 individual crania from all over the world. Ossenberg also links to the WW Howells craniometric dataset (thousands of cranial measurements of individuals all over dodge); I’m not sure if/how much Ossenberg’s and Howells’ datsets overlap, but the covariance of size, shape and non-metric traits could be a very interesting investigation (if it hasn’t been done already; sorry for my ignorance!).

Finally, if you’re looking to analyze these or any other tantalizing data, you’ll want to download and learn to use R. This free statistical computing program will let you analyze pretty much anything with either traditional statistics, or you can be a badass and make up your own custom tests. I’ve been blabbing incessantly about how awesome this program is since at least 2009, but here’s the link just in case. R takes some time to figure out how to use, but its help files are all online, and you can probably find out how to do anything else your dreams can concoct on the Internets.

Now you are ready to take on the world. Go forth!

One more great bioanthro resource

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Following up on yesterday’s post containing links to various online data and resources, Dr. Rebecca Jabbour brought the Human Origins Database to my attention today. As stated on the database’s home page:

Currently the Human Origins Database contains the measurements and skeletal element information present in the Koobi Fora Research Project. Volume 4: Hominid Cranial Remains by Bernard Wood (1991). In addition, a complete inventory of skeletal elements present for the chimpanzee and gorilla collections at the Powell-Cotton Museum is included, along with annotated data sheets providing information on epiphyseal fusion, element condition, etc.

Here’s a taste of the Powell-Cotton chimpanzee catalog & maturation info:

You have to register to access the database – which you should do since it’s free and appears immensely useful. Enjoy!

Online skeletal and dental datasets (links links links!)

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The TM 1517a fossil, from here

Jean Jacques Hublin has a commentary [1] in the current issue of Nature, about making fossils available for scanning, digital replication, and ultimately hopefully open dissemination. As Hublin points out, it’s a bit ridiculous that a fossil is a rare enough thing as it is, but even after their discovery, fossils “can become unreachable relics once they are in storage.” Fortunately, Hublin goes on to point to online collections that are available to anyone interested. Somewhat ironically, the article about free-ish data is behind a paywall, so here are the resources Hublin describes:

  • The Ditsong CT Archive, created by the collaboration of Hublin’s group at Max Planck and the Ditsong (formerly Transvaal) Museum in South Africa, which contains digitized hominin fossils from the site of Kromdraai (see also [ref 2]). Check out the type specimen of Paranthropus robustus, from this site, above!
  • You can download CT scans of the Skhul V early human fossil, thanks to the Harvard Peabody Museum.
  • Wanna see the the oldest possible animal embryos, early humans, insects, and other crazy fossils? Check out the European Synchrotron Radiation Facility’s microCT database.
  • Get free CT scans of 2 human skulls, thanks to the Virtual Anthropology program at the University of Vienna.
  • Finally, the NESPOS initiative is a large repository of Pleistocene hominin fossil scans, which I somehow don’t know enough about.

In addition to these sources, here are 2 other datasets that are pretty badass:

ResearchBlogging.orgI haven’t had much opportunity to look into these datasets Hublin pointed out, but they look promising. If you know of other good resources, please do share!

References
[1] Hublin, J. (2013). Palaeontology: Free digital scans of human fossils Nature, 497 (7448), 183-183 DOI: 10.1038/497183a

[2] Skinner MM, Kivell TL, Potze S, & Hublin JJ (2013). Microtomographic archive of fossil hominin specimens from Kromdraai B, South Africa. Journal of human evolution, 64 (5), 434-47 PMID: 23541384