Andy White Anthropology
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An Update on the Kirk Project

3/6/2017

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Without thinking about it too hard, it seems like a disproportionate amount of my work on the early hunting-gathering societies of the Eastern Woodlands has been done in the company of sick children. Today's update on the Kirk Project comes to you from a crowded chair, with my typing arms constrained by the presence of a 3-year-old in pajamas watching Fireman Sam. For the full effect, play this in the background while you read this post.

I have four updates, one of which includes an apology.

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South Carolina Antiquities Paper

The first salvo of analysis related to the Kirk Project comes in the form of a paper in South Carolina Antiquities titled "A Preliminary Analysis of Haft Variability in South Carolina Kirk Points." The paper uses morphometric data from 46 Kirk points, considering shape variability in the haft regions and asking which dimensions of that variability are most likely to be linked to change through time. The majority of the points are from the Larry Strong collection (from Allendale County, South Carolina), a surface assemblage that was presumably created over a long span time of time. I compare variability in the Larry Strong points to variability in points from the Nipper Creek cache (Richland County, South Carolina), which was presumably created over a very short period of time. You can find a link to the paper on my Annotated Journal Articles page. Eventually I'll add files with the data I used in the analysis.

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Morphometric Analysis on Two Tracks

Although based ultimately on 3D models, the analysis in the South Carolina Antiquities paper was done in 2D. I will continue working with the 3D models I'm producing, finding ways to capitalize on the richness of those data. At the same time, however, I plan to pursue a large scale 2D analysis that will allow me to make use of the large amount of data that I collected for my dissertation.  I've begun organizing and posting the "rough" scaled images of Kirk points from my Midcontinental data set by state here. It will take me a while to get all those photos in order, as there are over 600.

Once the images are assembled, I will be able to extract and analyze comparable 2D shape data from all the Kirk points in my dataset. At that point, we can finally start addressing questions about patterns of Kirk variability across large expanses of space. With a system in place, it will be much easier to feed new points from other regions into the analysis. That brings me to my next update . . .

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Apologies for My Sluggishness, Alabama . . . and Tennessee . . . and Georgia . . .

As I wrote several weeks ago, a mention of the Kirk Project in the newsletter of the Alabama Archaeological Society spurred several people to contact me about their collections. I have continued to get emails, but I haven't yet started assembling them in an attempt to take advantage of the offers for help and information. Starting to get back to people is next on my "to do" list today. I truly appreciate the communication, and I apologize for not responding to everyone in a more timely manner. The  "zero inbox" grail has always eluded me. It's a personal failing.

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Processing a Large Collection from Aiken County, South Carolina

Over the holiday break, SCIAA received a large, donated artifact collection from Aiken County, South Carolina. Processing the entire collection (which has taken over much of my lab) is a long term proposition. One of our highest priorities is inventorying and labeling the Paleoindian and Early Archaic materials so that we (by "we" I mean primarily Al Goodyear, Joe Wilkinson, and myself) can include them in analyses. Look for those materials to be incorporated into the Kirk Project in the future.


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Four for Friday

2/10/2017

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I have four quick updates to pass on today: two about archaeology and two about art.

Latest Issue of Legacy
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The latest issue of Legacy (December 2016) is now available online on the SCIAA website. Published by SCIAA twice a year, Legacy features short articles relevant to South Carolina archaeology. I wrote a short piece about the research value of large surface collections, focusing on how my work with the Larry Strong collection (from Allendale County, South Carolina) is connected to the Kirk Project.

Alabama Kirk Points
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I received a two emails this week about Kirk points from Alabama. Coincidence? No! There was a short mention of the Kirk Project in the latest issue of the newsletter of the Alabama Archaeological Society. I didn't know about it in advance, but I'm grateful for the exposure. I'll have an article about variability in Kirk points from Allendale County, South Carolina (see above) in the next issue of South Carolina Antiquities. As I continue to collect data from the Southeast, I plan to develop two "tracks" so I can utilize both 2D and 3D data (including all the data from my dissertation). Hopefully I'll have time to start incorporating more data from the Southeast (outside of South Carolina) as the semester moves along. Thank you, Alabama!

Upcoming Appearance on Palmetto Scene
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I'll be the subject of a short piece on Palmetto Scene that is scheduled to air on February 16th at 7:30 pm. The SCETV crew came by my workshop as I was working on Owl #1. I'm nervous to see myself on TV, as I will surely feel that I look and sound like an idiot. 

