App version: 0.1.16 (17 Feb 2020)
Database version: 1.0 [30 Jan 2020] — Total no. of dates: 1587 , sites: 368 , calibrations: 1584 , bibliographic references: 385

MedAfrica McDonald UCAM RCarbon Leverhulme ISMEO

About the MedAfrica project and MedAfriCarbon database

The MedAfrica Project set out to produce the first comprehensive, empirical and interpretative synthesis of long-term social and economic dynamics on the African flank of the Mediterranean between the beginning of the Holocene (ca. 9600 BC) and the arrival of Phoenicians and Greeks (between 800 and 600 BC), and to identify major factors shaping the patterns detected.

To address these questions, a large and up-to-date database of published radiocarbon dates was assembled with a systematic association of key cultural markers (e.g. presence/absence of domestic/wild species and material culture elements), allowing the first comprehensive chronological and cultural story for the prehistory of this region to emerge for a generation. These questions are explored as part of the interpretative synthesis presented in Broodbank and Lucarini (2019). The final database is presented here in the form of a user-friendly web app, to facilitate data exploration and informal analysis.

For more information about the database, see the open data publication Lucarini et al. (2020), or click on the Download tab.

MedAfricaCarbon

About the MedAfriCarbon web app

The MedAfricaCarbon web app provides a graphical interface to explore the MedAfrica database, based on the Shiny platform ([Chang et al. 2019][https://CRAN.R-project.org/package=shiny]). The app is structured as a tabbed dashboard with six major tabs (About; Map explorer; Dates explorer; Individual calibration; SPD (beta); Download; Bibliography). The default tab on opening the app is the Map explorer. Some of the tabs are synchronised, so that, for example, a filter selection made in the Map explorer will also appear in the Dates explorer and vice-versa. The Individual calibration and SPD tabs are linked but not synchronised to the explorer tabs.

About tab

This tab provides an overview and introductory information about the MedAfrica Project “Archaeological deep history and dynamics of Mediterranean Africa, ca. 9600-700 BC”, acknowledgements and credits as well as some basic tutorial instructions for use of the app.

Map explorer tab

In the Map explorer tab, the locations of radiocarbon dates are visualized on an interactive and zoomable map. Each date is represented by a single point; hovering over a point with the cursor shows the site name, and clicking on the point opens a popup with headline information about the date (unique identifier; uncalibrated date; median calibrated date; site name; material; site context). By clicking on More details, the user is transferred to the Individual calibration tab with all the fields related to that specific date (see below).

A number of filtering or search options are provided by the Map explorer (most of which are automatically synchronised in the Dates explorer tab). Dates can be visualised and filtered in two date formats: by uncalibrated bp or by median calibrated BP. Dates can be filtered geographically, either by entering the name of the site(s) in the “select sites” pane, or by using the polygon selection button on the top left of the page. Dates can also be filtered chronologically, by entering the maximum and minimum chronological bounds (the order is not important) using the two w/date range from: to: input boxes. Dates with overly large uncalibrated errors can be visually differentiated by adjusting the Max uncal. error menu box: in the map view, these dates will appear as small white dots instead of coloured ones.

The dates can be filtered out according to one or more economic or cultural using the Phase association(s) input box. The filter can match with one of two methods Any (union) or All (intersect). The first option is cumulative and shows all the radiocarbon dates associated to the two (or more) economic and/or cultural attributes, considered singularly. The second one shows instead all the radiocarbon dates in which the two (or more) economic and/or cultural attributes are associated to the same date(s). The associations that can be searched include presence/absence values for: domestic cattle; wild cattle; undetermined bovids; domestic sheep/goats; wild barbary sheep; domestic donkeys; wild donkeys / zebras; domestic horses; undetermined equids; domestic pigs; ostrich eggshells; ostrich bones; other wild terrestrial macrofauna; other wild terrestrial microfauna / avifauna; terrestrial / freshwater molluscs; marine molluscs; ichthyofauna / turtles; domestic cereals; domestic pulses; fruit crops; wild plants; pottery; lithics: backed tools / geometrics; lithics: notches / denticulates; lithics: bifacial tools; lithics: polished axes / adzes.

