diff --git a/joss.05811/10.21105.joss.05811.crossref.xml b/joss.05811/10.21105.joss.05811.crossref.xml
new file mode 100644
index 0000000000..cb403a548e
--- /dev/null
+++ b/joss.05811/10.21105.joss.05811.crossref.xml
@@ -0,0 +1,307 @@
+
+
+
+ 20231211T091253-f2ea8928bef7cfeb1884f6beedf73b4cb1111eca
+ 20231211091253
+
+ JOSS Admin
+ admin@theoj.org
+
+ The Open Journal
+
+
+
+
+ Journal of Open Source Software
+ JOSS
+ 2475-9066
+
+ 10.21105/joss
+ https://joss.theoj.org
+
+
+
+
+ 12
+ 2023
+
+
+ 8
+
+ 92
+
+
+
+ archeoViz: an R package for the Visualisation,
+Exploration, and Web Communication of Archaeological Spatial
+Data
+
+
+
+ Sébastien
+ Plutniak
+ https://orcid.org/0000-0002-6674-3806
+
+
+
+ 12
+ 11
+ 2023
+
+
+ 5811
+
+
+ 10.21105/joss.05811
+
+
+ http://creativecommons.org/licenses/by/4.0/
+ http://creativecommons.org/licenses/by/4.0/
+ http://creativecommons.org/licenses/by/4.0/
+
+
+
+ Software archive
+ 10.5281/zenodo.10200892
+
+
+ GitHub review issue
+ https://github.com/openjournals/joss-reviews/issues/5811
+
+
+
+ 10.21105/joss.05811
+ https://joss.theoj.org/papers/10.21105/joss.05811
+
+
+ https://joss.theoj.org/papers/10.21105/joss.05811.pdf
+
+
+
+
+
+ Interactive web-based data visualization with
+R, plotly, and shiny
+ Sievert
+ 10.1201/9780429447273
+ 978-1138331495
+ 2020
+ Sievert, C. (2020). Interactive
+web-based data visualization with R, plotly, and shiny. Chapman &
+Hall/CRC. https://doi.org/10.1201/9780429447273
+
+
+ BDA : une Base de Données Archéologique
+collaborative en ligne
+ Perrin
+ Bulletin de la Société préhistorique
+française
+ 1
+ 116
+ 10.3406/bspf.2019.14988
+ 1960
+ Perrin, T. (1960). BDA : une Base de
+Données Archéologique collaborative en ligne. Bulletin de la Société
+préhistorique française, 116(1), 159‑162.
+https://doi.org/10.3406/bspf.2019.14988
+
+
+ Integrated and interactive 4D system for
+archaeological stratigraphy
+ Ortega-Alvarado
+ Archaeological and Anthropological
+Sciences
+ 203
+ 14
+ 10.1007/s12520-022-01667-3
+ 2022
+ Ortega-Alvarado, G.-F., Lidia M.,
+Conde-Rodríguez, F., & Jurado-Rodríguez, J. M. (2022). Integrated
+and interactive 4D system for archaeological stratigraphy.
+Archaeological and Anthropological Sciences, 14(203).
+https://doi.org/10.1007/s12520-022-01667-3
+
+
+ Aspectus: A flexible collaboration tool for
+multimodal and multiscalar 3D data exploitation
+ Vurpillot
+ Studies in Digital Heritage
+ 2
+ 2
+ 10.14434/sdh.v2i2.24446
+ 2018
+ Vurpillot, D., Verriez, Q., &
+Thivet, M. (2018). Aspectus: A flexible collaboration tool for
+multimodal and multiscalar 3D data exploitation. Studies in Digital
+Heritage, 2(2), 150–165.
+https://doi.org/10.14434/sdh.v2i2.24446
+
+
+ Digital archaeology field recording in the
+4th dimension: ArchField c++ a 4D GIS for digital field
+work
+ Smith
+ 2015 digital heritage
+ 2
+ 10.1109/DigitalHeritage.2015.7419505
+ 2015
+ Smith, N. G., Howland, M., &
+Levy, T. E. (2015). Digital archaeology field recording in the 4th
+dimension: ArchField c++ a 4D GIS for digital field work. 2015 Digital
+Heritage, 2, 251–258.
