################################### # This file records the figure production ################################### load("cr_results_06_02_20corrected.Rdata") tbins <- sort(unique(baltic_binnings$bb)) tbins_upper <- as.numeric(c("484.5", "480", "472.5", "468.7", "460", "453.5", "448.5", "442.7", "438.5", "433.4", "427.4", "423", "419.2")) tbins_lower <- as.numeric(c("492.3", "484.5", "480", "472.5", "468.7", "460", "453.5", "448.5", "442.7", "438.5", "433.4", "427.4", "423")) tbins_mid <-(tbins_lower+tbins_upper)/2 tbins_dur <- tbins_lower-tbins_upper tbins_upper = tbins_upper*-1 tbins_lower = tbins_lower*-1 tbins_mid = tbins_mid*-1 baltic_stages <- c("Pakerort", "Varangu", "Hunneberg", "Billingen","Volkhov", "Kunda", "Aseri", "Lasnamägi", "Uhaku", "Kukruse", "Haljala", "Keila", "Oandu", "Rakvere", "Nabala", "Vormsi", "Pirgu", "Porkuni","Juuru", "Raikküla", "Adavere", "Jaani", "Jaagarahu", "Rootsiküla", "Paadla", "Kuuressaare", "Kaugatuma", "Ohesaare") baltic_lower <- c(485.4, 481.5, 479.7, 475, 472.5, 468.7, 464.7, 463.0, 460.0, 458.4, 457.5, 453.5, 452.5, 451.8, 450.3, 449.5, 448.5, 443.1, 442.7, 441.6, 438.8, 433.4, 432.2, 428.6, 427.4, 423.2, 423, 421.2) # baltic_upper <- c(481.5, 479.7, 475, 472.5, 468.7, 464.7, 463.0, 460.0, 458.4, 457.5, 453.5, 452.5, 451.8, 450.3, 449.5, 448.5, 443.1, 442.7, 441.6, 438.8, 433.4, 432.2, 428.6, 427.4, 423.2, 423, 421.2, 419.2) baltic_mid <- (baltic_lower + baltic_upper)/2 baltic_duration <- baltic_lower - baltic_upper baltic_lower = baltic_lower*-1 baltic_upper = baltic_upper*-1 baltic_mid = baltic_mid*-1 baltic_stage_times <- cbind(baltic_stages,baltic_lower , baltic_upper, baltic_mid, baltic_duration) baltic_stage_times <-as.data.frame(baltic_stage_times) baltic_stage_times$baltic_mid = baltic_mid baltic_stage_times$baltic_upper = baltic_upper baltic_stage_times$baltic_lower = baltic_lower Fig8_sqs_bio <- read.csv("CSVs_For_Figures/Fig8_iNEXT_bio_VS_sil_richness/sqs_div_brachs_bio_27_02_20.csv", row.names = 1, header =T) Fig8_sqs_sil <- read.csv("CSVs_For_Figures/Fig8_iNEXT_bio_VS_sil_richness/sqs_div_brachs_sil_27_02_20.csv", row.names = 1, header =T) Fig9_sqs_bios <- read.csv("CSVs_For_Figures/Fig9_iNEXT_bio_VS_sil_richness_stage_resolution/sqs_div_brachs_bio_stages_02_03_20.csv", row.names = 1, header =T) Fig9_sqs_sils <- read.csv("CSVs_For_Figures/Fig9_iNEXT_bio_VS_sil_richness_stage_resolution/sqs_div_brachs_sil_stages_02_03_20.csv", row.names = 1, header =T) Fig10_bio_mult_S <- read.csv("CSVs_For_Figures/Fig10_lithological_partitions/lith_mult_S_results_02_03_20.csv", row.names = 1, header =T) Fig10_lith_mult_shan <- read.csv("CSVs_For_Figures/Fig10_lithological_partitions/lith_mult_shan_results_02_03_20.csv", row.names = 1, header =T) Fig10_lith_mult_sim <- read.csv("CSVs_For_Figures/Fig10_lithological_partitions/lith_mult_sim_results_02_03_20", row.names = 1, header =T) Fig11_bio_mult_S <- read.csv("CSVs_For_Figures/Fig11_bio_partitions_2level/bio_mult_S_03_03_20.csv", row.names = 1, header =T) Fig11_bio_mult_shan <- read.csv("CSVs_For_Figures/Fig11_bio_partitions_2level/bio_mult_shan_03_03_20.csv", row.names = 1, header =T) Fig11_bio_mult_sim <- read.csv("CSVs_For_Figures/Fig11_bio_partitions_2level/bio_mult_sim_03_03_20.csv", row.names = 1, header =T) Fig12_sil_mult_S <- read.csv("CSVs_For_Figures/Fig12_sil_partitions_2level/sil_mult_S_03_03_20.csv", row.names = 1, header =T) Fig12_sil_mult_shan <- read.csv("CSVs_For_Figures/Fig12_sil_partitions_2level/sil_mult_shan_03_03_20.csv", row.names = 1, header =T) Fig12_sil_mult_sim <- read.csv("CSVs_For_Figures/Fig12_sil_partitions_2level/sil_mult_sim_03_03_20.csv", row.names = 1, header =T) ########################## ########################## # Fig xx CMR plot(tbins_mid[-(1:2)], gamma_bins_resis$estimate,col="blue", type="o", cex=0.6, pch=19, ylim=c(0,max(gamma_bins_resis$ucl))) arrows(tbins_mid[-(1:2)], (gamma_bins_resis$lcl), tbins_mid[-(1:2)], (gamma_bins_resis$ucl), col="blue",length=0.01, angle=90, code=3) lines(gamma_stage_resis$mid_age, gamma_stage_resis$estimate, col="red") points(gamma_stage_resis$mid_age, gamma_stage_resis$estimate,col="red", cex=0.6, pch=15) arrows(gamma_stage_resis$mid_age, (gamma_stage_resis$lcl), gamma_stage_resis$mid_age, (gamma_stage_resis$ucl), col="red",length=0.01, angle=90, code=3) abline(v = tbins_lower[-(1:2)], col="blue", lwd=1, lty=2) #abline(v = baltic_stage_times$baltic_lower[-(1:3)] , col="red", lwd=1, lty=2) ######################### ######################### #Fig 6 a-c fig6_temp_mult_S <- read.csv("CSVs_For_Figures/Fig6_temporal_partitions/temp_mult_S_results_02_03_20.csv", row.names = 1, header =T) fig6_temp_mult_shan <- read.csv("CSVs_For_Figures/Fig6_temporal_partitions/temp_mult_shan_results_02_03_20.csv", row.names = 1, header =T) fig6_temp_mult_sim <- read.csv("CSVs_For_Figures/Fig6_temporal_partitions/temp_mult_sim_results_02_03_20.csv", row.names = 1, header =T) fig6_temp_mult_S[,"tbins_mid"] = tbins_mid fig6_temp_mult_shan[,"tbins_mid"] = tbins_mid fig6_temp_mult_sim[,"tbins_mid"] = tbins_mid pdf(file="Rplot_afig6a.pdf", width=2.7, height=2.2) par(mar=c(1,1,1,1)) plot(fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$gamma)], fig6_temp_mult_S$gamma[!is.na(fig6_temp_mult_S$gamma)], type = 