Bayesian analyses question the role of climate in Chulmun demography: source code, data, and scripts

This repository contains all data and scripts required to fully reproduce all analyses presented in the following paper:

Kim,H., Lee,G., Crema, E.R. (2021) Bayesian analyses question the role of climate in Chulmun demography, Scientific Reports.

The repository is organised as follows:

./runscript ... contains R scripts for executing core analyses
./R_image_files ... contains R image files with results
./data ... contains all datasets required for the analysis
./figures_and_results ... contains all figures and results summaries and the R scripts required for their creation.

Data Sets and Data Preparation

Data Sets

The core dataset consists of:

a collection of radiocarbon dates gathered from various excavation reports and journal articles (./data/Neolithic_C14_dates.csv);
sediment data and associated radiocarbon dates from the SSDP-102 core (./data/Kim_etal_2004/*) originally published by Kim et al 2004 And retrieved from LiPDverse Global Holocene Repository.
arboreal to total pollen ratio and associated radiocarbon dates from the Pomaeho sediment core (./data/Constantine_etal_2020/*) originally published by Constantine et al 2020.
arboreal to total pollen ratio and associated radiocarbon dates from the GY-1 sediment core (./data/Park_etal_2019/*) originally published by Park et al 2019.
ESRI Shapefiles of the Korean Peninsula from GADM (/data/shp/*).

Pre-processing radiocarbon dates

The original set of radiocarbon dates have been processed using the R scipts ./runscript/data_clean.R and ./runscript/data_prep.R. The former processes ./data/Neolithic_C14_dates.csv by:

Removing all instances of dates without LabCode or a clear source
Removing all dates outside the time window 6200-2800 14C Age
Subsetting only to terrestial dates associated with charcoal or wood
Removing sites without geographic coordinates
Assigning a unique site identifier (SiteID)
Creating a new field milletAsso for all cases where the radiocarbon dates are associated to millets.
Keeping a subset of fields for the analysis and storing the output in the file ./data/Neolithic_C14_dates_cleaned.csv

The ./runscript/data_prep.R function processes ./data/Neolithic_C14_dates_cleaned.csv by grouping site into clusters using the DBSCAN algorithm (to control for CRM-based arbitrary definitions of archaeological sites) and subsequently assigning each cluster to either the coastal or inland region based on distance from coast. The function also calibrates all dates using IntCal20 and generates radiocarbon bins for each cluster to control for inter-site variation in sampling intensity. The results are store in the R image file /R_image_files/koreanC14.RData.

SPD Permutation Tests

The file ./runscript/statistical_tests.R contains R scripts for executing mark permutation tests for the Coastal vs Inland regions and for Millet vs non-Millet dates. Results are stored in the R image file /R_image_files/spd_test_results.RData

Age Depth Models

The file ./runscript/age_depth_model.R contains R scripts for fitting Compound Poisson-Gamma age-depth models for the SSDP-102, Pomaeho, and the GY-1 sedimentary data using the Bchron R package. Results are stored in the R image file ./R_image_files/kim2004_agedepthmodel.RData.

Bayesian Analysis

The files ./runscript/mcmc_coastal.R, ./runscript/mcmc_inland.R, and ./runscript/mcmc_all.R contains the scripts for fitting a bounded double exponential model via the nimble and nimbleCarbon R packages, whilst mcmc_diagnostic_ppc.R contains the R code for MCMC diagnostics and posterior predictive checks. R image files containing the MCMC outputs (mcmc_samples_inland.RData,mcmc_samples_coatsal.RData, and mcmc_samples_all.RData) and the posterior predictive checks (mcmcdiagnostic_postpredcheck.RData) are loacted in the R_image_files directory.