+https://doi.org/10.1109/DigitalHeritage.2015.7419505
+
+
+ Ten years of ArkeoGIS: Feedback on the
+challenges and benefits of digitally sharing archeological
+data
+ Bernard
+ 2019
+ Bernard, L. (2019). Ten years of
+ArkeoGIS: Feedback on the challenges and benefits of digitally sharing
+archeological data.
+https://hal.science/hal-02865759
+
+
+ archeoViz. Visualisation, exploration, and web
+communication of archaeological spatial data
+ Plutniak
+ 10.5281/zenodo.10200892
+ 2023
+ Plutniak, S., Araujo, R., Coltofean,
+L., Delsol, N., Giardino, S., & Laabs, J. (2023). archeoViz.
+Visualisation, exploration, and web communication of archaeological
+spatial data.
+https://doi.org/10.5281/zenodo.10200892
+
+
+ recexcavAAR: 3D reconstruction of
+archaeological excavations
+ Schmid
+ 2017
+ Schmid, C., & Serbe, B. (2017).
+recexcavAAR: 3D reconstruction of archaeological excavations.
+https://CRAN.R-project.org/package=recexcavAAR
+
+
+ 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
+ Couillet
+ Journal of Computer Applications in
+Archaeology
+ 1
+ 5
+ 10.5334/jcaa.81
+ 2022
+ Couillet, A., Rougier, H., Todisco,
+D., Marot, J., Gillet, O., & Crevecoeur, I. (2022). 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, 5(1), 19–34.
+https://doi.org/10.5334/jcaa.81
+
+
+ Generalized additive models: An introduction
+with R
+ Wood
+ 10.1201/9781315370279
+ 978-1315370279
+ 2017
+ Wood, S. N. (2017). Generalized
+additive models: An introduction with R (2nd ed.). Chapman; Hall/CRC.
+https://doi.org/10.1201/9781315370279
+
+
+ cxhull: Convex hull
+ Laurent
+ 2023
+ Laurent, S. (2023). cxhull: Convex
+hull. https://CRAN.R-project.org/package=cxhull
+
+
+ htmlwidgets: HTML widgets for R
+ Vaidyanathan
+ 2023
+ Vaidyanathan, R., Xie, Y., Allaire,
+J., Cheng, J., Sievert, C., & Russell, K. (2023). htmlwidgets: HTML
+widgets for R.
+https://CRAN.R-project.org/package=htmlwidgets
+
+
+ ggplot2: Elegant graphics for data
+analysis
+ Wickham
+ 10.1007/978-3-319-24277-4
+ 978-3-319-24277-4
+ 2016
+ Wickham, H. (2016). ggplot2: Elegant
+graphics for data analysis. Springer-Verlag.
+https://doi.org/10.1007/978-3-319-24277-4
+
+
+ SEAHORS: Spatial exploration of
+ArcHaeological objects in R shiny
+ Royer
+ Peer Community Journal
+ e55
+ 3
+ 10.24072/pcjournal.289
+ 2023
+ Royer, A., Discamps, E., Plutniak,
+S., & Thomas, M. (2023). SEAHORS: Spatial exploration of
+ArcHaeological objects in R shiny. Peer Community Journal, 3(e55).
+https://doi.org/10.24072/pcjournal.289
+
+
+ R: A language and environment for statistical
+computing
+ R Core Team
+ 2023
+ R Core Team. (2023). R: A language
+and environment for statistical computing. R Foundation for Statistical
+Computing. https://www.R-project.org/
+
+
+ shiny: Web application framework for
+R
+ Chang
+ 2020
+ Chang, W., Cheng, J., Allaire, J. J.,
+Xie, Y., & McPherson, J. (2020). shiny: Web application framework
+for R. https://CRAN.R-project.org/package=shiny
+
+
+ Visualiser et explorer la distribution
+spatiale du mobilier archéologique: l’application archeoViz et son
+portail web
+ Plutniak
+ Bulletin de la Société préhistorique
+française
+ 1
+ 120
+ 2023
+ Plutniak, S. (2023). Visualiser et
+explorer la distribution spatiale du mobilier archéologique:
+l’application archeoViz et son portail web. Bulletin de la Société
+préhistorique française, 120(1), 70–74.