'o', pch=19, cex=0.6, col="black", ylim= c(0,max(na.omit(fig6_temp_mult_S$gamma+fig6_temp_mult_S$gamma_CI)))) arrows(fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$gamma)], fig6_temp_mult_S$gamma[!is.na(fig6_temp_mult_S$gamma)]-fig6_temp_mult_S$gamma_CI[!is.na(!is.na(fig6_temp_mult_S$gamma_CI))], fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$gamma)], fig6_temp_mult_S$gamma[!is.na(fig6_temp_mult_S$gamma)]+fig6_temp_mult_S$gamma_CI[!is.na(!is.na(fig6_temp_mult_S$gamma_CI))], col="black",length=0.01, angle=90, code=3) lines(fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$beta1)], fig6_temp_mult_S$beta1[!is.na(fig6_temp_mult_S$beta1)], col="black") arrows(fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$beta_CI_1)], fig6_temp_mult_S$beta1[!is.na(fig6_temp_mult_S$beta1)]-fig6_temp_mult_S$beta_CI_1[!is.na(!is.na(fig6_temp_mult_S$beta_CI_1))], fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$beta1)], fig6_temp_mult_S$beta1[!is.na(fig6_temp_mult_S$beta1)]+fig6_temp_mult_S$beta_CI_1[!is.na(!is.na(fig6_temp_mult_S$beta_CI_1))], col="red",length=0.01, angle=90, code=3) points(fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$beta1)], fig6_temp_mult_S$beta1[!is.na(fig6_temp_mult_S$beta1)],cex=0.6, pch=22, col="black", bg="grey50") lines(fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$beta2)], fig6_temp_mult_S$beta2[!is.na(fig6_temp_mult_S$beta2)], col="black") arrows(fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$beta_CI_2)], fig6_temp_mult_S$beta2[!is.na(fig6_temp_mult_S$beta2)]-fig6_temp_mult_S$beta_CI_2[!is.na(!is.na(fig6_temp_mult_S$beta_CI_2))], fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$beta2)], fig6_temp_mult_S$beta2[!is.na(fig6_temp_mult_S$beta2)]+fig6_temp_mult_S$beta_CI_2[!is.na(!is.na(fig6_temp_mult_S$beta_CI_2))], col="red",length=0.01, angle=90, code=3) points(fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$beta2)], fig6_temp_mult_S$beta2[!is.na(fig6_temp_mult_S$beta2)],cex=0.6, pch=22, col="black", bg="white") lines(fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$alpha1)], fig6_temp_mult_S$alpha1[!is.na(fig6_temp_mult_S$alpha1)], col="black") arrows(fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$alpha1)], fig6_temp_mult_S$alpha1[!is.na(fig6_temp_mult_S$alpha1)]-fig6_temp_mult_S$alpha_CI_1[!is.na(!is.na(fig6_temp_mult_S$alpha_CI_1))], fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$alpha1)], fig6_temp_mult_S$alpha1[!is.na(fig6_temp_mult_S$alpha1)]+fig6_temp_mult_S$alpha_CI_1[!is.na(!is.na(fig6_temp_mult_S$alpha_CI_1))], col="grey",length=0.01, angle=90, code=3) points(fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$alpha1)], fig6_temp_mult_S$alpha1[!is.na(fig6_temp_mult_S$alpha1)],cex=0.6, pch=23 , col="black", bg="grey50") lines(fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$alpha2)], fig6_temp_mult_S$alpha2[!is.na(fig6_temp_mult_S$alpha2)], col="black") arrows(fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$alpha2)], fig6_temp_mult_S$alpha2[!is.na(fig6_temp_mult_S$alpha2)]-fig6_temp_mult_S$alpha_CI_2[!is.na(!is.na(fig6_temp_mult_S$alpha_CI_2))], fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$alpha2)], fig6_temp_mult_S$alpha2[!is.na(fig6_temp_mult_S$alpha2)]+fig6_temp_mult_S$alpha_CI_2[!is.na(!is.na(fig6_temp_mult_S$alpha_CI_2))], col="grey",length=0.01, angle=90, code=3) points(fig6_temp_mult_S$tbins_mid[!is.na(fig6_temp_mult_S$alpha2)], fig6_temp_mult_S$alpha2[!is.na(fig6_temp_mult_S$alpha2)],cex=0.6, pch=23, , col="black", bg="white") abline(v = tbins_lower, col="blue", lwd=1, lty=2) dev.off() pdf(file="Rplot_afig6b.pdf", width=2.7, height=2.2) par(mar=c(1,1,1,1)) plot(fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$gamma)], fig6_temp_mult_shan$gamma[!is.na(fig6_temp_mult_shan$gamma)], type = 'o', pch=19, cex=0.6, col="black", ylim= c(0,max(na.omit(fig6_temp_mult_shan$gamma+fig6_temp_mult_shan$gamma_CI)))) arrows(fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$gamma)], fig6_temp_mult_shan$gamma[!is.na(fig6_temp_mult_shan$gamma)]-fig6_temp_mult_shan$gamma_CI[!is.na(!is.na(fig6_temp_mult_shan$gamma_CI))], fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$gamma)], fig6_temp_mult_shan$gamma[!is.na(fig6_temp_mult_shan$gamma)]+fig6_temp_mult_shan$gamma_CI[!is.na(!is.na(fig6_temp_mult_shan$gamma_CI))], col="black",length=0.01, angle=90, code=3) arrows(fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$beta_CI_1)], fig6_temp_mult_shan$beta1[!is.na(fig6_temp_mult_shan$beta1)]-fig6_temp_mult_shan$beta_CI_1[!is.na(!is.na(fig6_temp_mult_shan$beta_CI_1))], fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$beta1)], fig6_temp_mult_shan$beta1[!is.na(fig6_temp_mult_shan$beta1)]+fig6_temp_mult_shan$beta_CI_1[!is.na(!is.na(fig6_temp_mult_shan$beta_CI_1))], col="black",length=0.01, angle=90, code=3) lines(fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$beta1)], fig6_temp_mult_shan$beta1[!is.na(fig6_temp_mult_shan$beta1)], col="black") points(fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$beta1)], fig6_temp_mult_shan$beta1[!is.na(fig6_temp_mult_shan$beta1)],cex=0.6, pch=22, col="black", bg="grey50") arrows(fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$beta_CI_2)], fig6_temp_mult_shan$beta2[!is.na(fig6_temp_mult_shan$beta2)]-fig6_temp_mult_shan$beta_CI_2[!is.na(!is.na(fig6_temp_mult_shan$beta_CI_2))], fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$beta2)], fig6_temp_mult_shan$beta2[!is.na(fig6_temp_mult_shan$beta2)]+fig6_temp_mult_shan$beta_CI_2[!is.na(!is.na(fig6_temp_mult_shan$beta_CI_2))], col="black",length=0.01, angle=90, code=3) lines(fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$beta2)], fig6_temp_mult_shan$beta2[!is.na(fig6_temp_mult_shan$beta2)], col="black") points(fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$beta2)], fig6_temp_mult_shan$beta2[!is.na(fig6_temp_mult_shan$beta2)],cex=0.6, pch=22, col="black", bg="white") arrows(fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$alpha1)], fig6_temp_mult_shan$alpha1[!is.na(fig6_temp_mult_shan$alpha1)]-fig6_temp_mult_shan$alpha_CI_1[!is.na(!is.na(fig6_temp_mult_shan$alpha_CI_1))], fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$alpha1)], fig6_temp_mult_shan$alpha1[!is.na(fig6_temp_mult_shan$alpha1)]+fig6_temp_mult_shan$alpha_CI_1[!is.na(!is.na(fig6_temp_mult_shan$alpha_CI_1))], col="black",length=0.01, angle=90, code=3) lines(fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$alpha1)], fig6_temp_mult_shan$alpha1[!is.na(fig6_temp_mult_shan$alpha1)], col="black") points(fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$alpha1)], fig6_temp_mult_shan$alpha1[!is.na(fig6_temp_mult_shan$alpha1)],cex=0.6, pch=23 , col="black", bg="grey50") arrows(fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$alpha2)], fig6_temp_mult_shan$alpha2[!is.na(fig6_temp_mult_shan$alpha2)]-fig6_temp_mult_shan$alpha_CI_2[!is.na(!is.na(fig6_temp_mult_shan$alpha_CI_2))], fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$alpha2)], fig6_temp_mult_shan$alpha2[!is.na(fig6_temp_mult_shan$alpha2)]+fig6_temp_mult_shan$alpha_CI_2[!is.na(!is.na(fig6_temp_mult_shan$alpha_CI_2))], col="black",length=0.01, angle=90, code=3) lines(fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$alpha2)], fig6_temp_mult_shan$alpha2[!is.na(fig6_temp_mult_shan$alpha2)], col="black") points(fig6_temp_mult_shan$tbins_mid[!is.na(fig6_temp_mult_shan$alpha2)], fig6_temp_mult_shan$alpha2[!is.na(fig6_temp_mult_shan$alpha2)],cex=0.6, pch=23 , col="black", bg="white") dev.off() pdf(file="Rplot_afig6c.pdf", width=2.7, height=2.2) par(mar=c(1,1,1,1)) plot(fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$gamma)], fig6_temp_mult_sim$gamma[!is.na(fig6_temp_mult_sim$gamma)], type = 'o', pch=19, cex=0.6, col="black", ylim= c(0,max(na.omit(fig6_temp_mult_sim$gamma+fig6_temp_mult_sim$gamma_CI)))) arrows(fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$gamma)], fig6_temp_mult_sim$gamma[!is.na(fig6_temp_mult_sim$gamma)]-fig6_temp_mult_sim$gamma_CI[!is.na(!is.na(fig6_temp_mult_sim$gamma_CI))], fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$gamma)], fig6_temp_mult_sim$gamma[!is.na(fig6_temp_mult_sim$gamma)]+fig6_temp_mult_sim$gamma_CI[!is.na(!is.na(fig6_temp_mult_sim$gamma_CI))], col="black",length=0.01, angle=90, code=3) arrows(fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$beta_CI_1)], fig6_temp_mult_sim$beta1[!is.na(fig6_temp_mult_sim$beta1)]-fig6_temp_mult_sim$beta_CI_1[!is.na(!is.na(fig6_temp_mult_sim$beta_CI_1))], fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$beta1)], fig6_temp_mult_sim$beta1[!is.na(fig6_temp_mult_sim$beta1)]+fig6_temp_mult_sim$beta_CI_1[!is.na(!is.na(fig6_temp_mult_sim$beta_CI_1))], col="black",length=0.01, angle=90, code=3) lines(fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$beta1)], fig6_temp_mult_sim$beta1[!is.na(fig6_temp_mult_sim$beta1)], col="black") points(fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$beta1)], fig6_temp_mult_sim$beta1[!is.na(fig6_temp_mult_sim$beta1)],cex=0.6, pch=22, col="black", bg="grey50") arrows(fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$beta_CI_2)], fig6_temp_mult_sim$beta2[!is.na(fig6_temp_mult_sim$beta2)]-fig6_temp_mult_sim$beta_CI_2[!is.na(!is.na(fig6_temp_mult_sim$beta_CI_2))], fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$beta2)], fig6_temp_mult_sim$beta2[!is.na(fig6_temp_mult_sim$beta2)]+fig6_temp_mult_sim$beta_CI_2[!is.na(!is.na(fig6_temp_mult_sim$beta_CI_2))], col="black",length=0.01, angle=90, code=3) lines(fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$beta2)], fig6_temp_mult_sim$beta2[!is.na(fig6_temp_mult_sim$beta2)], col="black") points(fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$beta2)], fig6_temp_mult_sim$beta2[!is.na(fig6_temp_mult_sim$beta2)], cex=0.6, pch=22, col="black", bg="white") arrows(fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$alpha1)], fig6_temp_mult_sim$alpha1[!is.na(fig6_temp_mult_sim$alpha1)]-fig6_temp_mult_sim$alpha_CI_1[!is.na(!is.na(fig6_temp_mult_sim$alpha_CI_1))], fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$alpha1)], fig6_temp_mult_sim$alpha1[!is.na(fig6_temp_mult_sim$alpha1)]+fig6_temp_mult_sim$alpha_CI_1[!is.na(!is.na(fig6_temp_mult_sim$alpha_CI_1))], col="black",length=0.01, angle=90, code=3) lines(fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$alpha1)], fig6_temp_mult_sim$alpha1[!is.na(fig6_temp_mult_sim$alpha1)], col="black") points(fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$alpha1)], fig6_temp_mult_sim$alpha1[!is.na(fig6_temp_mult_sim$alpha1)],cex=0.6, pch=23 , col="black", bg="grey50") arrows(fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$alpha2)], fig6_temp_mult_sim$alpha2[!is.na(fig6_temp_mult_sim$alpha2)]-fig6_temp_mult_sim$alpha_CI_2[!is.na(!is.na(fig6_temp_mult_sim$alpha_CI_2))], fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$alpha2)], fig6_temp_mult_sim$alpha2[!is.na(fig6_temp_mult_sim$alpha2)]+fig6_temp_mult_sim$alpha_CI_2[!is.na(!is.na(fig6_temp_mult_sim$alpha_CI_2))], col="black",length=0.01, angle=90, code=3) lines(fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$alpha2)], fig6_temp_mult_sim$alpha2[!is.na(fig6_temp_mult_sim$alpha2)], col="black") points(fig6_temp_mult_sim$tbins_mid[!is.na(fig6_temp_mult_sim$alpha2)], fig6_temp_mult_sim$alpha2[!is.na(fig6_temp_mult_sim$alpha2)],cex=0.6, pch=23 , col="black", bg="white") dev.off() ########################## ########################## # Fig 7a & b fig7_b_mult_S <- read.csv("CSVs_For_Figures/Fig7_iNEXT_shelf_VS_basin_richness/b_mult_S_results_30_03_20.csv", row.names = 1, header =T) fig7_p_mult_S <- read.csv("CSVs_For_Figures/Fig7_iNEXT_shelf_VS_basin_richness/p_mult_S_results_30_03_20.csv", row.names = 1, header =T) fig7_b_mult_S[,"tbins_mid"] = tbins_mid fig7_p_mult_S[,"tbins_mid"] = tbins_mid pdf(file="Rplot_afig7a.pdf", width=2.1, height=2) par(mar=c(1,1,1,1)) plot(fig7_b_mult_S$tbins_mid[!is.na(fig7_b_mult_S$gamma)],fig7_b_mult_S$gamma[!is.na(fig7_b_mult_S$gamma)], ,cex=0.6, pch=19 , col="black", type="o", xlim = c(-455,-420), ylim= c(0,50)) arrows(fig7_b_mult_S$tbins_mid[!is.na(fig7_b_mult_S$gamma_CI)], fig7_b_mult_S$gamma[!is.na(fig7_b_mult_S$gamma_CI)]-fig7_b_mult_S$gamma_CI[!is.na(!is.na(fig7_b_mult_S$gamma_CI))], fig7_b_mult_S$tbins_mid[!is.na(fig7_b_mult_S$gamma_CI)], fig7_b_mult_S$gamma[!is.na(fig7_b_mult_S$gamma_CI)]+fig7_b_mult_S$gamma_CI[!is.na(!is.na(fig7_b_mult_S$gamma_CI))], col="black",length=0.01, angle=90, code=3) arrows(fig7_b_mult_S$tbins_mid[!is.na(fig7_b_mult_S$alpha1)], fig7_b_mult_S$alpha1[!is.na(fig7_b_mult_S$alpha1)]-fig7_b_mult_S$alpha_CI_1[!is.na(!is.na(fig7_b_mult_S$alpha_CI_1 ))], fig7_b_mult_S$tbins_mid[!is.na(fig7_b_mult_S$alpha1)], fig7_b_mult_S$alpha1[!is.na(fig7_b_mult_S$alpha1)]+fig7_b_mult_S$alpha_CI_1[!is.na(!is.na(fig7_b_mult_S$alpha_CI_1 ))], col="black",length=0.01, angle=90, code=3) arrows(fig7_b_mult_S$tbins_mid[!is.na(fig7_b_mult_S$beta1)], fig7_b_mult_S$beta1[!is.na(fig7_b_mult_S$beta1)]-fig7_b_mult_S$beta1[!is.na(!is.na(fig7_b_mult_S$beta1))], fig7_b_mult_S$tbins_mid[!is.na(fig7_b_mult_S$beta1)], fig7_b_mult_S$beta1[!is.na(fig7_b_mult_S$beta1)]+fig7_b_mult_S$beta1[!is.na(!is.na(fig7_b_mult_S$beta1))], col="black",length=0.01, angle=90, code=3) lines(fig7_b_mult_S$tbins_mid[!is.na(fig7_b_mult_S$alpha1)], fig7_b_mult_S$alpha1[!is.na(fig7_b_mult_S$alpha1)], col="black") lines(fig7_b_mult_S$tbins_mid[!is.na(fig7_b_mult_S$beta1)], fig7_b_mult_S$beta1[!is.na(fig7_b_mult_S$beta1)], col="black") points(fig7_b_mult_S$tbins_mid[!is.na(fig7_b_mult_S$alpha1)], fig7_b_mult_S$alpha1[!is.na(fig7_b_mult_S$alpha1)],cex=0.6, pch=23, col="black", bg="gray50") points(fig7_b_mult_S$tbins_mid[!is.na(fig7_b_mult_S$beta1)], fig7_b_mult_S$beta1[!is.na(fig7_b_mult_S$beta1)],cex=0.6, pch=22, col="black", bg="grey50") dev.off() pdf(file="Rplot_afig7b.pdf", width=2.1, height=2) par(mar=c(1,1,1,1)) plot(fig7_p_mult_S$tbins_mid[!is.na(fig7_p_mult_S$alpha1)],fig7_p_mult_S$alpha1[!is.na(fig7_p_mult_S$alpha1)], cex=0.6, pch=23, col="black", bg="gray50", type="o", xlim = c(-455,-420), ylim= c(0,max(na.omit(fig7_p_mult_S$gamma+fig7_p_mult_S$gamma_CI)))) arrows(fig7_p_mult_S$tbins_mid[!is.na(fig7_p_mult_S$alpha1)], fig7_p_mult_S$alpha1[!is.na(fig7_p_mult_S$alpha1)]-fig7_p_mult_S$alpha_CI_1[!is.na(!is.na(fig7_p_mult_S$alpha_CI_1))], fig7_p_mult_S$tbins_mid[!is.na(fig7_p_mult_S$alpha1)], fig7_p_mult_S$alpha1[!is.na(fig7_p_mult_S$alpha1)]+fig7_p_mult_S$alpha_CI_1[!is.na(!is.na(fig7_p_mult_S$alpha_CI_1))], col="black",length=0.01, angle=90, code=3) arrows(fig7_p_mult_S$tbins_mid[!is.na(fig7_p_mult_S$beta1)], fig7_p_mult_S$beta1[!is.na(fig7_p_mult_S$beta1)]-fig7_p_mult_S$beta_CI_1[!is.na(!is.na(fig7_p_mult_S$beta_CI_1))], fig7_p_mult_S$tbins_mid[!is.na(fig7_p_mult_S$beta1)], fig7_p_mult_S$beta1[!is.na(fig7_p_mult_S$beta1)]+fig7_p_mult_S$beta_CI_1[!is.na(!is.na(fig7_p_mult_S$beta_CI_1))], col="black",length=0.01, angle=90, code=3) lines(fig7_p_mult_S$tbins_mid[!is.na(fig7_p_mult_S$beta1)], fig7_p_mult_S$beta1[!is.na(fig7_p_mult_S$beta1)], col="black") points(fig7_p_mult_S$tbins_mid[!is.na(fig7_p_mult_S$beta1)], fig7_p_mult_S$beta1[!is.na(fig7_p_mult_S$beta1)], cex=0.6, pch=22, col="black", bg="grey50") arrows(fig7_p_mult_S$tbins_mid[!is.na(fig7_p_mult_S$gamma)], fig7_p_mult_S$gamma[!is.na(fig7_p_mult_S$gamma)]-fig7_p_mult_S$gamma_CI[!is.na(!is.na(fig7_p_mult_S$gamma_CI))], fig7_p_mult_S$tbins_mid[!is.na(fig7_p_mult_S$gamma)], fig7_p_mult_S$gamma[!is.na(fig7_p_mult_S$gamma)]+fig7_p_mult_S$gamma_CI[!is.na(!is.na(fig7_p_mult_S$gamma_CI))], col="black",length=0.01, angle=90, code=3) lines(fig7_p_mult_S$tbins_mid[!is.na(fig7_p_mult_S$gamma)], fig7_p_mult_S$gamma[!is.na(fig7_p_mult_S$gamma)], col="black") points(fig7_p_mult_S$tbins_mid[!is.na(fig7_p_mult_S$gamma)], fig7_p_mult_S$gamma[!is.na(fig7_p_mult_S$gamma)], cex=0.6, pch=19) dev.off() ########################## # Fig 8a & b (9) Fig8_sqs_bio <- read.csv("CSVs_For_Figures/Fig8_iNEXT_bio_VS_sil_richness/sqs_div_brachs_bio_cam_O1_27_02_20.csv", row.names = 1, header =T) Fig8_sqs_sil <- read.csv("CSVs_For_Figures/Fig8_iNEXT_bio_VS_sil_richness/sqs_div_brachs_sil_cam_O1_27_02_20.csv", row.names = 1, header =T) Fig8_sqs_bio[,"tbins_mid"] = tbins_mid[-c(1:2)] Fig8_sqs_sil[,"tbins_mid"] = tbins_mid[-c(1:2)] Fig9_sqs_bios <- read.csv("CSVs_For_Figures/Fig9_iNEXT_bio_VS_sil_richness_stage_resolution/sqs_div_brachs_bio_stages_02_03_20.csv", row.names = 1, header =T) Fig9_sqs_sils <- read.csv("CSVs_For_Figures/Fig9_iNEXT_bio_VS_sil_richness_stage_resolution/sqs_div_brachs_sil_stages_02_03_20.csv", row.names = 1, header =T) Fig9_sqs_bios[,"baltic_mid"] = baltic_mid Fig9_sqs_sils[,"baltic_mid"] = baltic_mid pdf(file="Rplot_afig8a.pdf",width=2.7, height=2.2) par(mar=c(1,1,1,1)) plot(Fig8_sqs_bio$tbins_mid[!is.na(Fig8_sqs_bio$V1)],Fig8_sqs_bio$V1[!is.na(Fig8_sqs_bio$V1)], cex=0.6, pch=21, col="black", bg="black", type="o", xlim=c(-471,-420), ylim= c(0,100)) arrows(Fig8_sqs_bio$tbins_mid[!is.na(Fig8_sqs_bio$V2)], Fig8_sqs_bio$V2[!is.na(Fig8_sqs_bio$V2)], Fig8_sqs_bio$tbins_mid[!is.na(Fig8_sqs_bio$V3)], Fig8_sqs_bio$V3[!is.na(Fig8_sqs_bio$V3)], col="black",length=0.01, angle=90, code=3) arrows(Fig9_sqs_bios$baltic_mid[!is.na(Fig9_sqs_bios$V2)], Fig9_sqs_bios$V2[!is.na(Fig9_sqs_bios$V2)], Fig9_sqs_bios$baltic_mid[!is.na(Fig9_sqs_bios$V3)], Fig9_sqs_bios$V3[!is.na(Fig9_sqs_bios$V3)], col="black",length=0.01, angle=90, code=3) lines(Fig9_sqs_bios$baltic_mid[!is.na(Fig9_sqs_bios$V1)], Fig9_sqs_bios$V1[!is.na(Fig9_sqs_bios$V1)], col="black") points(Fig9_sqs_bios$baltic_mid[!is.na(Fig9_sqs_bios$V1)], Fig9_sqs_bios$V1[!is.na(Fig9_sqs_bios$V1)], cex=0.6, pch=22, col="black", bg="grey50") dev.off() pdf(file="Rplot_afig8b.pdf", width=2.7, height=2.2) par(mar=c(1,1,1,1)) plot(Fig8_sqs_sil$tbins_mid[!is.na(Fig8_sqs_sil$V1)],Fig8_sqs_sil$V1[!is.na(Fig8_sqs_sil$V1)], cex=0.6, pch=21, col="black", bg="black", type="o", xlim=c(-471,-420), ylim= c(0,100)) arrows(Fig8_sqs_sil$tbins_mid[!is.na(Fig8_sqs_sil$V2)], Fig8_sqs_sil$V2[!is.na(Fig8_sqs_sil$V2)], Fig8_sqs_sil$tbins_mid[!is.na(Fig8_sqs_sil$V3)], Fig8_sqs_sil$V3[!is.na(Fig8_sqs_sil$V3)], col="black",length=0.01, angle=90, code=3) arrows(Fig9_sqs_sils$baltic_mid[!is.na(Fig9_sqs_sils$V2)], Fig9_sqs_sils$V2[!is.na(Fig9_sqs_sils$V2)], Fig9_sqs_sils$baltic_mid[!is.na(Fig9_sqs_sils$V3)], Fig9_sqs_sils$V3[!is.na(Fig9_sqs_sils$V3)], col="black",length=0.01, angle=90, code=3) lines(Fig9_sqs_sils$baltic_mid[!is.na(Fig9_sqs_sils$V1)], Fig9_sqs_sils$V1[!is.na(Fig9_sqs_sils$V1)], col="black") points(Fig9_sqs_sils$baltic_mid[!is.na(Fig9_sqs_sils$V1)], Fig9_sqs_sils$V1[!is.na(Fig9_sqs_sils$V1)], cex=0.6, pch=22, col="black", bg="grey50") dev.off() ########################################### ########################################## # Fig. 10 a-c Fig10_lith_mult_S <- read.csv("CSVs_For_Figures/Fig10_lithological_partitions/lith_mult_S_results_02_03_20.csv", row.names = 1, header =T) Fig10_lith_mult_shan <- read.csv("CSVs_For_Figures/Fig10_lithological_partitions/lith_mult_shan_results_02_03_20.csv", row.names = 1, header =T) Fig10_lith_mult_sim <- read.csv("CSVs_For_Figures/Fig10_lithological_partitions/lith_mult_sim_results_02_03_20.csv", row.names = 1, header =T) Fig10_lith_mult_S[,"tbins_mid"] = tbins_mid Fig10_lith_mult_shan[,"tbins_mid"] = tbins_mid Fig10_lith_mult_sim[,"tbins_mid"] = tbins_mid pdf(file="Rplot_afig10a.pdf", width=2.7, height=2.2) par(mar=c(1,1,1,1)) plot(Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$gamma)], Fig10_lith_mult_S$gamma[!is.na(Fig10_lith_mult_S$gamma)], cex=0.6, pch=21, col="black", bg="black", type="o", xlim=c(-471,-420), ylim= c(0,max(na.omit(Fig10_lith_mult_S$gamma+Fig10_lith_mult_S$gamma_CI)))) arrows(Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$gamma)], Fig10_lith_mult_S$gamma[!is.na(Fig10_lith_mult_S$gamma)]-Fig10_lith_mult_S$gamma_CI[!is.na(!is.na(Fig10_lith_mult_S$gamma_CI))], Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$gamma)], Fig10_lith_mult_S$gamma[!is.na(Fig10_lith_mult_S$gamma)]+Fig10_lith_mult_S$gamma_CI[!is.na(!is.na(Fig10_lith_mult_S$gamma_CI))], col="black",length=0.01, angle=90, code=3) arrows(Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$beta_CI_1)], Fig10_lith_mult_S$beta1[!is.na(Fig10_lith_mult_S$beta1)]-Fig10_lith_mult_S$beta_CI_1[!is.na(!is.na(Fig10_lith_mult_S$beta_CI_1))], Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$beta1)], Fig10_lith_mult_S$beta1[!is.na(Fig10_lith_mult_S$beta1)]+Fig10_lith_mult_S$beta_CI_1[!is.na(!is.na(Fig10_lith_mult_S$beta_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$beta1)], Fig10_lith_mult_S$beta1[!is.na(Fig10_lith_mult_S$beta1)], col="black") points(Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$beta1)], Fig10_lith_mult_S$beta1[!is.na(Fig10_lith_mult_S$beta1)], cex=0.6, pch=22, col="black", bg="grey50") arrows(Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$beta_CI_2)], Fig10_lith_mult_S$beta2[!is.na(Fig10_lith_mult_S$beta2)]-Fig10_lith_mult_S$beta_CI_2[!is.na(!is.na(Fig10_lith_mult_S$beta_CI_2))], Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$beta2)], Fig10_lith_mult_S$beta2[!is.na(Fig10_lith_mult_S$beta2)]+Fig10_lith_mult_S$beta_CI_2[!is.na(!is.na(Fig10_lith_mult_S$beta_CI_2))], col="black",length=0.01, angle=90, code=3) lines(Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$beta2)], Fig10_lith_mult_S$beta2[!is.na(Fig10_lith_mult_S$beta2)], cex=0.6, pch=22, col="black", bg="white") points(Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$beta2)], Fig10_lith_mult_S$beta2[!is.na(Fig10_lith_mult_S$beta2)], cex=0.6, pch=22, col="black", bg="white") arrows(Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$alpha1)], Fig10_lith_mult_S$alpha1[!is.na(Fig10_lith_mult_S$alpha1)]-Fig10_lith_mult_S$alpha_CI_1[!is.na(!is.na(Fig10_lith_mult_S$alpha_CI_1))], Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$alpha1)], Fig10_lith_mult_S$alpha1[!is.na(Fig10_lith_mult_S$alpha1)]+Fig10_lith_mult_S$alpha_CI_1[!is.na(!is.na(Fig10_lith_mult_S$alpha_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$alpha1)], Fig10_lith_mult_S$alpha1[!is.na(Fig10_lith_mult_S$alpha1)], col="black") points(Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$alpha1)], Fig10_lith_mult_S$alpha1[!is.na(Fig10_lith_mult_S$alpha1)], cex=0.6, pch=23, col="black", bg="grey50") arrows(Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$alpha2)], Fig10_lith_mult_S$alpha2[!is.na(Fig