Browse by volume Browse by section Browse by topic Browse by conference

Section: Archaeology
Topic: Archaeology

SEAHORS: Spatial Exploration of ArcHaeological Objects in R Shiny

Royer, Aurélien1  ; Discamps, Emmanuel2 ; Plutniak, Sébastien3 ; Thomas, Marc2 
1 Biogéosciences, UMR 6282 CNRS, Université de Bourgogne, 6 Boulevard Gabriel, 21000 Dijon, France
2 UMR 5608 TRACES, CNRS & Université Toulouse Jean Jaurès, Toulouse 31058, France
3 CNRS/Université de Tours, UMR 7324 CITERES, Laboratoire Archéologie et Territoires, 40 Rue James Watt, ActiCampus 1, 37200, Tours, France

10.24072/pcjournal.289 - Peer Community Journal, Volume 3 (2023), article no. e55.

Get full text PDF Peer reviewed and recommended by PCI

This paper presents SEAHORS, an R shiny application available as an R package, dedicated to the intra-site spatial analysis of piece-plotted archaeological remains. This open-source script generates 2D and 3D scatter and density plots for archaeological objects located with cartesian coordinates. Many different GIS software already exist for this, but they mostly require specific skills and training to be used and are rarely designed for the particular needs of archaeological applications. The goal of SEAHORS is to make the two and three-dimensional intra-site spatial exploration of archaeological data as user-friendly as possible, in order to give the opportunity to researchers not familiar with GIS and R software to utilise such approaches. SEAHORS has an easily accessible interface and can import data from text and Excel files (.csv and .xls/xlsx respectively) without preformatting. The application includes functions to concatenate columns and to merge databases, for example when spatial data (XYZ coordinates) and analytical data (e.g. taxonomical attribution of faunal remains, typo-technological attributes of artifacts, etc.) are stored in separate files. SEAHORS can generate five types of plots: 3D, 2D and density plots, as well as 2D plots by slices (i.e. subdivisions according to a third dimension) and 2D plots with a modification of the angle of projection (i.e. to explore spatial organization without the constraints of the field grid orientation). SEAHORS has visualization tools with several sorting and formatting options (color, size, etc.) applicable to coordinates and all possible analytical variables (i.e. levels, spits, identified species, taphonomical alterations, etc.). Orthophotos can also be imported and directly used in the program. The application also allows the grouping of objects into new variables by selecting items on the interactive 2D plots. We present an overview of the application’s functions by using the case study of the Cassenade Paleolithic site (France).

Published online:
DOI: 10.24072/pcjournal.289
Type: Software tool
Keywords: archaeological methods; data visualization; spatial analysis; R shiny application; post-excavation stratigraphies
Royer, Aurélien 1; Discamps, Emmanuel 2; Plutniak, Sébastien 3; Thomas, Marc 2

1 Biogéosciences, UMR 6282 CNRS, Université de Bourgogne, 6 Boulevard Gabriel, 21000 Dijon, France
2 UMR 5608 TRACES, CNRS & Université Toulouse Jean Jaurès, Toulouse 31058, France
3 CNRS/Université de Tours, UMR 7324 CITERES, Laboratoire Archéologie et Territoires, 40 Rue James Watt, ActiCampus 1, 37200, Tours, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
@article{10_24072_pcjournal_289,
     author = {Royer, Aur\'elien and Discamps, Emmanuel and Plutniak, S\'ebastien and Thomas, Marc},
     title = {SEAHORS: {Spatial} {Exploration} of {ArcHaeological} {Objects} in {R} {Shiny}},
     journal = {Peer Community Journal},
     eid = {e55},
     publisher = {Peer Community In},
     volume = {3},
     year = {2023},
     doi = {10.24072/pcjournal.289},
     language = {en},
     url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.289/}
}
TY  - JOUR
AU  - Royer, Aurélien
AU  - Discamps, Emmanuel
AU  - Plutniak, Sébastien
AU  - Thomas, Marc
TI  - SEAHORS: Spatial Exploration of ArcHaeological Objects in R Shiny
JO  - Peer Community Journal
PY  - 2023
VL  - 3
PB  - Peer Community In
UR  - https://peercommunityjournal.org/articles/10.24072/pcjournal.289/
DO  - 10.24072/pcjournal.289
LA  - en
ID  - 10_24072_pcjournal_289
ER  - 
%0 Journal Article
%A Royer, Aurélien
%A Discamps, Emmanuel
%A Plutniak, Sébastien
%A Thomas, Marc
%T SEAHORS: Spatial Exploration of ArcHaeological Objects in R Shiny
%J Peer Community Journal
%D 2023
%V 3
%I Peer Community In
%U https://peercommunityjournal.org/articles/10.24072/pcjournal.289/
%R 10.24072/pcjournal.289
%G en
%F 10_24072_pcjournal_289
Royer, Aurélien; Discamps, Emmanuel; Plutniak, Sébastien; Thomas, Marc. SEAHORS: Spatial Exploration of ArcHaeological Objects in R Shiny. Peer Community Journal, Volume 3 (2023), article  no. e55. doi : 10.24072/pcjournal.289. https://peercommunityjournal.org/articles/10.24072/pcjournal.289/

Peer reviewed and recommended by PCI : 10.24072/pci.archaeo.100320

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

[1] Allaire, J.; Xie, Y.; McPherson, J.; Luraschi, J.; Ushey, K.; Atkins, A.; Wickham, H.; Cheng, J.; Chang, W.; Iannone, R. rmarkdown: Dynamic Documents for R. R package version 2.20, 2023 (https://github.com/rstudio/rmarkdown)