+
+
+ D2.2 second report on users’
+needs
+ Selhofer
+ 2015
+ Selhofer, H., & Geser, G. (2015).
+D2.2 second report on users’ needs [Ariadne WP15 Study]. Ariadne.
+http://legacy.ariadne-infrastructure.eu/wp-content/uploads/2019/01/ARIADNE_D2.2_Second_report_on_users_needs.pdf
+
+
+
+
+
+
diff --git a/joss.05811/10.21105.joss.05811.jats b/joss.05811/10.21105.joss.05811.jats
new file mode 100644
index 0000000000..5e673a8c10
--- /dev/null
+++ b/joss.05811/10.21105.joss.05811.jats
@@ -0,0 +1,761 @@
+
+
+
+
+
+
+
+Journal of Open Source Software
+JOSS
+
+2475-9066
+
+Open Journals
+
+
+
+5811
+10.21105/joss.05811
+
+archeoViz: an R package for the Visualisation,
+Exploration, and Web Communication of Archaeological Spatial
+Data
+
+
+
+https://orcid.org/0000-0002-6674-3806
+
+Plutniak
+Sébastien
+
+
+
+
+
+CNRS, CITERES-LAT, Université de Tours, Tours,
+France
+
+
+
+
+7
+12
+2023
+
+8
+92
+5811
+
+Authors of papers retain copyright and release the
+work under a Creative Commons Attribution 4.0 International License (CC
+BY 4.0)
+2022
+The article authors
+
+Authors of papers retain copyright and release the work under
+a Creative Commons Attribution 4.0 International License (CC BY
+4.0)
+
+
+
+R
+archaeology
+archeology
+data visualisation
+data vizualisation
+spatial analysis
+spatial statistics
+
+
+
+
+
+ Summary
+
archeoViz is an R Shiny application for the
+ visualisation, interactive exploration, and web communication of
+ archaeological spatial data
+ (Plutniak
+ et al., 2023;
+ Plutniak,
+ 2023). It generates interactive 3D plots, 2D cross sections and
+ 2D maps of archaeological objects and their refitting relationships,
+ and display an interactive timeline of the work made in a site.
+ Spatial statistics methods can be applied (convex hull, regression
+ surfaces, 2D kernel density estimation) and data can be directly
+ exported to other online applications to run other methods. This
+ application is designed as the building block of a decentralised web
+ edition network for archaeological data: 1) users can deploy
+ archeoViz instances specific to their datasets
+ on the server of their choice; 2) the archeoViz
+ Portal, a companion online application, references and
+ documents with metadata these archeoViz
+ instances, increasing their discoverability and audience on the web,
+ both for scientists and the general audience interested in
+ archaeology. It can also be used as an educational resource to
+ introduce learners to spatial analysis, data formats, reproducible
+ workflow, open science, and computational archaeology.
+
+
+ Statement of Need
+
For more than a century, archaeologists have generated spatially
+ coordinated data during fieldwork. However, the results of these
+ efforts are generally kept in inaccessible notebooks and hard drives,
+ or –in the best cases– analysed and summarised as figures in
+ publications, without providing the original data. Recent literature
+ stressed that the lack of
+
+
+
accessible and handy tools,
+
+
+
training in data management,
+
+
+
time to prepare data for publication, and
+
+
+
recognition related to data publishing
+
+
+
are factors explaining the insufficient availability of field
+ archaeological data
+ (Bernard,
+ 2019;
+ Selhofer
+ & Geser, 2015). Given the reluctance of archaeologists to
+ publish data, archeoViz indirectly fosters data
+ publication by demonstrating reuse, from the case of spatial
+ archaeological data at the site level
+ (Plutniak
+ et al., 2023;
+ Plutniak,
+ 2023).
