Data and Scripts for the manuscript "The importance of wild resources as a reflection of the resilience and changing nature of early agricultural systems in East Asia and Europe"
This repository contains data and scripts required for generating figures 2, 3, and 4 in the following paper:
Stevens, C.J.,Crema, E.R., Shoda, S. (2022). The importance of wild resources as a reflection of the resilience and changing nature of early agricultural systems in East Asia and Europe. Frontiers in Ecology and Evolution. DOI: 10.3389/fevo.2022.1017909
For East Asia, the core datasets are presence-absence tables of key taxa (rice, millets, and various wild nuts) from Japan and Korea stored in the CSV files SiteList_JP.csv and SiteList_KOR.csv. The Japanese dataset has been obtained by processing and partially translating (see prepareSiteList_JP for details) data downloaded from the Database of Plant Macrofossils from Archaeological Sites in Japan contained in the data folder (yayoi_abot.csv,kofun_abot.csv, and kodai_abot.csv). The Korean dataset was manually compiled by CJ Stevens from the "The Archaeobotanical Data in East Asia: Prehistoric Age".
The file presence_absence.R contains the R scripts for generatring figures 2 (korea_abot.pdf) and 3 (japan_abot.pdf) (see files in the figures folder).
SPD analyses for figure 4 was based on a renalyses of the dataset from Bevan et al 2017, downloaded from the associated data repository hosted on UCL discovery. The file spd.R contains all the script necessary for downloading, processing, analysing, and plotting the relevant dataset for generating figure 4 (see spd_gb.pdf in the figures folder).
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.0.9 RColorBrewer_1.1-3 rnaturalearth_0.1.0
[4] sf_1.0-8 rcarbon_1.4.4
loaded via a namespace (and not attached):
[1] spatstat.linnet_2.3-2 tidyselect_1.1.2 xfun_0.31
[4] purrr_0.3.4 splines_4.2.1 lattice_0.20-45
[7] spatstat.utils_2.3-1 vctrs_0.4.1 generics_0.1.2
[10] doSNOW_1.0.20 snow_0.4-4 mgcv_1.8-40
[13] utf8_1.2.2 rlang_1.0.2 spatstat.data_2.2-0
[16] e1071_1.7-11 pillar_1.7.0 spatstat_2.3-4
[19] glue_1.6.2 DBI_1.1.2 sp_1.5-0
[22] foreach_1.5.2 lifecycle_1.0.1 spatstat.core_2.4-4
[25] codetools_0.2-18 knitr_1.39 parallel_4.2.1
[28] class_7.3-20 fansi_1.0.3 Rcpp_1.0.8.3
[31] KernSmooth_2.23-20 tensor_1.5 classInt_0.4-7
[34] abind_1.4-5 deldir_1.0-6 spatstat.sparse_2.1-1
[37] polyclip_1.10-0 grid_4.2.1 cli_3.3.0
[40] tools_4.2.1 magrittr_2.0.3 goftest_1.2-3
[43] tibble_3.1.7 proxy_0.4-27 pkgconfig_2.0.3
[46] crayon_1.5.1 ellipsis_0.3.2 spatstat.random_2.2-0
[49] Matrix_1.4-1 assertthat_0.2.1 iterators_1.0.14
[52] R6_2.5.1 rpart_4.1.16 units_0.8-0
[55] spatstat.geom_2.4-0 nlme_3.1-157 compiler_4.2.1
This research was funded by the ERC grant Demography, Cultural Change, and the Diffusion of Rice and Millets during the Jomon-Yayoi transition in prehistoric Japan (ENCOUNTER) (Project N. 801953, PI: Enrico Crema) and by a Philip Leverhulme Prize (PLP-2019-304) in archaeology awarded to Enrico Crema.
CC-BY 3.0