File Structure

├── data
│   ├── Constantine_etal_2020
│   │   ├── pomaeho_constantine_etal_2020_aptp.csv
│   │   └── pomaeho_constantine_etal_2020_c14.csv
│   ├── Kim_etal_2004
│   │   ├── SSDP102_Kim_etlal_2004_c14.csv
│   │   └── SSDP102_Kim_etlal_2004_temp.csv
│   ├── koreanC14.RData
│   ├── Neolithic_C14_dates_cleaned.csv
│   ├── Neolithic_C14_dates.csv
│   ├── Park_etal_2019
│   │   ├── GY_Park_etal_2019_aptp.csv
│   │   └── GY_Park_etal_2019_c14.csv
│   └── shp
│       ├── polyline_korea.cpg
│       ├── polyline_korea.dbf
│       ├── polyline_korea.prj
│       ├── polyline_korea.sbn
│       ├── polyline_korea.sbx
│       ├── polyline_korea.shp
│       ├── polyline_korea.shp.xml
│       └── polyline_korea.shx
├── figures_and_results
│   ├── age_depth_hpd90.csv
│   ├── figure1.pdf
│   ├── figure2.pdf
│   ├── figure3.pdf
│   ├── figure4.pdf
│   ├── figureS10.pdf
│   ├── figureS11.pdf
│   ├── figureS12.pdf
│   ├── figureS13.pdf
│   ├── figureS1.pdf
│   ├── figureS2.pdf
│   ├── figureS3.pdf
│   ├── figureS4.pdf
│   ├── figureS5.pdf
│   ├── figureS6.pdf
│   ├── figureS7.pdf
│   ├── figureS8.pdf
│   ├── figureS9.pdf
│   ├── main_text_figures.R
│   ├── mcmc_summary.csv
│   ├── results_summary.R
│   └── supplementary_figures.R
├── NeolithicKoreaDemography.Rproj
├── README.md
├── R_image_files
│   ├── agedepthmodels.RData
│   ├── koreanC14.RData
│   ├── mcmcdiagnostic_postpredcheck.RData
│   ├── mcmc_samples_all.RData
│   ├── mcmc_samples_coastal.RData
│   ├── mcmc_samples_inland.RData
│   ├── spd_test_results.RData
│   └── test_results.RData
└── runscript
    ├── age_depth_model.R
    ├── data_clean.R
    ├── data_prep.R
    ├── mcmc_all.R
    ├── mcmc_coastal.R
    ├── mcmc_diagnostic_ppc.R
    ├── mcmc_inland.R
    └── statistical_tests.R

R SessionInfo

attached base packages:
[1] stats     graphics  grDevices utils     methods   base     

other attached packages:
 [1] latex2exp_0.4.0    Bchron_4.7.3       coda_0.19-4        truncnorm_1.0-8   
 [5] nimbleCarbon_0.1.2 nimble_0.10.1      raster_3.3-13      rgeos_0.5-3       
 [9] rgdal_1.5-18       maptools_1.0-1     rworldmap_1.3-6    dbscan_1.1-5      
[13] sp_1.4-5           rcarbon_1.4.1      here_0.1           dplyr_1.0.2       

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5            lattice_0.20-41       deldir_0.2-9         
 [4] snow_0.4-3            rprojroot_2.0.2       foreach_1.5.1        
 [7] ggforce_0.3.2         plyr_1.8.6            R6_2.5.0             
[10] ggridges_0.5.2        spam_2.5-1            ggplot2_3.3.2        
[13] tensor_1.5            pillar_1.4.7          rlang_0.4.8          
[16] rstudioapi_0.13       rpart_4.1-15          Matrix_1.2-18        
[19] goftest_1.2-2         startup_0.14.1        splines_4.0.3        
[22] stringr_1.4.0         foreign_0.8-80        igraph_1.2.6         
[25] polyclip_1.10-0       munsell_0.5.0         spatstat.data_1.7-0  
[28] compiler_4.0.3        xfun_0.20             pkgconfig_2.0.3      
[31] mgcv_1.8-31           doSNOW_1.0.19         tidyselect_1.1.0     
[34] tibble_3.0.4          codetools_0.2-16      crayon_1.3.4         
[37] MASS_7.3-51.6         grid_4.0.3            nlme_3.1-148         
[40] gtable_0.3.0          lifecycle_0.2.0       magrittr_2.0.1       
[43] scales_1.1.1          stringi_1.5.3         farver_2.0.3         
[46] spatstat_1.64-1       ellipsis_0.3.1        generics_0.1.0       
[49] vctrs_0.3.5           spatstat.utils_1.20-2 iterators_1.0.13     
[52] tools_4.0.3           glue_1.4.2            tweenr_1.0.1         
[55] purrr_0.3.4           maps_3.3.0            fields_10.3          
[58] abind_1.4-5           parallel_4.0.3        yaml_2.2.1           
[61] colorspace_2.0-0      dotCall64_1.0-0       knitr_1.30

Funding

This project was supported by the Korean Studies Promotion Service/Academy of Korean Studies (Laboratory Program for Korean Studies, AKS-2015-Lab-2250001)

Licence

CC-BY 3.0

ercrema / NeolithicKoreaDemography