+
Its minimal and multilingual interface (viz. issue 1) and the
+ simple data structure it requires (viz. issues 2, 3) make it handy to
+ use and fast to deploy on the web. This contributes to promoting
+ datasets as citable scientific outputs and also provides recognition
+ to their creators (viz. issue 4).
+
+
+ State of the Field
+
+ Archaeological Visualisation Software
+
First, archeoViz is related to other
+ archaeological visualisation software relying on similar
+ technologies. However, this software differs with regard to their
+ specialisations and are available in various formats as scripts,
+ applications, or packages:
+
+
+
Dataset-specific scripts or web applications:
+
+
+
Shannon McPherron’s R Shiny
+ Plot it
+ application (unpublished),
+
+
+
Anthony Sécher’s
+ PyCoCu
+ python script,
+
+
+
+
+
R Shiny application implementing specific statistical
+ methods, e.g.
+ (Couillet
+ et al., 2022),
+
+
+
R packages:
+
+
+
recexcavAAR
+ (Schmid
+ & Serbe, 2017) (no longer maintained)
+
+
+
SEAHORS
+ (Royer
+ et al., 2023), which offers more advanced
+ visualisation features than archeoViz
+ while being limited to this aspect.
+
+
+
+
+
+
+ Geographic Information Systems
+
Second, archeoViz is a lightweight,
+ complementary alternative to more complex archaeological software,
+ e.g. ArchField
+ (Smith
+ et al., 2015), Aspectus
+ (Vurpillot
+ et al., 2018), a “4D system”
+ (Ortega-Alvarado
+ et al., 2022) and to the more demanding association of GIS
+ software and export libraries,
+ e.g. Potree,
+ GeoNetwork
+ or QGIS and its
+ Qgis2threejs
+ plugin to export in HTML format.
+
+
+ Online Data Repositories
+
Third, regarding data publication and versioning,
+ archeoViz relates to web repositories that
+ include visualisation features,
+ e.g. arkeoGIS
+ (Bernard,
+ 2019),
+ BDA
+ (Perrin,
+ 1960),
+ Field,
+ and
+ CyberSW.
+ It differs in being a stand-alone application, in focusing on
+ intra-site data and the representation of individual archaeological
+ objects, and in taking into account the third spatial dimension.
+ Unlike these centralised repositories,
+ archeoViz is designed as the building block
+ of a decentralised web edition network for archaeological data, made
+ of as many archeoViz instances as there are
+ datasets.
+
+
+
+ The Building Block of a Decentralised Web Edition Network for
+ Archaeological Data
+
Since the 1960s, numerous attempts at building up standards and
+ repositories were made in archaeology. All projects tended to collect
+ as much data as possible and several independent databases existed
+ with the same themes. The pitfalls of this centralised approach were
+ addressed in the early 2000s with the development of the semantic web,
+ ontologies, and linked open data technologies.
+
archeoViz is designed along the same line.
+ Rather than collecting all data in the same place as in the
+ centralised approach, archeoViz users create a
+ particular instance of archeoViz for each
+ dataset to visualise and communicate. These instances can be deployed
+ on the server of their choice (e.g.,
+ shinyapps.io,
+ huma-num,
+ or any other institutional or personal server). Nevertheless,
+ archeoViz can be used in four ways, from purely
+ local (on the user’s machine), to purely remote, assuming or not data
+ publication on third-party repositories
+ ([fig:workflow]).
+
+
The four ways to use
+ archeoViz: local (green solid line),
+ remote and dynamic (dashed line), remote and static with data
+ publication on a third party service (black solid line), remote and
+ static without data publication (blue solid line).
+
+
+
+
+
+ Key Features
+
+ Interface and Functionalities
+
The archeoViz interface is available in
+ several languages, namely English, Italian, French, German, Spanish,
+ Portuguese, and Romanian. This interface has two parts
+ ([fig:interface]):
+
+
+
a left-side menu with options for data sub-selections
+
+
+
a right-side panel with tabs to display the results of the
+ functionalities.