We did not report the economic and cultural associations for the 14C dates coming from the early Egyptian royal and elite cemeteries along the Nile between Abu Roash and Illahun.

When at least one economic or cultural association is selected a with any following value(s) selection box appears. Multiple options can be chosen in an additive way (i.e. any values will be matched): the options are:- “definite presence”; “low presence” (definite presence in low frequency); “unconfirmed” (unconfirmed presence); “absence of evidence”; or “no data” (i.e. where specific study/analysis has not been carried out yet and so no data are available).

Finally, although we consider cultural-chronological phases problematic, dates can also be filtered according to traditional cultural phase definitions (e.g. “Bronze Age”), even if these periods should be treated with caution. In order to facilitate the grouping of different cultural classifications which fall within the same macro-cultural definition we also decided to set the cultural phasing hierarchically, up to 4 levels (e.g. cultural phasing 1: Bronze Age; 2: Middle Kingdom; 3: Dynasty 12; 4: Amenemhet III). For example, selecting the cultural phase level 1 (top right window), the web app will show all the radiocarbon dates that have been associate to different cultural definitions that can be included in the macro cultural group defined as Bronze Age).

Filters can be reset using the Clear sites filter and Reset other filters buttons at the bottom of the tab.

Once groups of dates have been filtered, spatially, chronologically or by phase association, these can also be viewed as a list by clicking on the -> as table button on the bottom right corner, which will open the Dates explorer tab, or transferred to the SPD tab in order to calculate a Summed Probability Distribution graph for the selected dates by clicking on the -> SPD button.

Dates explorer tab

In the Dates explorer tab, filtered dates are visualised using an interactive list table. The available filters are essentially identical to the Map explorer tab, and, moreover are synchronised so that the list shown on Dates explorer matches the points shown on the Map explorer. In the case of the Dates explorer, dates with errors above the selected maximum are shown in red text. Clicking on More detail opens the Individual calibration tab for that date, and clicking on Show on map opens the Map explorer tab at the site’s position. To select sites by spatial location, sites can be searched for, or the polygon tool on the Map explorer tab can first be used and then dates will be ready-filtered in the Dates explorer list. The listed radiocarbon dates can be downloaded in CSV format using the Download as CSV button; note this download includes only the basic information about the dates (e.g. identifier, CRA and error) and does not include the cultural phase associations or site information. The full database can be downloaded from the Download tab. The selected dates can also be transferred to the SPD tab for graphical analysis.

Individual calibration tab

The Individual calibration tab contains all the information relative to each radiocarbon date, i.e. Lab-ID, other Lab-ID (when applicable), CRA, error, possible isotopic signatures (e.g. δ13C), dated material and possible species, date method, calibration curve, local reservoir 14C and local reservoir 14C error; Sample ID; Site Context. All the cultural and economic associations (listed above) are also reported here. It also provides a single plot representing the probability distribution of the calibration of the date using the appropriate calibration curve. The calibration relies on the calibrate function in the rcarbon package (see stable version on CRAN or beta versions on GitHub).

Bibliographic references to the individual date, or to the relevant cultural phase are listed underneath the calibration plot.

SPD tab

The SPD tab enables the user to produce a Summed Probability Distribution graph using all dates in the database; the dates previously selected from the Map explorer or Dates explorer tabs; or by manually entering the unique Lab_ID identifiers for the date. [Explanation of What is SPD?]. The SPD graph, generated using the spd function in rcarbon, shows: raw SPD based on a selected bin value (in blue); a 200yr rolling average smoother function (in red) to remind users not to over-interpret narrow spikes; and a barcode indicator (in black) to visualise the density of dates along the range. Note that while some caching is used to speed up the calculation and plotting of SPD graphs, any novel SPDs (i.e. graphs which have not been previously generated) may be slow to load. The density binning value can be adjusted, and dates can be filtered by the maximum uncalibrated error value.

