“Gnu directions in r-chaeology”: innovations in the use of free and open source software (foss) to achieve an open archaeology

Posted on February 17, 2017

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A good way to start everyone weekend is with some open source work. Here is another video recorded session from the EAA conference:

Author – Orton, David, University of York, York, United Kingdom (Presenting author)
Co-author(s) – Birch, Thomas, UCL Qatar, Doha, Qatar
Co-author(s) – Ot rola-Castillo, Erik, Harvard University, Cambridge, MA, United States of America
Keywords: computing, methods, open-source

In recent years, considerable attention has been paid by archaeologists to the potential of an ‘open science’ approach within archaeology, focusing firstly upon open access publication, and more recently on the imperative for open data. Papers in this session address the third pillar of open science within archaeology: open methods, as underpinned by the use of Free and OpenSource Software (FOSS). The benefits of FOSS in archaeology are manifold, ranging from inclusivity, through transparency and research integrity, to practical issues such as cross-compatibility. Closed-source proprietary software has created a two-tier system, selectively disadvantaging individuals and institutions with more limited resources while hindering the free exchange of data, obfuscating methodological detail, and increasing the risk of digital obsolescence. By contrast, FOSS allows for universal access and encourages reproducibility and compatibility of research methods, while facilitating collaboration, archiving, and data re-use. The range of FOSS applications in archaeology has grown significantly in the last decade, expanding from traditional heartlands in GIS and spatial analysis into omics, morphometrics, bioarchaeology, and field recording, to name but a few. This session aims to draw attention to innovative ways in which archaeologists are applying the open source philosophy. Contributors will present cases in which the use of open software is instrumental in achieving objectives – whether in terms of expanding access to archaeology; developing reproducible methods; or enabling otherwise impractical research and collaborations. We also welcome papers showcasing innovative packages with the potential to facilitate such contributions. By raising awareness about the uses of FOSS in archaeology, we hope to promote the Freedom of Software movement within archaeological practice and to demonstrate how the discipline is developing towards a more democratic and egalitarian approach to information technology.

Digital media as an effective platform to archaeological data dissemination

https://youtu.be/WQrYbvzASqk Author – Eng. Botica, Natalia, Universidade do Minho, Braga, Portugal (Presenting author)
Co-author(s) – Bernardes, Paulo, Universidade do Minho, Braga, Portugal
Co-author(s) – Martins, Manuela, Universidade do Minho, Braga, Portugal
Co-author(s) – Madeira, Joaquim, Universidade de Aveiro, Aveiro, Portugal
Keywords: 3D models, Information System, open-source software

The Unit of Archaeology of the University of Minho (UAUM) start to be concerned about digital preserving of the archaeological data in the nineties, due to the large amount of records (both graphic and alphanumeric) mainly gathered during the rescue excavations carried out in the city of Braga since 1976. In order to facilitate the management and preservation after 1994 all the archaeological records start to be regularly digitized and stored in an Oracle DB. Later in 2000, as part of UAUM’s information system strategy, these data were migrated to a MySQL database. Simultaneously, to ensure a continuous update and management of the data, a web-based back-office was developed using HTML and PHP. This technological independence strategy enabled a controlled growth of the back-office, ensuring modularity, integration and customization facilities according to the user’s needs.

The designed Information System (2ArchIS) supports several modules, which range from the stratigraphy of any kind of excavations to the territory analysis and landscape characterization, connecting the alphanumeric data with images, vector graphics, cartographic documentation and bibliography. Furthermore, it can also integrate data resulting from the analysis and interpretation tasks.
The architecture of 2ArchIS also favours the data exchange with external applications. It is possible to export data to archED and ARCGIS enabling the automatic creation of a graph regarding the stratigraphic matrix and materials, that can be a valuable asset for the archaeological research.
This information system also integrates archaeological 3D models that are created either using constructive solid modelling techniques or computer vision techniques such as structure from motion (SfM) or dense stereo reconstruction algorithms. In fact it is possible to use artefacts, as coins, ceramics or architectural elements both for cooperative research and dissemination purposes.
All the 3D information is important not only for rendering and for 3D representation purposes, but also to be processed with visualization filters to enhance the knowledge about the archaeological record. This data is perfectly compatible to be processed with the Visualization Toolkit (VTK) from Kitware Inc., which is an open-source software system for 3D computer graphics and visualization. Some visualization procedures have already been implemented to filter scalar information of the archaeological data for contouring purposes or even to carry out manual segmentation over a 3D surface.

