Tutorial for the archeoViz application (R package)

Data download and upload

  • Chose and download one of these datasets :
    • Madjedebe (Paleolithic site, Australia), 9136 objects,
    • Bilzingsleben (Paleolithic site, Germany), 2439 objects and 61 refits
  • Open an archeoViz online instance:
  • Use the “Input data” tab to load the table(s)

Visualisation

  • Explore the 4 types of visualisation: 3D, map, Sections X and Y.
  • Display a map of all the remains.
  • Display a north-south section of the site (width = 50 cm, anywhere in the site)

Selections and export functions

Launch the “Cassenade” archeoViz instance and display the following selections:

  • A 3D view of “upper part” layer.
  • A map of the coprolithes remains between z=50 and z=100.
  • Export this map as a SVG file.
  • A 3D view of the faunal remains in the “upper part” layer.
  • A Section view of the refittings in X.
  • A Section view of the “silex” (=flint) remains and their refittings relationships.
  • Create a 3D visualisation that include three types of remains only; export it as an HTML file. Open it with a web browser.

Data analysis

Embedded methods

Explore the three methods included in the archeoViz application.

  1. In the “Map” tab, study the density of the spatial distribution of
    • all the remains
    • one type of remains only
    • deux types of remains in 1 layer only
  2. In the “3D plot” tab, display
    • the convex hull by layer
    • the convex hull of one type of remains.
  3. In the “3D plot” tab, display the regression surfaces by layer.

Export to external applications

Launch one of these instances:

  • Cassenade”, Upper Paleolithic site
  • MNK Skull T3”, Lower Paleolithic site
  • Select the “object_type” (for Cassenade) or the “object_subtype” variable (for MNK Skull)
  • In the “Statistics” tab, export the selected data set to the available software:
    • Seriograph, for seriation
    • AMADO, for seriation and classification
    • explor, for Correspondence analysis

The archeoViz Portal

  • Open the archeoViz Portal
  • Search the datasets related to sites located in Germany
  • Search the datasets related to Neolithic sites

More advanced use: Data formatting

  • Download the Camiac dataset (Paleolithic site, France), 1425 objects
  • Read the “Data Format” in the Guidelines tab
  • Edit the Camiac table with a spreadsheet editor to adapt it to the archeoViz format
  • Load the dataset in an archeoViz online instance.

Tutorial: Online Visualization and Graphic Exports of Archaeological Spatial Data, using the archeoViz Application

This document is intended for teachers introducing students in archaeology to spatial data visualisation. It presents the basics for a class syllabus, using the archeoViz application as a pedagogical resource.

  • Concepts: Representation in archaeology, Post-excavation stratigraphy, SVG and HTML file formats.
  • Audience: beginner.
  • Material:
    • a computer with an internet connection,
    • a web browser,
    • an SVG editor (e.g., Inkscape).

Data selection and visualisation

  • Launch the “PoeymaüarcheoViz instance.
  • Explore the 4 types of visualisation: 3D, map, Sections X and Y.
  • Display the following selections:
    • A 3D view of layer FSH.
    • A 3D view of the convex hull of all object types.
    • A 3D view of the convex hull of pottery objects.
    • A map of the faunal remains between z=300 and z=400.
    • A 3D view of the faunal remains in layer BI.
    • A Section view of the refittings in X.
    • Section view of the refittings in band X.
    • Generate a section view of the site in X and the same in Y: what is the difference?

Export Figures

  • Export a 3D view of the faunal and lithic remains as an SVG file. Open this file.
  • Export a map of the burned remains as an SVG file. Open this file.
  • Export a Section view in X of burned and not burned remains as an HTML file.
  • Export an HTML file of a 3D visualisation that allows to (un)select three types of remains.
    • Try it with a web browser;
    • Examine the files size: what do these files contain?
    • How this file could be used?

Reading

  • Gardin J.-C. & C. Peebles. 1992. Representations in Archaeology. Bloomington: Indiana University Press.
  • Opgenhaffen L. 2021. “Visualizing Archaeologists: A Reflexive History of Visualization Practice in Archaeology”, Open Archaeology, 7 (1), doi: 10.1515/opar-2020-0138.
  • Nakoinz, O., D. Knitter. 2016. Modelling Human Behaviour in Landscapes. Basic Concepts and Modelling Elements. Springer. DOI: 10.1007/978-3-319-29538-1.
  • Plutniak S. 2021. “Abstraction in Archaeological Stratigraphy: a Pyrenean Lineage of Innovation (late 19th-early 21th century)” in de Beaune, S. et al. (eds), New Advances in the History of Archaeology, Oxford: Archaeopress, p. 78-92, DOI: 10.31235/osf.io/2pgak.

Introduction to the R Programming Language and Reproducible Science, using the archeoViz Application

This document is intended for teachers introducing students in archaeology to scientific programming with R and to some principles of reproducible science. It presents the basics for a class syllabus, using the archeoViz application as a pedagogical resource.

  • Concepts: scientific programming, R language, Reproducible science.
  • Audience: intermediate, advanced.
  • Material:
    • a computer with an internet connection,
    • R and R Studio.

