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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.

archeoViz newsletter #1 Mai 2023

Chers et chères premiers inscrits à la lettre d’information archeoViz,

Voici la première lettre d’information archeoViz, faisant le point pour mai 2023.
Merci d’avoir bien voulu compter parmi les premiers et premières inscrits et/ou utilisateurs !

Ce premier envoi vient, malheureusement, avec une triste nouvelle : celle du récent décès de Grégor Marchand. Grégor avait compté parmi les premières personnes ayant répondu avec enthousiasme à mon appel à soutenir, avec des données, les débuts d’archeoViz. Partager, en pratique, constituait une évidence pour lui, ici en l’occurrence avec les données de l’Anse à Henry.

Comme annoncé, cette mailing list servira à diffuser les actualités relatives à l’application archeoViz et à son portail. En outre, la liste est paramétrée pour permettre les échanges entre abonné⋅e⋅s, donc n’hésitez pas à l’employer de cette manière (pour toute question ou suggestion d’intérêt général).

Les nouveautés du mois de mai sont présentées ci-dessous par rubrique.

Plus généralement, n’hésitez pas à soumettre toute suggestion concernant l’application et son interface, des jeux de données à intégrer, ou des personnes susceptibles d’être intéressées (écrire à : archeoviz-maintainers@services.cnrs.fr).

À bientôt,
Sébastien

Publications et documentations

Une courte publication, ainsi que les slides de la première présentation publiques, sont accessibles en ligne :

Ajouts de jeux de données sur le portail

Le portail vient de dépasser la barre des 300 000 objets, et celle des 10 000 relations de remontages, indexés.
Les ajouts du mois de mai incluent :

Améliorations du portail archeoViz

  • Citabilité : les instances statiques archeoViz sont désormais citables (la référence apparaît sur la page d’accueil de chaque instance),
  • Découvrabilité : la création de fiches HAL relatives aux instances d’archeoViz indexés sur le portail permettent de propager les références bibliographiques de ces instances dans d’autres systèmes documentaires (Google Scholar, BASE, etc.).
  • Les noms de personnes (de fouilleurs, de créateurs des données, d’éditeur des données) sont désormais alignées sur le référentiel VIAF.

Améliorations d’archeoViz

Nouveautés des versions 1.1.1 et 1.1.2 :

  • Il est désormais possible de visualiser les incertitudes des localisations des points (dans la visualisation 3D uniquement pour l’heure).
  • l’export des graphiques en format HTML interactif est désormais possible (comme option) pour tous les graphiques (3D, plan, coupes).
  • l’affichage d’informations en cliquant sur un point est désormais possible sur tous les graphiques (3D, plan, coupes).
  • Les balises HTML sont désormais possibles dans les tableaux de données. Cela permet notamment d’afficher des liens hypertextes vers les entrées correspondant aux objets dans leur base de données d’origine. C’est le cas, par exemple, pour
    • le site d’Erb Tanks, stocké sur tDAR.
    • Bilzingsleben, lié à sa base de données hébergée sur Internet Archaeology.

archeoViz newsletter #1 May 2023

Dear first subscribers to the archeoViz newsletter,

This is the first archeoViz newsletter, for May 2023.
Thank you much for subscribing to the archeoViz newsletter!

Unfortunately, this first message comes with sad news: the recent passing of Grégor Marchand. Grégor was among the first persons who responded my call to support the beginnings of archeoViz with data. Sharing –in practice– was essential for him, and so he did with the data from the l’Anse à Henry site he was excavating.

As announced, this mailing list will be used to share news and updates about archeoViz and the archeoViz portal. In addition, the list is set to allow for mails among subscribers, so do not hesitate to use it for requests, ideas, or question of general interest.

News from May is presented below by section.

More generally, feel free to submit any suggestions you may have concerning the application and its interface, data sets to be integrated, or people likely to be interested (write to: archeoviz-maintainers@services.cnrs.fr).

All the best
Sébastien

Publication and documentation

A short published note and the slides from the first public presentation are available online:

Recent additions to the archeoViz portal

Since May, the archeoViz instances references in the portal included more than 300,000 objects and 10,000 refitting relationships.
New additions include:

Improvements of the archeoViz portal

  • Citation: the static archeoViz instances can now be cited (the reference appears on the instance’s home page),
  • Discoverability: An HAL record is created for each for archeoViz instances indexed on the portal, enabling their bibliographic references be disseminated to other documentation systems (Google Scholar, BASE, etc.).
  • Persons names (excavators, data creator, data editor) are now aligned on the VIAF repository

Improvements of the archeoViz application

New features of the 1.1.1 and 1.1.2 versions:

  • The uncertainty of the points locations can now be displayed: inaccurate locations are represented as lines, surfaces, of volumes (only in the 3D view so far).
  • All the plots can now be exported as interactive stand-alone HTML files (this features can be disabled).
  • The display (below the plots) of additional information when clicking on a point is now available in all tabs (3D, Sections, Map)
  • HTML markup is now supported in input data tables, and are visible in the table with additional information about the clicked point. These hyperlinks can –among other– be used to link the points with their corresponding record in their original database. See for example:
    • Erb Tanks, linked to its original dataset on tDAR
    • Bilzingsleben, linked to its original dataset on Internet Archaeology