Photo of Rooster -- I Mean "Gamecock" -- Sculpture in USC Today
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USC Today is a daily online publication of the University of South Carolina. They did a story on my welding art back in July of 2016 and recently sent a photographer over to take a few more pictures. The action shots turned out great (I'm using one at the top of of my Sculpture page). The photographer also took some photos of things I've made since the earlier story, including my rooster sculpture.

I'm learning that talking about "roosters" around here is basically a non-starter: they're "gamecocks," plain and simple. I find myself resistant to that, as my understanding is that "gamecock" refers specifically to roosters with "physical and behavioral traits suitable for cockfighting." What if my rooster is gentle and not prone to rooster-on-rooster violence? I'm not sure I'm likely to ever win that argument in this town.

I'm working on another rooster sculpture right now. It will probably a be a couple more weeks until it's done. If you like gamecocks -- actual gamecocks -- you're going to want to see it.
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In Press: "A Preliminary Analysis of Haft Variability in South Carolina Kirk Points"

11/28/2016

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The gears of science almost always turn more slowly then I would like. It was about a year ago that I first hatched the idea of the Kirk Project, and I've just now submitted my first formal publication related to describing and understanding variability in Kirk points from the Southeast.  The paper, titled "A Preliminary Analysis of Haft Variability in South Carolina Kirk Points," will be published in the next issue of South Carolina Antiquities.

The paper considers haft variation in a sample (n = 46 total) of Kirk points from the Larry Strong Collection (n = 41, Allendale County, South Carolina) and the Nipper Creek cache (n = 5, Richland County, South Carolina). The Larry Strong portion of the sample is a large "long time” assemblage that contains Kirk points from the full range of time those points were produced in the region. The Nipper Creek cache, in contrast, is a “short time” assemblage that was produced during a small window of time.  Comparison of these assemblages can be used to explore which aspects of haft morphology may be carrying useful stylistic information that is sensitive to change through time and, potentially, patterned in ways that can eventually tell us something meaningful about Kirk societies. This table summarizes the sample and provides links to the downloadable 3D models that I used (I also posted the table on my Data page). 

My analysis focuses on various aspects of shape as characterized by a series of landmarks placed on 3D models. Although 3D models are the starting point, I purposefully performed the preliminary analysis in the paper in only two dimensions (i.e., utilizing just the shape of the outline of the haft region and getting rid of data related to thickness).
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The main take-away point from the paper is that shape variation in the lateral haft margins appears to be a better candidate for capturing stylistic change through time (and potentially also stylistic variability across space) than the the morphology of the basal edge and the overall length:width proportions of the haft. The "short time" Nipper Creek assemblage is more consistent in the degree of haft flare and shape of the lateral/basal junction than the "long time" Larry Strong assemblage, which is what one would expect if design of the lateral haft margins was strongly influenced by some kind of cultural-bound choice (i.e, if lateral haft morphology is essentially isochrestic). This is a potentially important observation, as basal edge shape and treatment are often thought to be good attributes upon which to base “type” distinctions that are presumed to have temporal significance. While basal edge morphology appears to account for the greatest amount of variability overall in the shape analysis, it may not be strongly linked to style within the Kirk Corner Notched cluster (and may, in fact, be linked to function through haft repair and maintenance). It will be important to sort this out going forward to avoid inclusion of non-stylistic variability in a stylistic analysis.

I'll let you know when the paper is available. In the meantime, I'll be working on expanding the analysis in several different directions. I'm hoping that making my primary data sources (i.e., the 3D models) available as freely downloadable files will encourage others to do the same. We're really not doing ourselves any favors by not taking better advantage of the data-sharing potential offered by the digital age.

Funds to support inventorying and analysis of the Larry Strong Collection were provided by the Archaeological Research Trust.
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"Social Implications of Large-Scale Demographic Change During the Early Archaic Period in the Southeast"

11/1/2016

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I've loaded a pdf version of my 2016 SEAC presentation "Social Implications of Large-Scale Demographic Change During the Early Archaic Period in the Southeast" onto my Academia.edu page (you can also access a copy here). Other than a few minor alterations to complete the citations and adjust the slides to get rid of the animations, it's what I presented at the meetings last Friday. I tend to use slides as prompts for speaking, so some of the information that I tried to convey isn't directly represented on the slides. There's enough there that you can get a pretty good idea, I hope, of what I was going for.
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Some Very Preliminary Kirk Morphometric Data

10/4/2016

14 Comments

 
I've spent some time over the last few days generating some basic morphometric data from the 3D models of Kirk points that I've processed so far (n = about 50) . I'd like to have about double that for a formal analysis to publish, but I also would like to discuss some preliminary results as part of my presentation at the SEAC (Southeastern Archaeological Conference) meeting that's coming up in a few weeks. So you go to war with the Kirk assemblage you've got, not the Kirk assemblage you want.

