Data and code for 'Biogeography of crop progenitors and wild plant resources in the terminal Pleistocene and Early Holocene of West Asia, 14.7–8.3 ka'
This research compendium contains the data and code accompanying our paper:
Roe, Joe and Amaia Arranz-Otaegui, 2026. Biogeography of crop progenitors and wild plant resources in the terminal Pleistocene and Early Holocene of West Asia, 14.7–8.3 ka. Open Quaternary 12: 2. https://doi.org/10.5334/oq.163
It is a Quarto manuscript written in Markdown with embedded R code.
To rerender the manuscript (in PDF format), use quarto render paper.qmd.
Executing the R code requires that R and the packages listed at the top of
paper.qmd are installed.
The GBIF occurrence data used in the published analysis can be accessed at
https://www.gbif.org/occurrence/download/0007320-250811113504898. Download and
copy this data to analysis/data/derived_data/gbif/ to reproduce the analysis
as-published.
If no GBIF data download is present, the script will reacquire it based on the given filters, but since GBIF is constantly updated, the result will probably differ.
Reacquiring data from GBIF via R requires credentials to be given as environment
variables, which will be
automatically loaded from /.env if
present. See rgbif's vignette, Set Up Your GBIF Username and Password
for details.
This analysis uses a number of large, remote raster files that cannot be conveniently packaged here in their original forms. These include data from Paleoclim, SoilGrids, and OpenTopography (SRTM DEM). Please see the respective source repositories for license and usage information for this data.
Where possible, the cropped versions of these datasets used in the analysis are
cached in the respective folders analysis/data/derived_data/. The code used
to acquire this data is found under analysis/data/ and can be used to
regenerated these files as long as the external APIs used are still working.
Reacquiring data from OpenTopography requires an API key specified in the
environment variable OPENTOPO_KEY, which will be automatically loaded
from /.env if present.
Please cite this analysis as:
Roe, Joe and Amaia Arranz-Otaegui, 2026. Biogeography of crop progenitors and wild plant resources in the terminal Pleistocene and Early Holocene of West Asia, 14.7–8.3 ka. Open Quaternary 12: 2. https://doi.org/10.5334/oq.163
Preliminary results were presented at the 18th conference of the International Workgroup for Palaeoethnobotany (IWGP), Lecce, 3–8 June, 2019:
Arranz-Otaegui, A., Roe, J., Pantos, G. A., Santana, J., Araus-Cabrera, J. L., Le Roux, P., & Richter, T. 2019. Locally available or imported? Identifying the provenance of Natufian plant food and fuel resources at Shubayqa 1 (northeastern Jordan). Presented at the 18th conference of the International Workgroup for Palaeoethnobotany (IWGP), Lecce, 3–8 June.