ArchSeries: an R package for transparent estimation of chronological frequency distributions

https://youtu.be/Wp88QhPXKeQ Author – Dr. Orton, David, University of York, York, United Kingdom (Presenting author)
Keywords: chronology, R, uncertainty

Archaeologists often wish to plot the chronological frequency distribution of a given entity – for example a feature category, a plant or animal species, or an artefact type – within a specific site or region. Since each archaeological occurrence is subject to chronological uncertainty, and since dating resolution varies widely, estimating a single distribution from numerous occurences is a non-trivial task. This is particularly problematic where data are combined from multiple sites or interventions with a wide range of different chronological break points and sources of dating information – for example sites with a long history of excavation, or urban areas with complex stratigraphy and a high concentration of development-led archaeology. Researchers are often forced to fall back on a lowest-common-denominator approach, trading resolution for comparability by combining data into broad period categories.
This paper presents an R package for dealing with this situation without surrendering the original dating resolution. Designed originally for meta-analysis of zooarchaeological remains from numerous historical-period sites across London (used here as a case study), archSeries is built around functions for estimating frequency distributions using either (a) aoristic analysis or (b) simulation. Initially based upon uniform probability distributions within archaeologically defined limits, the simulation approach is currently being expanded to allow integration of archaeological chronologies with radiocarbon dates. The package also features a variety of functions for plotting the resulting frequency distributions along with their associated uncertainty. Finally, there is a tool for adjusting results according to the chronological distribution of research intensity.
With raw, context-level archaeological datasets increasingly being made publicly available, it is hoped that archSeries will facilitate transparent re-use and meta-analysis of frequency data while allowing researchers to retain the full available chronological resolution.

Consumption patterns and morphology of cattle in a Late Neolithic settlement Polg r–Csoszhalom

https://youtu.be/iiSddmmCyFk Author – Dr. Csippan, Péter, Eötvös Lor nd University of Sciences, Budapest, Hungary (Presenting author)
Keywords: Free software, Statistics, R, Zooarchaeology

In the last decades the zooarchaeological analysis of large sites shed lights on the limits of the interpretation of animal bones and required new technologies and methods in the research. The main question is, how we can interpretting these huge datasets? Which methods can help us to visualize this incredible sample size? And finally which sofware(s) can help us in this quest? For the evaluation of raw data from the Late Neolithic (5th millennium BC) settlement of Polg r–Cs szhalom is a perfect case study for the archaeological adaptation of one of the widely applied opensource statistical software: R.
Through the wildrange analysis of animal bones I focused on the meet consumption of the main domestic species at the site, the cattle. But the question is, how can we earn more information about these animals with using only a FOSS to the research? R offers numerous possibilities and ways for the data analysis and visualisation, but in this case study I would like to show the whole process from the birth of the research question until the answers with the help of R.

Can we have that on a map? Open Source options for the dissemination of archaeological spatial data

https://youtu.be/ArrjVCIZwEc Author – Dr. Evans, Tim, Archaeology Data Service, York, United Kingdom (Presenting author)
Keywords: Open Source, Web mapping

Perhaps more than any other data type, geospatial information appeals to the archaeologist. The ability to plot a dataset in its geographical and chronological context offers a myriad of possibilities for interpretation, understanding and presentation. For over twenty years the Archaeology Data Service (ADS) has curated and disseminated such datasets, the latter through an increased use of tools for Web-based mapping. However, the practice of such dissemination has not always run smoothly, early work with proprietary software and middleware such as ArcIMS, ArcGIS Server and ArcSDE have proved problematic and on occasion, unsustainable. Thus in more recent years the ADS have moved towards utilising the wide range of Open Source libraries, tools and standards to disseminate this data. Use of innovations such as OpenLayers, GeoServer and WMS has facilitated a new wave of simple and efficient re-use potentials and coincided with a wider trend in a more unrestricted dissemination of archaeological and non-archaeological data alike. Indeed, as such methods of presentation become more easily achievable, if not expected, then so does an increased need to re-examine the potential of working online. This potential is not only limited to WMS publishing and consumption, but also the possibilities for use of linked data and API lookups for historic and modern place names and boundaries to spatially locate other data such as reports and journal articles. The long term effect of such moves may be less about building complex, and arguably unsustainable, Web-based GIS, but towards a more literal Webmapping to facilitate resource discovery.

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