Before I talk about the data, I'd like to congratulate myself on having the forethought to take a day last spring to write down the workflow right after I got it figured out. There were a few details that I neglected to mention in that blog post, but overall it was a huge time saver. Figuring out the steps was enough of a pain-in-the-ass the first time. Let us never do it again.​

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I defined seven landmarks on each point (s0 through s6).

​To define these landmarks consistently, I first oriented the point to minimize the horizontal distance between s0 and s1. Generally, that resulted in s0 and s1 falling on roughly the same plane. I then defined s2 and s3 to mark the maximum deviation of the lateral haft edges proximal to maximum constriction of the haft (marked by s0 and s1).  

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I used s0, s1, s2, and s3 to define the axial plane (in the "View" pulldown menu). This superimposes an asymmetrical grid on the point and defines a set of three planes: axial, coronal, and sagittal (named following conventions for anatomy, which is what this software was designed for). 

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I turned on the sagittal plane to locate landmark s4. The sagittal plane splits the axial plane down the middle. Landmark s4 is defined as the location where the sagittal plane intersects with the basal edge of the point when the sagittal plane bisects the axial plane. If the point is symmetrical, s4 will fall in the center of the basal edge.

Note: the sagittal plane is movable. When you initially turn it "on," it's automatically centered in reference to the axial plane. If it gets moved you can recenter it simply by turning it off and then on again.

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Finally, I turned on the coronal plane to locate landmarks s5 and s6. Landmarks s5 and s6 are defined as the locations were the coronal plane intersects the lateral edges of the haft when the coronal plane bisects the axial plane.

For each point, you have to tell the software how the landmarks correspond to those on the "atlas" model. The simplest thing to do is to always place the landmarks in the same order. You still have to manually define the correspondence between each model and the atlas ("View Correspondences" in the "View" menu).

I followed the same steps I described in the previous post to export and edit the data so that I could import it into MorphoJ. I used MorphoJ to perform a principal components analysis (PCA), the purpose of which is take all the variability in the 3D data and boil it down to its most important components. PCA lets you flatten the variability in a dataset into scores that you can plot in two dimensions.

Here are the basic results of the PCA performed on the points currently in the sample:
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I haven't spent any significant time digging into the data yet, but my initial reaction is that the first principal component may well be measuring variability related to time. If you look at the examples of points that fall at the far left end of the plot, they look very Taylor- or Thebes-like, with relatively long hafts, deep notches, and small/shallow basal concavities/indentations separating broad convex basal edge segments. The points at the far right of the plot, conversely, have relatively short hafts, shallow notches, and broad basal concavities. If you squint a little, maybe, you can see how that end of the Kirk spectrum is trending toward a bifurcate/lobed haft morphology. In the center of the plot are points like 5947, which I think we can agree is a "modal" Kirk Corner Notched.

With the exception of the Nipper Creek cache points (shown in green), all the points in the sample are from Allendale County, South Carolina, and are made from Allendale chert. This all but eliminates the possibility that the variability is due to space or raw material.

My next step is to explore the possible "time" component of the PCA by gathering some data from the point forms that bracket Kirk: Taylor (on the earlier side) and lobed/bifurcate points (on the later side). If I'm correct that the first principal component shown above is telling us something about time, the Taylor points should plot to the left and the bifurcate/lobed points should plot to the right.  It's notable that four of the five points from the Nipper Creek cache plot close together. Those points were almost certainly produced during a short period of time (but so was 5963 NC 4, so . . . something to think about).
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Three-Headed Research Monster: A Brief Update

9/8/2016

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We're now into the fourth week of the semester here at the University of South Carolina. As usual I've been writing for this blog less than I'd like (I have several unfinished draft posts and ideas for several more, and there's currently a backlog of Fake Hercules Swords). A good chunk of my time/energy is going into the Forbidden Archaeology class (you can follow along on the course website if you like -- I've been writing short synopses, and student-produced content will begin to appear a few weeks from now). Much of the remainder has gone into pushing forward the inter-locking components of my research agenda. This is a brief update about those pieces.


