Data and R scripts for the paper 'Culinary continuity in central Japan across the transition to agriculture'
This repository contains data and R scripts for the following paper:
Lundy,J.,Bondetti,M.,Lucquin,A.,Talbot,H.M.,Murakami,N.,Nakayama,S.,Harada,M.,Suzuki,M.,Endo,E.,Stevens,C.,Crema,E.R.,Craig,O.E.,Shoda,S.(2024).Culinary continuity in central Japan across the transition to agriculture. Anthropological and Archaeological Sciences.https://doi.org/10.1007/s12520-024-01992-9
The repository is organised into four main directories: data, scripts, and results. The data directory contains the organic residue analysis summary data, human isotope and seed impression data, a pre-processing script for C14 radiocarbon dates, and a radiocarbon date dataset; scripts contains all R scripts for executing the analyses, and results contains output CSV and R image files.
ORAresults.csv... Spreadsheet containing ceramic information and organic residue analysis summary data.JAPREF.csv... Spreadsheet containing ceramic information and organic residue analysis summary data.Humanisotope.csv... Spreadsheet containing previously published human isotope data from Tokai and Central Highlands ceramic information and organic residue analysis summary data.data_prep_c14_rice.R... R scripts for pre-processing rice radiocarbon dates from Crema et al 2022. Generates the R image filec14rice.RData.prefecture_region_match.csv... lookup table to aggregate geographic regions.c14rice.RData... R image file containing R objects required for analyses. Generated usingdata_prep_c14_rice.Randprefecture_region_match.csv.seeds_2.10. csv... Spreadsheet containing previously published seed impression data from Tokai and Central Highlands. Based on Endo and Leipe 2022 with additional fields on sherd counts.
phase_sitemap.R... Contains R scripts for estimating arrival dates of rice in Tokai and Central Highlands and a site map for fig. 1 in the manuscript.ORAscript.R... Contains R scripts for statistical analyses and basic visualisation of ORA.seeds.R... Contains R scripts for the analyses of seed impressions data.rice_arrival.R... Contains R scripts for the reanalysis of Crema et al 2022 dataset.
arrival_estimates.RData... output ofrice_arrival.R, containing arrival dates in Chubu Highlands and Tokai.table_seed_freq.csv... output generated from the analyses of seed impression data (seeds.R)
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/London
tzcode source: system (glibc)
attached base packages:
[1] grid parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] marmap_1.0.10 rnaturalearth_0.3.3 gridBase_0.4-7
[4] cowplot_1.1.1 raster_3.6-26 sp_2.0-0
[7] sf_1.0-14 elevatr_0.99.0 scales_1.2.1
[10] brms_2.19.0 Rcpp_1.0.11 dunn.test_1.3.5
[13] dplyr_1.1.2 ggstar_1.0.4 ggplot2_3.4.2
[16] coda_0.19-4 rcarbon_1.5.1 nimbleCarbon_0.2.5
[19] nimble_1.0.1
loaded via a namespace (and not attached):
[1] shape_1.4.6 jsonlite_1.8.5 tensorA_0.36.2
[4] magrittr_2.0.3 estimability_1.4.1 spatstat.utils_3.0-4
[7] farver_2.1.1 vctrs_0.6.2 memoise_2.0.1
[10] spatstat.explore_3.2-5 base64enc_0.1-3 terra_1.7-39
[13] htmltools_0.5.5 distributional_0.3.2 StanHeaders_2.26.26
[16] pracma_2.4.2 KernSmooth_2.23-22 htmlwidgets_1.6.2
[19] plyr_1.8.8 cachem_1.0.8 emmeans_1.8.9
[22] zoo_1.8-12 igraph_1.5.1 mime_0.12
[25] lifecycle_1.0.4 iterators_1.0.14 pkgconfig_2.0.3
[28] colourpicker_1.2.0 Matrix_1.6-1.1 R6_2.5.1
[31] fastmap_1.1.1 shiny_1.7.4 digest_0.6.31
[34] numDeriv_2016.8-1.1 colorspace_2.1-0 ps_1.7.5
[37] tensor_1.5 RSQLite_2.3.1 crosstalk_1.2.0
[40] spatstat.linnet_3.1-3 progressr_0.14.0 gdistance_1.6.4
[43] fansi_1.0.4 spatstat.sparse_3.0-3 httr_1.4.6
[46] polyclip_1.10-6 abind_1.4-5 mgcv_1.9-0
[49] compiler_4.3.1 proxy_0.4-27 bit64_4.0.5
[52] withr_2.5.0 backports_1.4.1 inline_0.3.19
[55] shinystan_2.6.0 DBI_1.1.3 spatstat.model_3.2-8
[58] pkgbuild_1.4.0 classInt_0.4-10 gtools_3.9.4
[61] loo_2.6.0 tools_4.3.1 units_0.8-4
[64] httpuv_1.6.11 threejs_0.3.3 goftest_1.2-3
[67] glue_1.6.2 callr_3.7.3 nlme_3.1-163
[70] promises_1.2.0.1 checkmate_2.2.0 reshape2_1.4.4
[73] generics_0.1.3 snow_0.4-4 gtable_0.3.3
[76] spatstat.data_3.0-3 class_7.3-22 utf8_1.2.3
[79] spatstat.geom_3.2-7 foreach_1.5.2 pillar_1.9.0
[82] markdown_1.7 stringr_1.5.0 posterior_1.4.1
[85] later_1.3.1 splines_4.3.1 lattice_0.22-5
[88] bit_4.0.5 deldir_1.0-9 tidyselect_1.2.0
[91] miniUI_0.1.1.1 knitr_1.45 gridExtra_2.3
[94] stats4_4.3.1 xfun_0.41 adehabitatMA_0.3.16
[97] bridgesampling_1.1-2 matrixStats_1.0.0 DT_0.28
[100] rstan_2.21.8 stringi_1.7.12 codetools_0.2-19
[103] spatstat_3.0-7 tibble_3.2.1 cli_3.6.1
[106] RcppParallel_5.1.7 rpart_4.1.21 shinythemes_1.2.0
[109] xtable_1.8-4 munsell_0.5.0 processx_3.8.1
[112] doSNOW_1.0.20 spatstat.random_3.2-1 rstantools_2.3.1.1
[115] ellipsis_0.3.2 blob_1.2.4 prettyunits_1.1.1
[118] dygraphs_1.1.1.6 bayesplot_1.10.0 Brobdingnag_1.2-9
[121] mvtnorm_1.2-2 xts_0.13.1 e1071_1.7-13
[124] ncdf4_1.21 purrr_1.0.1 crayon_1.5.2
[127] rlang_1.1.2 shinyjs_2.1.0
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 the JSPS KAKENHI (grant numbers 21H04370, 20H05820 and 17H04777).