Download tab

From this tab the user can find a link to download the full MedAfriCarbon database.

Bibliography tab

This tab provides a comprehensive bibliography of all references in the database. Where URLs were available, links to the publications are also made, so that such references are clickable.

References

Broodbank, C and Lucarini, G. 2019. The Dynamics of Mediterranean Africa, ca. 9600-1000 BC: An Interpretative Synthesis of Knowns and Unknowns. Journal of Mediterranean Archaeology, 32.2: 195-268.

Chang, W, Cheng, J, Allaire JJ, Xie, Y and McPherson J. 2019. shiny: Web Application Framework for R. R package version 1.3.2. https://CRAN.R-project.org/package=shiny

Giulio Lucarini, Toby Wilkinson, Enrico R. Crema, Augusto Palombini, Andrew Bevan, Cyprian Broodbank. 2020. The MedAfriCarbon radiocarbon database and web application. Archaeological dynamics in Mediterranean Africa, ca. 9600-700 BC. Journal of Open Archaeology Data. https://dx.doi.org/10.5281/zenodo.3630620.

Project Funding

We would like to acknowledge our gratitude to the MedAfrica project funders. The Leverhulme Trust provided the core funding for the Archaeological deep history and dynamics of Mediterranean Africa, ca. 9600-700 BC, “MedAfrica” Research Project (RPG-2016-261). Additional financial support to the project came from the McDonald Institute for Archaeological Research and the Italian Ministry of Foreign Affairs and International Cooperation, and IPOCAN, MIUR project, via the ISMEO (International Association for Mediterranean and Oriental Studies).

Acknowledgements

We warmly thank Nabiha Aouadi, Louiza Aoudia, Nadia Bahra, Barbara E. Barich, Graeme Barker, Lotfi Belhouchet, Youssef Bokbot, Abdeljalil Bouzouggar, Alfredo Coppa, Katerina Douka, Julie Dunne, Lucy Farr, Evan Hill, Christopher Hunt, Mary Jackes, Karin Kindermann, Jörg Linstädter, Veerle Linseele, David Lubell, Agnieszka Mączyńska, Katie Manning, Abdeslam Mikdad, Simone Mulazzani, Giuseppina Mutri, Thomas Perrin, Giacoma Petrullo, Heiko Riemer, Joanne Rowland, and Geoffrey J. Tassie†. Our gratitude also goes to Kimberley Watt for her work on the reference database, and to David Redhouse for his technical support in setting up the Cambridge Shiny server.

Future updates

Colleagues who wish to share new published archaeological 14C dates from the Mediterranean Africa, or to report any missing or incorrect information in the already published dataset of dates and economic/cultural associations are very much welcome to contact Giulio Lucarini at giulio.lucarini@cnr.it.

We plan to update the web app and public database approximately every 6 months, where there are new additions.


Web App Technical Appendix and Acknowledgements

This web app was written using R using the Shiny web app framework and a number of additional packages. The full dependencies are acknowledged below.

Development on a package to generalise the interface for other databases is currently being undertaken. Watch this space.


App dependencies

This web app depends on a number of open source R-packages; as ever, we therefore stand on the shoulders of giants. This server is running the following versions of these packages:


Select sites:

View the selected dates as

Data compiled for the MedAfrica project.




SPD plot

Note that user-defined dynamically generated charts can be very slow to load since summed probabilities are calculated on the fly. Please be patient!
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Included Dates

Note: Dates with maximum errors above the selected max error threshold (displayed as red) are NOT included in SPD calculations and the resultant plot.
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Database version: 1.0 [30 Jan 2020]

Download full database from: https://doi.org/10.5281/zenodo.3630619

MedAfriCarbon database

MedAfriCarbon radiocarbon database and web app are outcomes of the MedAfrica Project —Archaeological deep history and dynamics of Mediterranean Africa, ca. 9600-700 BC. The dataset presented here includes a collection of 1584 calibrated archaeological 14C dates from 1587 samples collected from 368 sites located in Mediterranean Africa (plus some additional dates whose published information is incomplete). The majority of the dates are linked to cultural and environmental variables, notably the presence/absence of different domestic/wild species and specific material culture.