+
+
+
These functionalities include:
+
+
+
Interactive visualisations and exports (SVG and HTML) of:
+
+
+
3D plot
+
+
+
2D map plot
+
+
+
2D section plot on the X axis
+
+
+
2D section plot on the Y axis
+
+
+
+
+
Summary statistics and data export to third-party
+ applications
+
+
+
+
Reproducibility features, i.e. automatic generation of the
+ command line to reproduce the current setting of the
+ application
+
+
+
Timeline of the findings discovery
+
+
+
Guidelines for the application
+
+
+
+
archeoViz interface.
+
+
+
+
+
+ Data Input
+
Input data must be CSV files, loaded either through the
+ application interface or in the command line, using the launching
+ function’s parameters. The data structure is kept as simple as
+ possible, with (few) mandatory and some optional variables
+ (Table 1).
+
+
+
Example of an input CSV file. Mandatory variables are in bold
+ type. “max” coordinates are for objects inaccurately located
+ within a range. An unlimited number of variables named using the
+ “object_” prefix can be added.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
id
+
square_x
+
square_y
+
xmin
+
xmax
+
ymin
+
ymax
+
zmin
+
zmax
+
layer
+
object_type
+
object_misc
+
+
+
+
+
1
+
A
+
1
+
50
+
54
+
66
+
70
+
20
+
+
1
+
lithic
+
biface
+
+
+
2
+
B
+
2
+
130
+
+
144
+
+
30
+
35
+
2a
+
fauna
+
deer antler
+
+
+
+
+
+
+
+ Research Using <monospace>archeoViz</monospace>
+
So far, 43 datasets have been edited on the web using
+ archeoViz instances. They include about 370,000
+ objects and 11,000 refitting relationships (between fragments of
+ broken objects). To increase their discoverability and audience, the
+ archeoViz
+ Portal gathers their references and metadata, and
+ makes it possible to browse the list of instances with keywords and
+ through a map.
+
Interoperability between software tools is key to their diffusion
+ and adoption. The SEAHORS package
+ (Royer
+ et al., 2023) can generate CSV files in the
+ archeoViz format and send them to an online
+ archeoViz instance. Data can be exported from
+ archeoViz to
+
+
+
the
+ archeofrag
+ application for refitting analysis
+
+
+
the
+ seriograph
+ application for seriation
+
+
+
an online instance of the
+ explor
+ R package / Shiny application for correspondence analysis
+
+
+
the
+ AMADO online
+ application, for seriation and classification.
+
+
+
+
+ Resources and Examples
+
archeoViz is available on
+ CRAN
+ and the code of the development version is available on
+ Github.
+ Documentation is made available embedded in the application
+ (Guidelines tab) and as
+ Vignettes,
+ in English, French, and Spanish. A website presents the application in
+ a less technical way,
+ https://archeoviz.hypotheses.org.
+ Users can receive news and find support by subscribing to the
+ archeoViz
+ mailing list. Multiple use cases can be browsed through the
+ archeoViz
+ Portal, that are also referenced in the
+ HAL.science
+ and
+ Isidore
+ repositories.
+
+
+ Acknowledgements
+
archeoViz is an R Shiny
+ (Chang
+ et al., 2020) application embedded in an R package
+ (R
+ Core Team, 2023). It relies on the
+ plotly
+ (Sievert,
+ 2020), ggplot2
+ (Wickham,
+ 2016), and htmlwidgets
+ (Vaidyanathan
+ et al., 2023) packages for the graphical outputs, and spatial
+ statistics use functions from the cxhull
+ (Laurent,
+ 2023) and mgcv
+ (Wood,
+ 2017) packages.