Small-Scale Archaeological Data

At the beginning of the summer I spent a little time in the field doing some preliminary excavation work at a site that contains (minimally) an intact Archaic component buried about 1.9 meters below the surface (see this quick summary).  Based on the general pattern here in the Carolina Piedmont and a couple of projectile points recovered from the slump at the base of the profile, my guess is that buried cultural zone dates to the Middle Archaic period (i.e., about 8000-5000 years ago).​

My daughter washed some of the artifacts from the site over the summer, and I've now got an undergraduate student working on finishing up the washing before moving on to cataloging and labeling. Once the lithics are labeled we'll be able to spread everything out and start fitting the quartz chipping debris back together. Because I piece-plotted the large majority of the lithic debris, fitting it back together will help us understand how the deposit was created. I'm hoping we can get some good insights into the very small-scale behaviors that created the lithic deposit (i.e.,perhaps the excavated portion of the deposit was created by just one or two people over the course of less than an hour).
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Drawing of the deposits exposed in profile. The numbers in the image are too small to read, but the (presumably) Middle Archaic zone is the second from the bottom if you look at the left edge of the drawing. Woodland/Mississippian pit features are also exposed in the profile nearer the current ground surface.
When the archaeology faculty met to discuss the classes we'd be offering in the spring semester, I pitched the idea of running a one-day-per-week field school at the site. Assuming I can get sufficient enrollment numbers, that looks like it's going to happen. The site is within driving distance of Columbia, so we'll be commuting every Friday (leaving campus at 8:00 and returning by 4:00). The course will be listed as ANTH 322/722. It's sand, it's three dimensional, and it's pretty complicated -- it's going to be a fun excavation. I'll be looking to hire a graduate student to assist me on Fridays, and I'll be applying for grant monies to cover the costs of the field assistant's wages, transportation, and other costs associated with putting a crew in the field. 

Large-Scale Archaeological Data

Some parts of my quest to assemble several different large-scale datasets are creeping along, some are moving forward nicely, and some are still on pause.
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​In the "creeping along" department is the Eastern Woodlands Radiocarbon Compilation. My daughter did some work on the bibliography over the summer, so that was helpful. I'm still missing data from big chunks of the Southeast and Midwest. I've got some sources in mind to fill some of those gaps, and I've also got a list of co-conspirators. Our plan is to combine everything we've got ASAP and make it available ASAP.  I don't really have a timeline in mind for doing that, but for selfish reasons I'm going to try to make it sooner rather than later: I'm going to be using information from the radiocarbon compilation in the paper I'm going to give at this year's SEAC meeting in October. So . .  Georgia, Alabama, Arkansas, Missouri, Indiana, Illinois . . . I'll be coming for you.
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I've got two undergraduate students working on processing the Larry Strong Collection, a large collection of artifacts (mostly chipped stone projectile points) from Allendale County, South Carolina.  Mr. Strong, who gathered the materials himself over the course of decades, donated the collection to SCIAA in the 1990's. Large surface collections such as this have significant research potential. I'm most interested in this collection for two reasons: (1) it provides a large sample of Kirk points from a single geographical area made from a single raw material, improving the possibility of teasing apart functional, stylistic, and temporal dimensions of variability (the large majority of 3D models of Kirk points I've produced so far have come from the Larry Strong collection for just this reason); (2) it provides a basis for making robust statements about the relative frequencies of various point types. When you have an n in the many thousands, you can have some confidence that the patterns you're seeing (such as drop in the numbers of points following the Kirk Horizon) are real. That will also factor into my SEAC paper. Curation of the Larry Strong collection is being funded by a grant from the Archaeological Research Trust.
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Finally, in the "paused" category there is the Eastern Woodlands Household Archaeology Data Project. That effort has been on hold since early last year (I have money to support it and I had an assistant hired, but she moved on to a greener pasture). I'd really like to get this going again but I need to find someone who can work on it more-or-less independently. And I need a bit more office furniture and another computer. Hopefully I can get the EWHADP moving again after things stabilize with my new crop of employees and I have time to take a trip to the surplus building and see what I can scrape up.

Complex Systems Theory and Computer Modeling

Complex systems theory is what will make it possible to bridge the small and large scales of data that I'm collecting. Last year, I invested some effort into transferring my latest computer model (FN3_D_V3) into Repast Simphony and getting it working. I also started building a brand new, simpler model to look at equifinality issues associated with interpreting patterns of lithic transport (specifically to address the question of whether or not we can differentiate patterns of transport produced via group mobility, personal mobility between groups, and exchange).  