[2] Chadelle, J.-P.; Geneste, J.-M.; Texier, J.-P. Les gisements paléolithiques récemment découverts à Pombonne (Lembras, Dordogne), Paléo, Revue d'archéologie préhistorique, Volume 8 (1996) no. 1, pp. 279-291 | DOI

[3] Chang, W.; Cheng, J.; Allaire, J.; Xie, Y.; McPherson, J.; Dipert, A.; Borges, B. shiny: Web Application Framework for R. R package version 1.7.4, 2022 (https://cran.r-project.org/web/packages/shiny/index.html)

[4] Couillet, A.; Rougier, H.; Todisco, D.; Marot, J.; Gillet, O.; Crevecoeur, I. New Visual Analytics Tool and Spatial Statistics to Explore Archeological Data: The Case of the Paleolithic Sequence of La Roche-à-Pierrot, Saint-Césaire, France, Journal of Computer Applications in Archaeology, Volume 5 (2022) no. 1, pp. 19-34 | DOI

[5] Dibble, H. L.; McPherron, S. P. On the Computerization of Archaeological Projects, Journal of Field Archaeology, Volume 15 (2013) no. 4, pp. 431-440 | DOI

[6] Discamps, E.; Bachellerie, F.; Baillet, M.; Sitzia, L. The use of spatial taphonomy for interpreting Pleistocene palimpsests: an interdisciplinary approach to the Châtelperronian and carnivore occupations at Cassenade (Dordogne, France)., Paleoanthropology (2019) | DOI

[7] Discamps, E.; Thomas, M.; Dancette, C.; Gravina, B.; Plutniak, S.; Royer, A.; Angelin, A.; Bachellerie, F.; Beauval, C.; Bordes, J.-G.; Deschamps, M.; Ducasse, S.; Langlais, M.; Laroulandie, V.; Mallye, J.-B.; Michel, A.; Perrin, T.; Rendu, W. Breaking free from field layers: the interest of Post-Excavation Stratigraphies (PES) for producing reliable archaeological interpretations and increasing chronological resolution, Research Square Preprint | DOI

[8] Houllier, J.-R.; Arnoux, T. Informatisation d’une fouille : réalisation et déploiement du logiciel d’acquisition de données « FrAcTool » (Fressignes Acquisition Tool), Paléo (2001) no. 13, pp. 251-264 | DOI

[9] Lacrampe-Cuyaubere, F. Utilisation du logiciel Data Desk™ pour la construction de projections de vestiges archéologiques: une application automatisée à l'usage des préhistoriens, Paléo, Volume 9 (1997) no. 1, pp. 335-349 | DOI

[10] Laplace-Jauretche, G.; Méroc, L. Application des coordonnées cartésiennes à la fouille d'un gisement, Bulletin de la Société préhistorique de France, Volume 51 (1954) no. 1, pp. 58-66 | DOI

[11] Morehouse, S. ARC/INFO: A geo-relational model for spatial information, Auto-Carto 7, 1985

[12] Plutniak, S. Abstraction in Archaeological Stratigraphy: a Pyrenean Lineage of Innovation (late 19th-early 21th century) In: New Advances in the History of Archaeology, Archaeopress, Oxford (2021), pp. 78-92 (https://hal.archives-ouvertes.fr/hal-03338343v2)

[13] Plutniak, S. Virtual Poeymaü: a web application to explore the archaeological data from the excavation archives of the Poeymaü cave (France) (v0.2), Zenodo, 2021 | DOI

[14] Plutniak, S. archeoViz. Visualisation, Exploration, and Web Communication of Archaeological Excavation Data, R package v0.2.1, 2023 (https://cran.r-project.org/web/packages/archeoViz/index.html.) | DOI

[15] Plutniak, S. Visualiser et explorer la distribution spatiale du mobilier archéologique : l’application archeoViz et son portail web, Bulletin de la Société préhistorique française, Volume 120 (2023)

[16] QGIS Development Team QGIS Geographic Information System. QGIS Association, 2002 (https://www.qgis.org)

[17] Ripley, B.; Venables, B.; Bates, D.; Hornik, K.; Gebhardt, A.; Firth, D.; Ripley, M. Package ‘MASS’, R Cran, Volume 538, 2013 (https://cran.r-project.org/web/packages/MASS/index.html)

[18] Sécher, A.; Langlais, M.; Berlioz, É.; Delvigne, V.; Pétillon, J.-M.; Renou, S. Combe-Cullier (Lacave, Lot) : une séquence oubliée du Magdalénien. Rapport de deuxième année d’aide à la préparation de publication, DRAC Occitanie, 2020

[19] Sievert, C.; Parmer, C.; Hocking, T.; Chamberlain, S.; Ram, K.; Corvellec, M.; Despouy, P. plotly: Create Interactive Web Graphics via ‘plotly. js’. R package version, R Cran, Volume 4, 2017 (https://cran.r-project.org/web/packages/plotly/)

[20] R Core Team R: A language and environment for statistical computing, 2022 (https://www.r-project.org/)

[21] Wickham, H.; Chang, W.; Henry, L.; Lin Pedersen, T.; Takahashi, K.; Wilke, C.; Woo, K.; Yutani, H.; Dunnington, D. Package ‘ggplot2’. Create elegant data visualisations using the grammar of graphics, Volume 2, 2016 (https://cran.r-project.org/web/packages/ggplot2/index.html)

Cited by Sources: