nakagawa2021

Scripts for: Nakagawa, T., Tamura, K., Yamaguchi, Y., Matsumoto, N., Matsugi, T., Nakao, H. (2021) Population pressure and prehistoric violence in the Yayoi period of Japan. Journal of Archaeological Science　132: 105420. (doi: 10.1016/j.jas.2021.105420)

The number in the name of a directory corresponds to the section number of the supplementary material.

1_chi_squared

• chisq.R: a script to calculate the chi-squared test. The results of the chi-squared test and the effect size (Cramer’s V) are shown.

3_effect_of_aggregation

• simulation.R: a simulation model to investigate possible effects of aggregation.
• examine_adjustment.R: a script to compare the results of the logistic regression with and without the adjustment.
• plot_figure1.R: a script to make figure 1 in SI.
• plot_figure2.R: a script to make figure 2 in SI.
• make_figure3.R: a script yo make figure 3 in SI.

4-1_logistic_regression

• logistic_regression.R: a script to carry out the logistic regression.
• make_figure5.R: a script to make figure 5 in the main text.

4-2_glmm

• table3_glmm_subregion.R: a script to carry out the GLMM where subregion is used as a random effect.
• table4_glmm_subset_subregion.R: a script to carry out the GLMM where subregion is used as a random effect. Only data points with longer time intarvals (70, 80, and 100 years) are used.
• table5_glmm_subphase.R: a script to carry out the GLMM where subphase is used as a random effect.
• table6_glmm_subset_subphase.R: a script to carry out the GLMM where subphase is used as a random effect. Only data points with longer time intarvals (70, 80, and 100 years) are used.
• table7_glmm_ID.R: a script to carry out the GLMM where ID is used as a random effect.
• table8_glmm_subset_ID.R: a script to carry out the GLMM where ID is used as a random effect. Only data points with longer time intarvals (70, 80, and 100 years) are used.

4-3_zero-inflated_poisson

• table9_zero_inflated.R: a script to carry our the zero-inflated poisson model.
• table10_zero_inflated_subset.R: a script to carry our the zero-inflated poisson model. Only data points with longer time intarvals (70, 80, and 100 years) are used.
• table11_zero_inflated_population_pressure.R: a script to carry our the zero-inflated poisson model.　Population pressure is used as a independent variable in zero-inflation model.
• table12_zero_inflated_population_pressure_subset.R: a script to carry our the zero-inflated poisson model.　Population pressure is used as a independent variable in zero-inflation model. Only data points with longer time intarvals (70, 80, and 100 years) are used.

5_GIS

A directory correpsonds to a subregion. Currently, the directory for DEM files are blank. Please download files listed in filelist.txt from Geospatial Information Authority of Japan (https://fgd.gsi.go.jp/download/menu.php). calc_area.R is a script to calculate area suitable for cultivation.

6_logistic_regression_with_GIS_in_R

• logistic_regression.R: a script to carry out the logistic regression using arable area calculated with R.