10_lith_mult_S$alpha2)]-Fig10_lith_mult_S$alpha_CI_2[!is.na(!is.na(Fig10_lith_mult_S$alpha_CI_2))], Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$alpha2)], Fig10_lith_mult_S$alpha2[!is.na(Fig10_lith_mult_S$alpha2)]+Fig10_lith_mult_S$alpha_CI_2[!is.na(!is.na(Fig10_lith_mult_S$alpha_CI_2))], col="black",length=0.01, angle=90, code=3) lines(Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$alpha2)], Fig10_lith_mult_S$alpha2[!is.na(Fig10_lith_mult_S$alpha2)], col="black") points(Fig10_lith_mult_S$tbins_mid[!is.na(Fig10_lith_mult_S$alpha2)], Fig10_lith_mult_S$alpha2[!is.na(Fig10_lith_mult_S$alpha2)], cex=0.6, pch=23, col="black", bg="white") dev.off() pdf(file="Rplot_afig10b.pdf", width=2.7, height=2.2) par(mar=c(1,1,1,1)) plot(Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$gamma)],Fig10_lith_mult_shan$gamma[!is.na(Fig10_lith_mult_shan$gamma)], cex=0.6, pch=21, col="black", bg="black", type="o", xlim=c(-471,-420), ylim= c(0,max(na.omit(Fig10_lith_mult_shan$gamma+Fig10_lith_mult_shan$gamma_CI)))) arrows(Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$gamma)], Fig10_lith_mult_shan$gamma[!is.na(Fig10_lith_mult_shan$gamma)]-Fig10_lith_mult_shan$gamma_CI[!is.na(!is.na(Fig10_lith_mult_shan$gamma_CI))], Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$gamma)], Fig10_lith_mult_shan$gamma[!is.na(Fig10_lith_mult_shan$gamma)]+Fig10_lith_mult_shan$gamma_CI[!is.na(!is.na(Fig10_lith_mult_shan$gamma_CI))], col="black",length=0.01, angle=90, code=3) arrows(Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$beta_CI_1)], Fig10_lith_mult_shan$beta1[!is.na(Fig10_lith_mult_shan$beta1)]-Fig10_lith_mult_shan$beta_CI_1[!is.na(!is.na(Fig10_lith_mult_shan$beta_CI_1))], Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$beta1)], Fig10_lith_mult_shan$beta1[!is.na(Fig10_lith_mult_shan$beta1)]+Fig10_lith_mult_shan$beta_CI_1[!is.na(!is.na(Fig10_lith_mult_shan$beta_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$beta1)], Fig10_lith_mult_shan$beta1[!is.na(Fig10_lith_mult_shan$beta1)], col="black") points(Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$beta1)], Fig10_lith_mult_shan$beta1[!is.na(Fig10_lith_mult_shan$beta1)], cex=0.6, pch=22, col="black", bg="grey50") arrows(Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$beta_CI_2)], Fig10_lith_mult_shan$beta2[!is.na(Fig10_lith_mult_shan$beta2)]-Fig10_lith_mult_shan$beta_CI_2[!is.na(!is.na(Fig10_lith_mult_shan$beta_CI_2))], Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$beta2)], Fig10_lith_mult_shan$beta2[!is.na(Fig10_lith_mult_shan$beta2)]+Fig10_lith_mult_shan$beta_CI_2[!is.na(!is.na(Fig10_lith_mult_shan$beta_CI_2))], col="black",length=0.01, angle=90, code=3) lines(Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$beta2)], Fig10_lith_mult_shan$beta2[!is.na(Fig10_lith_mult_shan$beta2)], col="black") points(Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$beta2)], Fig10_lith_mult_shan$beta2[!is.na(Fig10_lith_mult_shan$beta2)], cex=0.6, pch=22, col="black", bg="white") arrows(Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$alpha1)], Fig10_lith_mult_shan$alpha1[!is.na(Fig10_lith_mult_shan$alpha1)]-Fig10_lith_mult_shan$alpha_CI_1[!is.na(!is.na(Fig10_lith_mult_shan$alpha_CI_1))], Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$alpha1)], Fig10_lith_mult_shan$alpha1[!is.na(Fig10_lith_mult_shan$alpha1)]+Fig10_lith_mult_shan$alpha_CI_1[!is.na(!is.na(Fig10_lith_mult_shan$alpha_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$alpha1)], Fig10_lith_mult_shan$alpha1[!is.na(Fig10_lith_mult_shan$alpha1)], col="black") points(Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$alpha1)], Fig10_lith_mult_shan$alpha1[!is.na(Fig10_lith_mult_shan$alpha1)], cex=0.6, pch=23, col="black", bg="grey50") arrows(Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$alpha2)], Fig10_lith_mult_shan$alpha2[!is.na(Fig10_lith_mult_shan$alpha2)]-Fig10_lith_mult_shan$alpha_CI_2[!is.na(!is.na(Fig10_lith_mult_shan$alpha_CI_2))], Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$alpha2)], Fig10_lith_mult_shan$alpha2[!is.na(Fig10_lith_mult_shan$alpha2)]+Fig10_lith_mult_shan$alpha_CI_2[!is.na(!is.na(Fig10_lith_mult_shan$alpha_CI_2))], col="black",length=0.01, angle=90, code=3) lines(Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$alpha2)], Fig10_lith_mult_shan$alpha2[!is.na(Fig10_lith_mult_shan$alpha2)], col="black") points(Fig10_lith_mult_shan$tbins_mid[!is.na(Fig10_lith_mult_shan$alpha2)], Fig10_lith_mult_shan$alpha2[!is.na(Fig10_lith_mult_shan$alpha2)], cex=0.6, pch=23, col="black", bg="white") dev.off() pdf(file="Rplot_afig10c.pdf", width=2.7, height=2.2) par(mar=c(1,1,1,1)) plot(Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$gamma)],Fig10_lith_mult_sim$gamma[!is.na(Fig10_lith_mult_sim$gamma)], cex=0.6, pch=21, col="black", bg="black", type="o", xlim=c(-471,-420), ylim= c(0,max(na.omit(Fig10_lith_mult_sim$gamma+Fig10_lith_mult_sim$gamma_CI)))) arrows(Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$gamma)], Fig10_lith_mult_sim$gamma[!is.na(Fig10_lith_mult_sim$gamma)]-Fig10_lith_mult_sim$gamma_CI[!is.na(!is.na(Fig10_lith_mult_sim$gamma_CI))], Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$gamma)], Fig10_lith_mult_sim$gamma[!is.na(Fig10_lith_mult_sim$gamma)]+Fig10_lith_mult_sim$gamma_CI[!is.na(!is.na(Fig10_lith_mult_sim$gamma_CI))], col="black",length=0.01, angle=90, code=3) arrows(Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$beta_CI_1)], Fig10_lith_mult_sim$beta1[!is.na(Fig10_lith_mult_sim$beta1)]-Fig10_lith_mult_sim$beta_CI_1[!is