As it currently sits, the FN3_D_V3 model is mainly demographic, lacking a spatial component. Over the summer I used it to produce data relevant to understanding the minimum viable population (MVP) size of human groups. Those data, which I'm currently in the process of analyzing, suggest to me that the "magic number of 500" is probably much too large: I have yet to find evidence in my data that human populations limited to about 150 people are not demographically viable over spans of several hundred years even under constrained marriage rules. But I've just started the analysis, so we'll see. I submitted a paper on this topic years ago with a much cruder model and didn't have the stomach to attempt to use that model to address the reviewers' comments. I'm hoping to utilize much of the background and structure of that earlier paper and produce a new draft for submission quickly. I also plan to put the FN3_D_V3 code online here and at OpenABM.org once I get it cleaned up a bit. I also discuss this model in a paper in a new edited volume titled Uncertainty and Sensitivity Analysis in Archaeological Computational Modeling (edited by Marieka Brouwer Burg, Hans Peeters, and William Lovis). 
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How big does a human population have to be to remain demographically viable over a long span of time? Perhaps not as big as we think. The numbers along the bottom axis code for marriage rules (which will be explained in the paper). Generally, the rules get more strict from left to right within each category: 2-0-1 basically means there are no rules, while 2-3-8 means that you are prohibited from marrying people within a certain genetic distance and are compelled to choose marriage partners from within certain "divisions" of the population.
It will be a relatively simple thing to use the FN3_D_V3 model in its non-spatial configuration to produce new data relevant to the Middle Paleolithic mortality issue I discussed at the SAA meetings a couple of years ago. I'm also going to be working toward putting the guts of the demographic model into a spatial context. That's going to take some time.
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Kirk Project: Workflow from Point to 3D Morphometric Data

5/6/2016

2 Comments

 
I've spent most of today and yesterday trying to find a workflow path that gets me from the collection of 3D data (which I've been doing for months now) to a set of numbers that I can do meaningful analysis on.  This has involved, mostly, a lot of trial and error with various software programs. I think I've finally found a series of reasonable steps that will let me go from the 3D models to characterizations of shape data that I can examine visually and statistically.

This is post is mostly a way to document these steps for my own benefit, so that I can refer back to them in a week or a month when I've forgotten what I just figured out. This may not be the final procedure that I end up using for a large scale analysis. I'm putting this out there in public in case anyone finds it useful. Or in case I get hit by a bus and someone else needs to carry on with this important work.
Acquiring 3D Data
PictureScan in progress.
I'm using a NextEngine Desktop 3D scanner (UltraHD, Model 2020i). I'm scanning each point in two orientations: (A) one that exposes all the edges and (B) one that exposes the faces. Before scanning, I use a red pen (supplied with the scanner) to place a series of small dots along the edges of the point. These dots are used to align scan sets A and B into a single model (three points are required for alignment), so they should be placed in locations likely to show up in both scans.

I'm using the autodrive (rather than the multidrive) to rotate the points as they are scanned. I use part of an eraser to elevate the point off of the platform, and the padded to gripper to hold it firmly in place without damaging it.

For each scan set, I've got the scanner set to rotate the point through 10 divisions at the middle HD setting (67k points/square inch).  This may be overkill, but it's been working so far and I've been producing models far faster than I've been processing them (I've scanned about 90 points but have only processed the models for about 40). I scan with texture capture on, because I need to be able to see the red dots to do the alignment.

Processing 3D Data
PictureExample of raw scan data.
I keep copies of the raw (unprocessed) scan data in an archive folder. At the settings I'm using, the raw data for a set of scans from a single point occupies about 300-450 MB. I copy the files for each point and put them in a "processing folder."

​Processing is done in the ScanStudio software that came with scanner. The first thing I do is trim away the non-point things that were captured in the scan. This is a simple operation: you just select what you don't want and delete it. Because I'm scanning in two different orientations, it doesn't matter if a small bit of the actual point gets deleted where it's touching the eraser and gripper - data for those areas will be contained in the other set of scans.

PictureAlignment in process.
After the two sets of scans are trimmed, I align A and B. This is done by determining which of my red dots I can most reliably locate on both scan sets and marking them with color-coded pins. Again, this is a fairly simple process. I've found that some care in this step can significantly reduce the amount of time you have spend cleaning up the model later. 

