Code and Data for "Resource access, mobility, and the location of pre-Qin copper-smelting sites in China: a replicated MaxEnt study"

Data and Code Package for the Journal of Archaeological Science Submission Created: 2026-06-18 Manuscript Resource access, mobility, and the location of pre-Qin copper-smelting sites in China: a replicated MaxEnt study Purpose This package contains the data and code needed to rerun the Java MaxEnt workflow used in the manuscript. Directory Layout maxent/maxent.jar: Java MaxEnt executable. data/occurrences/: occurrence CSV files used as presence records. data/predictors/{HX,SS,SEH,JL,DL}/: ASCII environmental predictor rasters used by Java MaxEnt. scripts/: R scripts for data checks, baseline Java MaxEnt runs, output collection, predictor synthesis, site-background tests, predictor correlations, sensitivity checks, and figure/table generation. outputs/: generated by the scripts when the workflow is rerun. AOI Codes HX: Hexi SS: Southern Shanxi SEH: Southeast Hubei JL: Jianping-Liaoxi DL: Dajing Occurrence Files Each occurrence CSV is named {AOI}_samples.csv and contains: species: model class label. The retained value is smelting. lon: x coordinate in the coordinate reference system used by that AOI's predictor rasters. lat: y coordinate in the coordinate reference system used by that AOI's predictor rasters. Predictor Raster Files Each AOI folder contains the same ten ASCII raster predictors: 01_dem.asc: elevation. 02_slope.asc: slope. 03_channel.asc: channel or valley-related terrain parameter. 04_planar.asc: planar curvature. 05_ridge.asc: ridge-related terrain parameter. 06_lcp_density_2500_2000.asc: least-cost-path density surface. 07_outgoing_viewshed.asc: outgoing visibility index. 08_incoming_viewshed.asc: incoming visibility index. 09_walking_time_to_mines.asc: modeled walking time to copper/mineral sources. 10_walking_time_to_water.asc: modeled walking time to water. Requirements Java available on PATH. Test with: java -version R with the following packages: terrasfdplyrtidyrpurrrreadrggplot2 Quick Check From this folder in R: setwd("PATH/TO/JAS_data_code_upload_20260618")source("scripts/01_check_data.R") Full Baseline Workflow From this folder in R: setwd("PATH/TO/JAS_data_code_upload_20260618")source("scripts/run_pipeline.R") Optional Sensitivity and Null-Model Scripts These are slower and can be run after the baseline workflow: source("scripts/07_background_sensitivity_optional.R")source("scripts/08_dajing_null_model_optional.R") Windows Shortcut Double-click RUN_FULL_PIPELINE.bat or run it from PowerShell/CMD. It starts Rscript in this folder and runs: scripts/run_pipeline.R Notes The workflow uses Java MaxEnt, not maxnet, for the manuscript's final AUC values, response curves, jackknife outputs, suitability maps, and variable contributions. All required predictor layers are stored inside this package, so the workflow does not require the original local working directory. Runtime can be substantial because the baseline uses replicated Java MaxEnt runs. Java MaxEnt outputs, diagnostics, cached rasters, and figures are generated under outputs/ when the workflow is rerun. They are not required as source inputs. Third-Party Software The package includes maxent/maxent.jar for direct reproducibility. MaxEnt is third-party software distributed by the American Museum of Natural History: https://biodiversityinformatics.amnh.org/open_source/maxent/ License Note The current open-source MaxEnt release is distributed under an MIT license according to the AMNH MaxEnt project page. Suggested MaxEnt Software Citation Phillips, S. J., Dudik, M., and Schapire, R. E. MaxEnt software for modeling species niches and distributions. Available from https://biodiversityinformatics.amnh.org/open_source/maxent/.