.na(!is.na(Fig10_lith_mult_sim$beta_CI_1))], Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$beta1)], Fig10_lith_mult_sim$beta1[!is.na(Fig10_lith_mult_sim$beta1)]+Fig10_lith_mult_sim$beta_CI_1[!is.na(!is.na(Fig10_lith_mult_sim$beta_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$beta1)], Fig10_lith_mult_sim$beta1[!is.na(Fig10_lith_mult_sim$beta1)], col="black") points(Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$beta1)], Fig10_lith_mult_sim$beta1[!is.na(Fig10_lith_mult_sim$beta1)], cex=0.6, pch=22, col="black", bg="grey50") arrows(Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$beta_CI_2)], Fig10_lith_mult_sim$beta2[!is.na(Fig10_lith_mult_sim$beta2)]-Fig10_lith_mult_sim$beta_CI_2[!is.na(!is.na(Fig10_lith_mult_sim$beta_CI_2))], Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$beta2)], Fig10_lith_mult_sim$beta2[!is.na(Fig10_lith_mult_sim$beta2)]+Fig10_lith_mult_sim$beta_CI_2[!is.na(!is.na(Fig10_lith_mult_sim$beta_CI_2))], col="black",length=0.01, angle=90, code=3) lines(Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$beta2)], Fig10_lith_mult_sim$beta2[!is.na(Fig10_lith_mult_sim$beta2)], col="black") points(Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$beta2)], Fig10_lith_mult_sim$beta2[!is.na(Fig10_lith_mult_sim$beta2)], cex=0.6, pch=22, col="black", bg="white") arrows(Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$alpha1)], Fig10_lith_mult_sim$alpha1[!is.na(Fig10_lith_mult_sim$alpha1)]-Fig10_lith_mult_sim$alpha_CI_1[!is.na(!is.na(Fig10_lith_mult_sim$alpha_CI_1))], Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$alpha1)], Fig10_lith_mult_sim$alpha1[!is.na(Fig10_lith_mult_sim$alpha1)]+Fig10_lith_mult_sim$alpha_CI_1[!is.na(!is.na(Fig10_lith_mult_sim$alpha_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$alpha1)], Fig10_lith_mult_sim$alpha1[!is.na(Fig10_lith_mult_sim$alpha1)], col="black") points(Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$alpha1)], Fig10_lith_mult_sim$alpha1[!is.na(Fig10_lith_mult_sim$alpha1)], cex=0.6, pch=23, col="black", bg="grey50") arrows(Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$alpha2)], Fig10_lith_mult_sim$alpha2[!is.na(Fig10_lith_mult_sim$alpha2)]-Fig10_lith_mult_sim$alpha_CI_2[!is.na(!is.na(Fig10_lith_mult_sim$alpha_CI_2))], Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$alpha2)], Fig10_lith_mult_sim$alpha2[!is.na(Fig10_lith_mult_sim$alpha2)]+Fig10_lith_mult_sim$alpha_CI_2[!is.na(!is.na(Fig10_lith_mult_sim$alpha_CI_2))], col="black",length=0.01, angle=90, code=3) lines(Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$alpha2)], Fig10_lith_mult_sim$alpha2[!is.na(Fig10_lith_mult_sim$alpha2)], col="black") points(Fig10_lith_mult_sim$tbins_mid[!is.na(Fig10_lith_mult_sim$alpha2)], Fig10_lith_mult_sim$alpha2[!is.na(Fig10_lith_mult_sim$alpha2)], cex=0.6, pch=23, col="black", bg="white") dev.off() ########################################### ########################################## # Fig. 11 a-c Fig11_bio_mult_S <- read.csv("CSVs_For_Figures/Fig11_bio_partitions_2level/bio_mult_S_03_03_20.csv", row.names = 1, header =T) Fig11_bio_mult_shan <- read.csv("CSVs_For_Figures/Fig11_bio_partitions_2level/bio_mult_shan_03_03_20.csv", row.names = 1, header =T) Fig11_bio_mult_sim <- read.csv("CSVs_For_Figures/Fig11_bio_partitions_2level/bio_mult_sim_03_03_20.csv", row.names = 1, header =T) Fig11_bio_mult_S[,"tbins_mid"] = tbins_mid Fig11_bio_mult_shan[,"tbins_mid"] = tbins_mid Fig11_bio_mult_sim[,"tbins_mid"] = tbins_mid pdf(file="Rplot_afig11a.pdf", width=2.7, height=2.2) par(mar=c(1,1,1,1)) plot(Fig11_bio_mult_S$tbins_mid[!is.na(Fig11_bio_mult_S$gamma)],Fig11_bio_mult_S$gamma[!is.na(Fig11_bio_mult_S$gamma)], cex=0.6, pch=21, col="black", bg="black", type="o", ylim= c(0,max(na.omit(Fig11_bio_mult_S$gamma+Fig11_bio_mult_S$gamma_CI)))) arrows(Fig11_bio_mult_S$tbins_mid[!is.na(Fig11_bio_mult_S$gamma)], Fig11_bio_mult_S$gamma[!is.na(Fig11_bio_mult_S$gamma)]-Fig11_bio_mult_S$gamma_CI[!is.na(!is.na(Fig11_bio_mult_S$gamma_CI))], Fig11_bio_mult_S$tbins_mid[!is.na(Fig11_bio_mult_S$gamma)], Fig11_bio_mult_S$gamma[!is.na(Fig11_bio_mult_S$gamma)]+Fig11_bio_mult_S$gamma_CI[!is.na(!is.na(Fig11_bio_mult_S$gamma_CI))], col="black",length=0.01, angle=90, code=3) arrows(Fig11_bio_mult_S$tbins_mid[!is.na(Fig11_bio_mult_S$beta_CI_1)], Fig11_bio_mult_S$beta1[!is.na(Fig11_bio_mult_S$beta1)]-Fig11_bio_mult_S$beta_CI_1[!is.na(!is.na(Fig11_bio_mult_S$beta_CI_1))], Fig11_bio_mult_S$tbins_mid[!is.na(Fig11_bio_mult_S$beta1)], Fig11_bio_mult_S$beta1[!is.na(Fig11_bio_mult_S$beta1)]+Fig11_bio_mult_S$beta_CI_1[!is.na(!is.na(Fig11_bio_mult_S$beta_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig11_bio_mult_S$tbins_mid[!is.na(Fig11_bio_mult_S$beta1)], Fig11_bio_mult_S$beta1[!is.na(Fig11_bio_mult_S$beta1)], col="black") points(Fig11_bio_mult_S$tbins_mid[!is.na(Fig11_bio_mult_S$beta1)], Fig11_bio_mult_S$beta1[!is.na(Fig11_bio_mult_S$beta1)], cex=0.6, pch=22, col="black", bg="grey50") arrows(Fig11_bio_mult_S$tbins_mid[!is.na(Fig11_bio_mult_S$alpha1)], Fig11_bio_mult_S$alpha1[!is.na(Fig11_bio_mult_S$alpha1)]-Fig11_bio_mult_S$alpha_CI_1[!is.na(!is.na(Fig11_bio_mult_S$alpha_CI_1))], Fig11_bio_mult_S$tbins_mid[!is.na(Fig11_bio_mult_S$alpha1)], Fig11_bio_mult_S$alpha1[!is.na(Fig11_bio_mult_S$alpha1)]+Fig11_bio_mult_S$alpha_CI_1[!is.na(!is.na(Fig11_bio_mult_S$alpha_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig11_bio_mult_S$tbins_mid[!is.na(Fig11_bio_mult_S$alpha1)], Fig11_bio_mult_S$alpha1[!is.na(Fig11_bio_mult_S$alpha1)], col="black") points(Fig11_bio