After at least three pins are placed (I'm not sure that placing more than three actually leads to better results), you hit the "align" button and see what you get. I find it helpful to switch the display mode to "solid" at this point (removing the photo-like surface texture) because it is much easier to see how the two scan sets actually lined up. If the alignment is bad, you can tell. Sometimes an alignment issue can be mitigated by just going back and re-setting the pins and doing the alignment again. Other times it is apparent that the best solution is to go back to square one and re-generate the raw scan data (i.e., put the thing on the scanner and start over).

PictureFused model.
Assuming the alignment is okay, I fuse the two scan sets together with the "fuse" command. This is a one-button operation.  This is another one button operation. I'm using these fuse settings:
  • Volume Merge,
  • Resolution Ratio 0.5 
  • "Create Watertight Model" unchecked
  • "Include Textures" checked
  • Texture Blending 5 pixels
Fusing scan sets A and B produces a new mesh, conveniently labeled "C." If I'm satisfied with the way C looks, I go ahead and delete A and B at this point.

The fused model requires some clean up. There are often small bits "floating" around the edges and at locations on the surface were data from A and B overlapped. These can be removed using the trim tool. The cleaner the model, the less time this will take, obviously. I really feel like the scanner has good days and bad days: sometimes it seems like the scans are really messy no matter what you do, and sometimes things just work out easily. Regardless, I'm not sweating pixel-level details on these models because it won't affect the kind of morphometric analysis I'm planning on doing. I just need the models to be fairly good approximations of the actual point.

After cleaning up the fused model, I run the "remesh" operation (resolution ratio = 0.9) to fill the holes and even things out a bit. Sometimes this reveals a few more defects that can be addressed through limited trimming. In that case, I'll run the "fill holes" operation ("smooth" and "smooth boundaries" checked) afterward to fill any remaining holes in the mesh.

The file I'm working with to produce these images is about 23 MB at this point. I use the "simplify" tool (set at 0.0050") to reduce the file size to about 5 MB. Then I create a .STL file for exporting the model to Sketchfab and a .PLY file to use for analysis in Landmark.  Here is the model on Sketchfab:

Kirk 5984 by aawhite on Sketchfab

Deriving 3D Landmark Coordinates
This is the part of the equation I just figured out the other day. I discovered the Landmark software package (available here) that allows you position sets of landmarks on the surfaces of 3D models. The software was designed with three-dimensional, irregular biological structures (such as bones) in mind, but will work great for projectile points as well. It is mainly a software to acquire, rather than analyze, coordinate data (at least in my plan). 

Even though the manual says the software will work with .STL files, it didn't seem to want to do it for me. So I converted a batch of 10 Kirk models into .PLY files so I could import them into Landmark and work my way through the process of generating data. I added the model I just created above to the batch to illustrate the steps in this software.
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For a trial run, I defined five replicable landmarks that can be placed in the haft region when the point is orientated with the tip pointing up: the points of greatest constriction (s0 and s1), the points of greatest width below the notches (s2 and s3), and the point of greatest divergence from horizontal along the basal edge (s5). The labels are automatically applied to the points as you place them.

As in other software like this, you place the landmarks in the same order each time because the end result is to going to be a file of numbers with XYZ coordinates corresponding to the locations of those landmarks on each of the objects in your assemblage. The next software that reads that file is going to assume that the coordinates are all in the same order, so they better be or you'll get nonsense back. Landmark helps with this by making the process of applying consistent sets of landmarks to different objects semi-automated.

Here is a close up showing the landmarks placed on the surface of the model. You can use your mouse to drag them around and get them exactly where you want them:


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After I placed the five landmarks on a group of ten Kirk point models, I exported the coordinates of the landmarks by highlighting all the models (listed in the pane on the left) and using the "export" function (in the Project menu). I had to play around with several different options to get a file that would eventually work in the analysis software I found (see below). Supposedly I should be able to export files in a format that can be read directly by MorphoJ, but I couldn't get it to work. I had to export the data in the .DTA format and then just edit the text file myself to a format that MorphoJ could read. The .DTA format has the advantage of being a single file with all the coordinates clearly organized, so editing it was no big deal.

Analysis of 3D Coordinate Data 

Once you have 3D coordinate data, what do you do with them? I was surprised to find that my most beloved data analysis package, JMP, doesn't seem to be able to hand 3D coordinate data. Some of software that can do tricks with 3D data, like EVAN, costs money (which I'd like to avoid spending on a product that I'm not sure is actually going to do what I want it to do).  I downloaded various free software packages and played around with several of them. The one I finally got work is called MorphoJ (available here).