Basics of R Language

  • Install and load the archeoViz package (introduction to CRAN and the following functions: install.packages(), library()).
  • Download the Cassenade dataset.
  • Load the dataset in R (functions: read.csv(), read.table(), <-)
  • Data edition:
    • convert the coordinates values to centimetres (functions: *, $)
    • subset (columns and rows selection; functions: indexing with [,]):
      • remove the “spitid” column,
      • keep only the objects excavated in 2013.
  • Launch archeoViz with the edited dataset (function: archeoViz()) and explore it.

Reproducible Research

  • If the raw table changes, the script we have written so far enables us to edit it quickly and seamlessly.
  • However, what about the operations made through the archeoViz graphic interface?
    • The results of the manipulation made through the graphic interface can be shared as figures and HTML files (cf. the tutorial on visualisation).
    • archeoViz includes an additional feature for reproducible science: explore the “Reproducibility” tab:
      • What does this tab offer?
      • Examine the parameters: what type of data is represented? (variable types: character, integer, logical; functions: c()).

Functions and Parameters

  • After interacting with the archeoViz interface, copy-paste the function in the “Reproducibility” tab in R Studio and execute it.
  • Read the about the archeoViz() parameters.
  • Edit the function’s parameters to:
    • display only lithic objects,
    • disable data export as HTML and CSV files,
    • change the title and homepage contents.

Reading

Introduction to Archaeological Data Curation, Description, and Edition, using the archeoViz Application

This document is intended for teachers introducing students in archaeology to basic principles of data curation and web edition. It presents the basics for a class syllabus, using the archeoViz application as a pedagogical resource.

  • Concepts: metadata, data publication, data editorialisation, data alignment, Interoperability.
  • Audience: intermediate, advanced.
  • Material:
    • a computer with an internet connection,
    • a spreadsheet editor.

Concepts

  • Explore the archeoViz Portal and the archeoViz instances.
    • Examine and interpret the “metadata” section in one of the instances (e.g., the Barger Gulch dataset).
    • Advanced students: download, examine, and comment on the “metadata table” available on the archeoViz Portal page.
  • Examine the archeoViz workflow chart:
    • What difference do you observe in the four options?
    • What does it mean (or should mean) to “publish” data?
    • What is the difference between data publication and data editorialisation?
  • Examine the archeoViz ecosystem chart:
    • What mean the two types of arrows?
    • What are the types of services composing this ecosystem?
    • Analyse the archeoViz ecosystem in terms of centralisation / decentralisation.
    • Explore the website of the reference systems used in this ecosystem: PACTOLS, ORCID, VIAF, Geonames.

Interoperability

  • Explore the Bilzingsleben instance. Describe how the data in this archeoViz instance is linked to the original database. Compare it with the Erb Tanks instance.
  • Read the archeoViz documentation about the use of URL parameters.
  • Use URL parameters to load the Cassenade dataset in an online archeoViz instance.
  • Conversely, data can be transmitted from an archeoViz instance to third-party applications. Using the options in the “Statistics” tab, try to:
    • analyse the refitting data with the archeofrag application;
    • analyse the object types distribution in the stratigraphy of the Poeymaü cave with the Seriograph application.

Data alignment

For Advanced students:

  • In the PACTOLS thesaurus, find the “lithic” and “pottery” concepts and their unique identifier.
  • In SEAHORS, load the Cassenade dataset, and export it to the archeoViz format in a CSV file.
  • Edit the CSV file to recode the “object_type” variable and align it with the PACTOLS concepts.
  • Load the resulting CSV file in archeoViz and check if the link between the objects and the PACTOLS concepts is correct.

Readings

  • Kansa, E. C., S. W. Kansa. 2013. “We All Know That a 14 Is a Sheep: Data Publication and Professionalism in Archaeological Communication”. Journal of Eastern Mediterranean Archaeology and Heritage Studies, 1 (1), p. 88-97. DOI: 10.1353/ema.2013.0007
  • Marwick B. 2017. “Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of their Implementation”. Journal of Archaeological Method and Theory, 24 (4), p. 1-27. DOI: 10.1007/s10816-015-9272-9

Introduction to File Formats and Archeological Data Preparation, using the archeoViz Application

This document is intended for teachers introducing students in archaeology to basic concepts related to computer file formats. It presents the basics for a class syllabus, using the archeoViz application as a pedagogical resource.

  • Concepts: file formats, tabular data, CSV format, archaeological field data.
  • Audience: beginners, intermediate.
  • Material:
    • a computer with an internet connection, a spreadsheet editor, an unzipper software,
    • the example Excel file.

File formats

  • Download the XLSX file and open it.
  • Examine the data structure and interpret the variables.
  • Convert it into a CSV file (pay attention to the delimiters).
  • Compare the size of the two files.

For intermediate audience:

  • unzip the XLSX file, examine its structure;
  • open the CSV file with a text editor.]

Data formatting for archeoViz

  • Read the archeoViz guidelines about data format.
  • Method 1: Use the SEAHORS application to load, prepare, and download the file.
  • Method 2: edit the CSV file:
    • rename the variable names,
    • split the values of the square labels into two columns “square_x” and “square_y”,
  • Upload and test the file in an online archeoViz instance.

Readings

  • Wikipedia’s page on the CSV format.
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