+
I thank Anaïs Vignoles and Élisa Caron-Laviolette (co-maintainers
+ of the archeoViz Portal), Renata Araujo (Portuguese
+ translation), Laura Coltofean (Romanian translation), Nicolas Delsol
+ (Spanish translation), Sara Giardino (Italian translation), Julian
+ Laabs (German translation), and the early users for their feedback and
+ support: Astolfo Araujo, Jean-Pierre Chadelle, Elsa Defranoult, Solène
+ Denis, Emmanuel Discamps, Mathieu Langlais, Maureen Le Doaré, Grégor
+ Marchand, Jean-Claude Marquet, Alexandre Michel, Thomas Perrin,
+ Anthony Sécher, Peter Tóth. Finally, I acknowledge the
+ tDAR
+ team at the
+ Center
+ for Digital Archaeology, where this paper was written and
+ the
+ SEADDA
+ European COST action that funded this research stay.
+
+
+
+
+
+
+
+ SievertCarson
+
+ Interactive web-based data visualization with R, plotly, and shiny
+ Chapman & Hall/CRC
+ Boca Raton (Fla.)
+ 2020
+ 978-1138331495
+ https://plotly-r.com
+ 10.1201/9780429447273
+
+
+
+
+
+ PerrinThomas
+
+ BDA : une Base de Données Archéologique collaborative en ligne
+ Bulletin de la Société préhistorique française
+ 1960
+ 116
+ 1
+ 10.3406/bspf.2019.14988
+ 159‑162
+
+
+
+
+
+
+ Ortega-AlvaradoGarcía-FernándezLidia M.
+ Conde-RodríguezFrancisco
+ Jurado-RodríguezJuan M.
+
+ Integrated and interactive 4D system for archaeological stratigraphy
+ Archaeological and Anthropological Sciences
+ 2022
+ 14
+ 203
+ 10.1007/s12520-022-01667-3
+
+
+
+
+
+ VurpillotDamien
+ VerriezQuentin
+ ThivetMatthieu
+
+ Aspectus: A flexible collaboration tool for multimodal and multiscalar 3D data exploitation
+ Studies in Digital Heritage
+ 2018
+ 2
+ 2
+ 10.14434/sdh.v2i2.24446
+ 150
+ 165
+
+
+
+
+
+ SmithNeil G.
+ HowlandMatthew
+ LevyThomas E.
+
+ Digital archaeology field recording in the 4th dimension: ArchField c++ a 4D GIS for digital field work
+ 2015 digital heritage
+ 2015
+ 2
+ 10.1109/DigitalHeritage.2015.7419505
+ 251
+ 258
+
+
+
+
+
+ BernardLoup
+
+ Ten years of ArkeoGIS: Feedback on the challenges and benefits of digitally sharing archeological data
+ 2019
+ https://hal.science/hal-02865759
+
+
+
+
+
+ PlutniakSébastien
+ AraujoRenata
+ ColtofeanLaura
+ DelsolNicolas
+ GiardinoSara
+ LaabsJulian
+
+ archeoViz. Visualisation, exploration, and web communication of archaeological spatial data
+ 2023
+ https://CRAN.R-project.org/package=archeoViz
+ 10.5281/zenodo.10200892
+
+
+
+
+
+ SchmidClemens
+ SerbeBenjamin
+
+ recexcavAAR: 3D reconstruction of archaeological excavations
+ 2017
+ https://CRAN.R-project.org/package=recexcavAAR
+
+
+
+
+
+ CouilletArmelle
+ RougierHélène
+ TodiscoDominique
+ MarotJosserand
+ GilletOlivier
+ CrevecoeurIsabelle
+
+ 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
+ 2022
+ 5
+ 1
+ 10.5334/jcaa.81
+ 19
+ 34
+
+
+
+
+
+ WoodSimon N.
+
+ Generalized additive models: An introduction with R
+ Chapman; Hall/CRC
+ Boca Raton
+ 2017
+ 2
+ 978-1315370279
+ 10.1201/9781315370279
+
+
+
+
+
+ LaurentStéphane
+
+ cxhull: Convex hull
+ 2023
+ https://CRAN.R-project.org/package=cxhull
+
+
+
+
+
+ VaidyanathanRamnath
+ XieYihui
+ AllaireJJ
+ ChengJoe
+ SievertCarson
+ RussellKenton
+
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