The first trick is getting the 3D coordinate data exported from Landmark to be read properly in MorphoJ. As I said above, this wasn't as easy as advertised (here's the relevant section of the MorphoJ manual). Eventually I gave up on the "easy" route and just edited the data from Landmark into a standard comma-delimited text file using Notepad. For future reference, the input data file should look like this:
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The first line gives MorphoJ the column labels. Each line after that contains data for a single Kirk point: the label of the point, the XYZ coordinates of the first landmark, the XYZ coordinates of the second landmark, etc. Don't put commas at the end of lines, don't put in any tabs, etc.

After you create the data file, you import it into MorphoJ using File-->Create New Project. In the dialog that comes up, click "3 dimensions," select "text" as file type, and then navigate to the text file with the coordinate data. If there are no problems with the import it will tell you so. 

Once the data are in there, they'll show up on the Project Tree. Select the data set, go to the Preliminaries menu, and choose "New Procrustes Fit." This performs a Procrustes analysis that rotates, translates, and scales the objects in space to minimize their differences:
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The graphic above shows the results of the Procrustes analysis, with the numbered points representing the centroids and clouds of smaller points around them representing the spread of actual data values. Notice that the points are flipped vertically and horizontally from the way I showed them in the images above, and also that s0 is now "1," s1 is now "2," etc. The results can be viewed along three different axes.

The Procrustes data can be used to do a Principal Components Analysis, which reduces the three axes down to two.  Here is what that looks like:
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Now we're getting somewhere!  The last hurdle will be to figure out if/how I can export the raw principal component data so I can analyze it in another software package.

Working my way through these steps was a "proof of concept" exercise that I needed to do before scaling the analysis up to the full sample. I've been down a lot of dead ends with software.  I'm hoping this is the combination that gets me to a full-scale analysis. The five landmarks I used for the test run really don't take advantage of the 3D model data that I have, so I'll need to start thinking in three dimensions rather than two. And I still don't know how to make use of the data from curves. Once I get those things sorted out, it will be really interesting to see how variation patterns out with a much larger sample (I'm aiming for 100) from a single county and a single raw material. Based on what I've seen as I've been creating the 3D models, I will be surprised if some component of temporal variation is not detectable.  

And then, of course, I'll need to do about 10,000 more of these to see what's going on in the rest of the country.
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My Thursday: Radiocarbon and Kirk

5/5/2016

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I submitted the final grades for my class yesterday, so barring some kind of last minute disaster, my first academic year at South Carolina is done. I'm spending the last part of the week working on the radiocarbon compilation (which I'll need for my paper at SEAC in the fall), moving forward with analysis for a couple of publications I'm working on, and prepping to go in the field and then give a talk next week. My blog has been getting a lot of traffic related to the posts I wrote about the ethnographic megalithic societies of India and Indonesia last year (most of them should come up if you search on "megaliths").  I wish I had time to look at that stuff again right now, but I don't.

I wanted to post this histogram showing the distribution of the ~9,100 dates (intercepts) currently in the radiocarbon compilation (here's the map of the dates I made yesterday). There's a pretty clear trend of an increasing number of dates through time.  Part of that, I think, almost certainly reflects the emphasis that archaeology in the Eastern Woodlands places on the Woodland and Late Prehistoric/Mississippian societies that largely post-date 2000 RCYBP (and the fact that those societies tend to produce large sites with lots of datable deposits). But I think the chart below, as unrefined as it is, is probably also telling us something very basic about demographic change.  There's an inflection point in the number of dates toward the end of the Middle Archaic period (about 5500 RCYBP) that corresponds in time to when we see (generally) more intensively occupied sites, indicators of decreasing mobility, and increasing use of plants that are later domesticates. Yes, I'm saying intensification.
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Distribution of the RCYBP intercepts of 9,129 radiocarbon dates from the Eastern Woodlands.
I think I've found a path forward that will let me extract morphometric data from the 3D models of Kirk points that I've been producing (I've got 41 models uploaded to Sketchfab so far, with a goal of 100 from Allendale County, South Carolina, to serve as the basis for a paper). I found a software package called Landmark (available here for free) that was developed at UC Davis for use with biological materials (i.e., irregularly shaped things).  It allows you to load in a 3D model, place markers and curves on the surface, and export the coordinates of the points for analysis.  I've spent the day learning how to use the software, and have generated a small data set of five points and four curves from ten of my Kirk point models.  The next step is to figure out how to go from the XYZ coordinates that the software exports into something that I can meaningfully analyze.  I don't think that the data analysis package I use (JMP) will do things like Procrustes analysis and, honestly, I've never attempted to analyze a 3D dataset and will need to do some reading to figure out how to start.  If any of my bioanthropology friends have done this sort of thing with morphometric data from skeletal remains and have some advice, I'm listening. Please do not tell me to learn how to use R.
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Screenshot of a couple of Kirk models in Landmark. The software lets you define a set of landmarks on one item and then semi-automatically transfer them to another. Then you can export the XYZ coordinates that describe the locations of the points and, somehow, can be used to describe the shapes of curves that are defined.
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One Procedure for Generating Linear Measurements from 3D Models

