From the Margins to the Mainstream: Code, Data, and Results

This repository contains all of the data and R scripts necessary to reproduce the analyses presented in From the margins to the Mainstream: understanding the Polychrome Tradition Expansion in Central Amazon through spatial and chronological modelling, currently in review (16/06/2023).

The repository is organised into four folders:

• Code - containing R scripts
• Data - containing the radiocarbon and spatial data
• Figures - comprising the images presented in the manuscript and its supplementary information
• R_Images - .RData files of the modelling output, for visualisation and diagnostics

R session information

R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default


locale:
[1] LC_COLLATE=English_United Kingdom.utf8  LC_CTYPE=English_United Kingdom.utf8   
[3] LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.utf8    

time zone: Europe/London
tzcode source: internal

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

other attached packages:
 [1] MCMCvis_0.16.0     patchwork_1.1.2    latex2exp_0.9.6    coda_0.19-4        truncnorm_1.0-9   
 [6] nimbleCarbon_0.2.1 nimble_1.0.0       ggsn_0.5.0         ggplot2_3.4.2      rgdal_1.6-7       
[11] sf_1.0-13          rworldmap_1.3-6    sp_1.6-1           rcarbon_1.5.0     

loaded via a namespace (and not attached):
  [1] bitops_1.0-7           DBI_1.1.3              deldir_1.0-9           gridExtra_2.3         
  [5] rlang_1.1.1            magrittr_2.0.3         maptools_1.1-7         cAIC4_1.0             
  [9] e1071_1.7-13           compiler_4.3.0         spatstat.geom_3.2-1    mgcv_1.8-42           
 [13] spatstat.model_3.2-4   png_0.1-8              spatstat.linnet_3.1-1  vctrs_0.6.2           
 [17] maps_3.4.1             reshape2_1.4.4         stringr_1.5.0          pkgconfig_2.0.3       
 [21] backports_1.4.1        utf8_1.2.3             pracma_2.4.2           nloptr_2.0.3          
 [25] purrr_1.0.1            xfun_0.39              goftest_1.2-3          sjmisc_2.8.9          
 [29] ggeffects_1.2.2        spatstat.utils_3.0-3   jpeg_0.1-10            broom_1.0.4           
 [33] R6_2.5.1               stringi_1.7.12         spatstat.data_3.0-1    car_3.1-2             
 [37] boot_1.3-28.1          rpart_4.1.19           numDeriv_2016.8-1.1    estimability_1.4.1    
 [41] Rcpp_1.0.10            iterators_1.0.14       knitr_1.43             tensor_1.5            
 [45] modelr_0.1.11          fields_14.1            snow_0.4-4             igraph_1.4.3          
 [49] Matrix_1.5-4           splines_4.3.0          tidyselect_1.2.0       abind_1.4-5           
 [53] viridis_0.6.3          codetools_0.2-19       spatstat.random_3.1-5  spatstat.explore_3.2-1
 [57] RLRsim_3.1-8           sjlabelled_1.2.0       lattice_0.21-8         tibble_3.2.1          
 [61] plyr_1.8.8             withr_2.5.0            spatstat_3.0-6         bayestestR_0.13.1     
 [65] foreign_0.8-84         units_0.8-2            proxy_0.4-27           polyclip_1.10-4       
 [69] pillar_1.9.0           carData_3.0-5          KernSmooth_2.23-20     foreach_1.5.2         
 [73] stats4_4.3.0           insight_0.19.2         generics_0.1.3         munsell_0.5.0         
 [77] scales_1.2.1           minqa_1.2.5            class_7.3-21           glue_1.6.2            
 [81] sjPlot_2.8.14          emmeans_1.8.6          tools_4.3.0            lme4_1.1-33           
 [85] mvtnorm_1.2-1          dotCall64_1.0-2        cowplot_1.1.1          tidyr_1.3.0           
 [89] colorspace_2.1-0       nlme_3.1-162           performance_0.10.4     RgoogleMaps_1.4.5.3   
 [93] cli_3.6.1              spatstat.sparse_3.0-1  ggmap_3.0.2            spam_2.9-1            
 [97] fansi_1.0.4            viridisLite_0.4.2      sjstats_0.18.2         dplyr_1.1.2           
[101] doSNOW_1.0.20          gtable_0.3.3           classInt_0.4-9         lifecycle_1.0.3       
[105] httr_1.4.6             MASS_7.3-58.4