archeofrag.gui: Spatial Analysis in Archaeology from Refitting Fragments (GUI)

An R 'Shiny' application to access the functionalities and datasets of the 'archeofrag' package for spatial analysis in archaeology from refitting data. Quick and seamless exploration of archaeological refitting datasets, focusing on connection relationships only (i.e. physical refits). Features include: built-in documentation and convenient workflow, plot generation and export, R code generation to re-execute the simulations in R and ensure reproducibility, support for parallel computing to speed up computation. A demonstration version of the app is available online.

Summary

This R Shiny application implements and complements some features of the archeofrag package R package for spatial analysis in archaeology from the study of refitting fragments of objects. Based on the TSAR method (Topological Study of Archaeological Refitting), it includes functions to evaluate and validate the distinction between archaeological spatial units (e.g. layers), from the distribution and the topology of the refitting relationships between the fragments contained in these units.

Contents

• Installation
• About archeofrag
• archeofrag.gui features
  • Reporting bugs
  • Suggesting changes
• Data input
• Spatial units merging
• Comparison with simulated data to test formation scenarios
• Community guidelines
• References

Installation

The package can be installed from CRAN with:

install.packages("archeofrag.gui")

The development version is available from GitHub and can be installed with:

if ( ! requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_github("sebastien-plutniak/archeofrag.gui")

The determination of graph planarity in the archeofrag package requires the RBGL package, available through Bioconductor: This feature is optional, because

1. even if archaeological fragmentation graphs are planar in most of the cases, there are exceptions
2. RBGL is a very large package.

if ( ! requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("RBGL")

About archeofrag

Please refer to the archeofrag package documentation on CRAN or github to learn about its methods and functions for spatial and refitting analysis.

archeofrag.gui features

• Exclusive focus on connection relationships (i.e. physical refits)
• Integrated workflow for quick and efficient use of archeofrag functionalities
• Convenient access to refitting datasets included in archeofrag
• Built-in documentation
• Charts generation and export as SVG
• R code generation
• openMOLE code generation, a model exploration software
• Interoperability: data can be exported to archeofrag.gui from the archeoViz application for archaeological spatial data visualisation.

Data input

Either load one of the built-in example data sets or upload your data. Use the menu on the left to upload your 'relationships' and 'fragments' data as CSV files.

• The relationships table must have a row for each refitting relationship, and two columns containing the identifiers of the two fragments.
• The fragments table must have a row for each fragment, the first column is for fragments identifier and the second column contains the spatial unit they are associated to.

Spatial units merging

Archaeological spatial units are likely to be recombined, for example when there are reasons to merge stratigraphic layers. The 'Spatial units optimisation' tab helps in this task. It draws on the measurement of the difference between the cohesion values of a pair of spatial units: the lower this difference, the more balanced the archaeological information about them (regardless of their possible admixture). Given a series of spatial units, this functionality:

1. determines the list of possible combinations of pair of spatial units
2. computes the cohesion values for each combination and summarises it by calculating its median values
3. return and sort the solutions.

Merging solutions with lower median values reflect spatial divisions for which the archaeological information is best balanced.

Comparison with simulated data to test formation scenarios

Hypotheses about two aspects of site formation processes are of particular interest and can be studied by generating series of fragmentation graphs to compare:

1. the number of deposition events and
2. the direction of fragments transport between the first and second spatial units considered.

Select the pair of spatial units to compare in the left menu, set the number of simulated data sets to generate, and click on the “Run” button. Depending on the size of the data set, the computing time can be long. Charts are generated for various parameters measured on the fragmentation graphs: the value observed on the empirical graph is represented by a vertical bar, the distribution of values for each hypotheses are represented by dark (H1) and light (H2) grey shades.

1. Number of deposition events

Fragmentation graphs can be generated for two hypotheses regarding the number of deposition events involved in the formation of the considered pair of spatial units:

• H1. The objects were buried during one deposition event forming a single spatial unit, were subsequently fragmented and moved, and were discovered in two spatial units according to the archaeologists;
• H2. The objects were buried during two deposition events forming two spatial units, were subsequently fragmented and moved, and were discovered in two spatial units according to the archaeologists.

2. Direction of fragments transport

The 'Unidirectional transport from unit...' parameter makes it possible to constrain the direction of fragments transport between the two spatial units under study.

The observed data can be compared to similar simulated data for two formation hypothesis:

Community guidelines

Reporting bugs

If you find a bug, please fill an issue with all the details needed to reproduce it.

Suggesting changes

Suggestions of changes to archeofrag.gui are very welcome. These requests may concern additional functions, changes to documentation, additional examples, new features, etc. They can be made by filling an issue and, even better, using pull requests and the GitHub Fork and Pull model.

References

Please use Plutniak 2022a to cite archeofrag.gui.

For more details, see the following publications:

• Plutniak, S. 2021. “The Strength of Parthood Ties. Modelling Spatial Units and Fragmented Objects with the TSAR Method – Topological Study of Archaeological Refitting”, Journal of Archaeological Science, 136, p. 105501. DOI: 10.1016/j.jas.2021.105501.
• Plutniak, S. 2022a. “Archeofrag: an R package for Refitting and Spatial Analysis in Archaeology”, Journal of Open Source Software, 7 (75), p. 4335. DOI: 10.21105/joss.04335.
• Plutniak, S. 2022b. “Archeofrag: un package R pour les remontages et l'analyse spatiale en archéologie”, Rzine.
• Plutniak, S. 2022c. “L'analyse topologique des remontages archéologiques : la méthode TSAR et le package R archeofrag”, Bulletin de la Société préhistorique française, 119 (1), p. 110-113.
• Plutniak, S., J. Caro, C. Manen 2023. “Four Problems for Archaeological Fragmentation Studies. Discussion and Application to the Taï Cave’s Neolithic Pottery Material (France)”, in A. Sörman et al., Broken Bodies, Places and Objects. New Perspectives on Fragmentation in Archaeology, London: Routledge, DOI: 10.4324/9781003350026-10.