4/6/2016

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Things are busy as usual around here, so I don't have time to write much myself today. I wanted to make available to you, however, a nice document produced by Ken Lentz.  Lentz took it upon himself to explore how to go from the 3D models that I'm producing for the Kirk Project to a set of linear measurements. As I wrote recently, getting those linear measurements is something I'm going to need to start doing again in short order. I used a freeware landmark-based program (tpsDIG, which I see is still available here) to derive linear measurements from images for my disseration. The program worked fine, but it was a bit labor intensive and I'm hoping to find an alternate path to getting the same measurements that takes advantage of the fact that I've got a detailed, scaled 3D model sitting right there in front of me. 

Lentz succeeded in getting linear measurements (including angles, which I would really like to be able to measure) from a CAD program, but he had to go through a lot of time-consuming steps to do it.  I'm grateful for his efforts, as I have had zero time myself to seriously explore the issues involved in going from 3D back to 2D. Thanks, Ken, for all your work on this (and taking the time to explain what you did).
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SEAC 2016 Symposium: Hunter-Gatherer Societies of the Early Holocene Southeast

4/4/2016

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PictureI Googled "hunter-gatherer Athens Georgia" and I found this picture of the drummer of a band called "Hunter Gatherer" playing in Athens, GA. That's good enough for a blog post about a symposium abstract.
The annual meeting of the Society for American Archaeology (SAA) is in Orlando, Florida, this week, running from Wednesday through Sunday. I'm not giving a paper this time around (though I did just sign up to do a 3 minute lighting talk in the Digital Data Interest Group), but I'm looking forward to driving down and hearing about what others have been up to lately.

I'm also going to be asking around (and maybe, although I've never been very good at it, attempting to twist a few arms) to try to lock in some participants for a symposium I'm working on for the 2016 Southeastern Archaeology Conference (SEAC) meeting that will be held in Athens, Georgia, in October.  Here is the draft of an abstract I wrote this morning:

Hunter-Gatherer Societies of the Early Holocene Southeast
Societies are groups of people defined by persistent social interaction.  While the characteristics of the early Holocene (> 5000 RCYBP) hunter-gatherer societies of the American Southeast undoubtedly varied across time and space, archaeological data generally suggest that they were often geographically extensive.  Patterns of artifact variability and transport, for example, demonstrate that small-scale elements (e.g., individuals, families, and foraging groups) of these Early and Middle Archaic societies were situated within much larger social fabrics. The goal of this session is to explore the size, structure, and characteristics of these early Holocene hunter-gatherer societies, asking how patterns of face-to-face interactions at human scales “map up” to and are affected by larger social spheres. Theoretical and methodological diversity are welcome, as is an interest in integrating various scales of archaeological data analysis.  
​

I'm hoping this will appeal to a range of scholars, especially those who like to work on multiple scales and address difficult questions.  Ideally, we can get a group of papers together that will be suitable for an edited volume. The first job, however, is seeing what kind of interest there is and who I can get commitments from.  Everything will have to be decided and submitted by the end of August. If you read this and you're interested, please let me know:  aawhite@mailbox.sc.edu.   

I've got several ideas for what I'll contribute to the session. Something related to Kirk is an obvious one, but I've also been spending more time thinking about the Early/Middle Archaic transition after reading Ken Sassaman's book.  I'm wondering if we can: (1) use multiple lines of evidence to identify an abandonment of the Southeast during the late Early Archaic; (2) generate some explanations for that abandonment; (3) understand how social structure would have affected (and been affected by) whatever the causes of an abandonment were and whatever processes were in operation.  And I'm also in the last stages of writing a new agent-based model that I'm going to use to try to attack the equifinality problem that hampers our ability to differentiate among group mobility, personal mobility, and exchange as mechanisms for the very-long-distance transport of stone artifacts.
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