Citation

Please cite this database using the following reference:

Giulio Lucarini, Toby Wilkinson, Enrico R. Crema, Augusto Palombini, Andrew Bevan, Cyprian Broodbank (2020) The MedAfriCarbon radiocarbon database and web application. Archaeological dynamics in Mediterranean Africa, ca. 9600-700 BC. Version 1.0. Journal of Open Archaeology Data. [in press, volume and doi pending].

Version history

The latest Zenodo version should always be accessible from: https://doi.org/10.5281/zenodo.3630619

  • 1.0 _30 Jan 2020_— First public release of the dataset on Zenodo, doi:10.5281/zenodo.3630620.
  • 0.9 15 Dec 2019 — Peer review version.
  • 0.x — Pre-release versions.

Database Contents

The main database tables and link tables are stored in a series of CSV files, plus a single BibTeX database file.

  • cultureLink.csv
  • cultureTable.csv
  • cultureRefLink.csv
  • dateRefLink.csv
  • dateTable.csv
  • phaseTable.csv
  • siteTable.csv
  • bibliography.bib

In addition the LICENSE for the database and its re-use is described in a single Markdown file, LICENSE.md.

Metadata: schema description for tables

Key relationships between tables in the database can be visualised as follows:

Database relationships diagram

Table schema descriptions

Explanations for the meaning of fields used in the database are described within individual CSV files per table or link table, prefixed by schema_.

  • metadata/schema_cultureLink.csv
  • metadata/schema_cultureTable.csv
  • metadata/schema_cultureRefLink.csv
  • metadata/schema_dateRefLink.csv
  • metadata/schema_dateTable.csv
  • metadata/schema_phaseTable.csv
  • metadata/schema_siteTable.csv

These files are structured with the following fields:

  • “Field” - Field or column name for this table (no spaces used)
  • “Key” - Defines whether this field is a key of any kind. Options are: “PK” (primary key) or “FK” (foreign key), “EK” (external key, e.g. for BibTeX) or “OL” (option list)
  • “VariableType” - A machine-readable categorisation of the content type of the field (e.g. “String”,“Integer”,“Decimal”)
  • “Description” - Human-readable description of field meaning, use or derivation
  • “OptionsMetaSchema” - For “OL” keys or lists. Name of the option schema/file to be used to define options/factors for the field (only used for fields with structured options or are lists)
  • “ForeignKeyLink” - For “FK” keys. Name of key in foreign table

Options descriptions

Some fields are effectively structured or predefined lists. In this case, the description of the meaning of the possible options are provided in a separate options_ csv file.

  • metadata/options_contentType.csv
  • metadata/options_country.csv
  • metadata/options_culturalAssociation.csv
  • metadata/options_locationQuality.csv
  • metadata/options_phaseByExcavator.csv

These files are structured with the following fields:

  • “Option” - Potential value of field as it appears in the raw database (effectively an option “key”)
  • “OptionDescription” - Human-readable description of the meaning of this value

Important Keys

  • “Date_ID” - unique radiocarbon date identifiers are based on laboratory-defined unique date identifiers where available
  • “Site_ID” - unique site identifiers are based on abbreviated identifier , international code of the country where the site is located followed by a sequential number (e.g. DZ021)
  • “Phase_ID” - unique local cultural phase identifier from a certain site using a combination of the site code followed by a sequential number corresponding to the number of phases detected, and with 1 as the oldest one (e.g. DZ021-1)
  • “Culture_ID” - unique culture key is defined a textual identifier of the culture (or cultural phase), usually identical to the lowest level of cultural phase definition (e.g. 1st Intermediate Period)
  • “BibTexKey” - unique BibTeX-style identifiers for bibliographic references reference the bibliography.bib file

Shiny app settings

Settings for the linked Shiny app are contained within shinyapp and are documented elsewhere.


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