_mult_S$tbins_mid[!is.na(Fig11_bio_mult_S$alpha1)], Fig11_bio_mult_S$alpha1[!is.na(Fig11_bio_mult_S$alpha1)], cex=0.6, pch=23, col="black", bg="grey50") dev.off() pdf(file="Rplot_afig11b.pdf", width=2.7, height=2.2) par(mar=c(1,1,1,1)) plot(Fig11_bio_mult_shan$tbins_mid[!is.na(Fig11_bio_mult_shan$gamma)], Fig11_bio_mult_shan$gamma[!is.na(Fig11_bio_mult_shan$gamma)], cex=0.6, pch=21, col="black", bg="black", type="o", ylim= c(0,max(na.omit(Fig11_bio_mult_shan$gamma+Fig11_bio_mult_shan$gamma_CI)))) arrows(Fig11_bio_mult_shan$tbins_mid[!is.na(Fig11_bio_mult_shan$gamma)], Fig11_bio_mult_shan$gamma[!is.na(Fig11_bio_mult_shan$gamma)]-Fig11_bio_mult_shan$gamma_CI[!is.na(!is.na(Fig11_bio_mult_shan$gamma_CI))], Fig11_bio_mult_shan$tbins_mid[!is.na(Fig11_bio_mult_shan$gamma)], Fig11_bio_mult_shan$gamma[!is.na(Fig11_bio_mult_shan$gamma)]+Fig11_bio_mult_shan$gamma_CI[!is.na(!is.na(Fig11_bio_mult_shan$gamma_CI))], col="black",length=0.01, angle=90, code=3) arrows(Fig11_bio_mult_shan$tbins_mid[!is.na(Fig11_bio_mult_shan$beta_CI_1)], Fig11_bio_mult_shan$beta1[!is.na(Fig11_bio_mult_shan$beta1)]-Fig11_bio_mult_shan$beta_CI_1[!is.na(!is.na(Fig11_bio_mult_shan$beta_CI_1))], Fig11_bio_mult_shan$tbins_mid[!is.na(Fig11_bio_mult_shan$beta1)], Fig11_bio_mult_shan$beta1[!is.na(Fig11_bio_mult_shan$beta1)]+Fig11_bio_mult_shan$beta_CI_1[!is.na(!is.na(Fig11_bio_mult_shan$beta_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig11_bio_mult_shan$tbins_mid[!is.na(Fig11_bio_mult_shan$beta1)], Fig11_bio_mult_shan$beta1[!is.na(Fig11_bio_mult_shan$beta1)], col="black") points(Fig11_bio_mult_shan$tbins_mid[!is.na(Fig11_bio_mult_shan$beta1)], Fig11_bio_mult_shan$beta1[!is.na(Fig11_bio_mult_shan$beta1)], cex=0.6, pch=22, col="black", bg="grey50") arrows(Fig11_bio_mult_shan$tbins_mid[!is.na(Fig11_bio_mult_shan$alpha1)], Fig11_bio_mult_shan$alpha1[!is.na(Fig11_bio_mult_shan$alpha1)]-Fig11_bio_mult_shan$alpha_CI_1[!is.na(!is.na(Fig11_bio_mult_shan$alpha_CI_1))], Fig11_bio_mult_shan$tbins_mid[!is.na(Fig11_bio_mult_shan$alpha1)], Fig11_bio_mult_shan$alpha1[!is.na(Fig11_bio_mult_shan$alpha1)]+Fig11_bio_mult_shan$alpha_CI_1[!is.na(!is.na(Fig11_bio_mult_shan$alpha_CI_1))], col="green",length=0.01, angle=90, code=3) lines(Fig11_bio_mult_shan$tbins_mid[!is.na(Fig11_bio_mult_shan$alpha1)], Fig11_bio_mult_shan$alpha1[!is.na(Fig11_bio_mult_shan$alpha1)], col="black") points(Fig11_bio_mult_shan$tbins_mid[!is.na(Fig11_bio_mult_shan$alpha1)], Fig11_bio_mult_shan$alpha1[!is.na(Fig11_bio_mult_shan$alpha1)], cex=0.6, pch=23, col="black", bg="grey50") dev.off() pdf(file="Rplot_afig11c.pdf", width=2.7, height=2.2) par(mar=c(1,1,1,1)) plot(Fig11_bio_mult_sim$tbins_mid[!is.na(Fig11_bio_mult_sim$gamma)],Fig11_bio_mult_sim$gamma[!is.na(Fig11_bio_mult_sim$gamma)], cex=0.6, pch=21, col="black", bg="black", type="o", ylim= c(0,max(na.omit(Fig11_bio_mult_sim$gamma+Fig11_bio_mult_sim$gamma_CI)))) arrows(Fig11_bio_mult_sim$tbins_mid[!is.na(Fig11_bio_mult_sim$gamma)], Fig11_bio_mult_sim$gamma[!is.na(Fig11_bio_mult_sim$gamma)]-Fig11_bio_mult_sim$gamma_CI[!is.na(!is.na(Fig11_bio_mult_sim$gamma_CI))], Fig11_bio_mult_sim$tbins_mid[!is.na(Fig11_bio_mult_sim$gamma)], Fig11_bio_mult_sim$gamma[!is.na(Fig11_bio_mult_sim$gamma)]+Fig11_bio_mult_sim$gamma_CI[!is.na(!is.na(Fig11_bio_mult_sim$gamma_CI))], col="black",length=0.01, angle=90, code=3) arrows(Fig11_bio_mult_sim$tbins_mid[!is.na(Fig11_bio_mult_sim$beta_CI_1)], Fig11_bio_mult_sim$beta1[!is.na(Fig11_bio_mult_sim$beta1)]-Fig11_bio_mult_sim$beta_CI_1[!is.na(!is.na(Fig11_bio_mult_sim$beta_CI_1))], Fig11_bio_mult_sim$tbins_mid[!is.na(Fig11_bio_mult_sim$beta1)], Fig11_bio_mult_sim$beta1[!is.na(Fig11_bio_mult_sim$beta1)]+Fig11_bio_mult_sim$beta_CI_1[!is.na(!is.na(Fig11_bio_mult_sim$beta_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig11_bio_mult_sim$tbins_mid[!is.na(Fig11_bio_mult_sim$beta1)], Fig11_bio_mult_sim$beta1[!is.na(Fig11_bio_mult_sim$beta1)], col="black") points(Fig11_bio_mult_sim$tbins_mid[!is.na(Fig11_bio_mult_sim$beta1)], Fig11_bio_mult_sim$beta1[!is.na(Fig11_bio_mult_sim$beta1)], cex=0.6, pch=22, col="black", bg="grey50") arrows(Fig11_bio_mult_sim$tbins_mid[!is.na(Fig11_bio_mult_sim$alpha1)], Fig11_bio_mult_sim$alpha1[!is.na(Fig11_bio_mult_sim$alpha1)]-Fig11_bio_mult_sim$alpha_CI_1[!is.na(!is.na(Fig11_bio_mult_sim$alpha_CI_1))], Fig11_bio_mult_sim$tbins_mid[!is.na(Fig11_bio_mult_sim$alpha1)], Fig11_bio_mult_sim$alpha1[!is.na(Fig11_bio_mult_sim$alpha1)]+Fig11_bio_mult_sim$alpha_CI_1[!is.na(!is.na(Fig11_bio_mult_sim$alpha_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig11_bio_mult_sim$tbins_mid[!is.na(Fig11_bio_mult_sim$alpha1)], Fig11_bio_mult_sim$alpha1[!is.na(Fig11_bio_mult_sim$alpha1)], col="black") points(Fig11_bio_mult_sim$tbins_mid[!is.na(Fig11_bio_mult_sim$alpha1)], Fig11_bio_mult_sim$alpha1[!is.na(Fig11_bio_mult_sim$alpha1)], cex=0.6, pch=23, col="black", bg="grey50") dev.off() ########################################### ########################################## # Fig. 12 a-c Fig12_sil_mult_S <- read.csv("CSVs_For_Figures/Fig12_sil_partitions_2level/sil_mult_S_03_03_20.csv", row.names = 1, header =T) Fig12_sil_mult_shan <- read.csv("CSVs_For_Figures/Fig12_sil_partitions_2level/sil_mult_shan_03_03_20.csv", row.names = 1, header =T) Fig12_sil_mult_sim <- read.csv("CSVs_For_Figures/Fig12_sil_partitions_2level/sil_mult_sim_03_03_20.csv", row.names = 1, header =T) Fig12_sil_mult_S[,"tbins_mid"] = tbins_mid Fig12_sil_mult_shan[,"tbins_mid"] = tbins_mid Fig12_sil_mult_sim[,"tbins_mid"] = tbins_mid pdf(file="Rplot_afig12a.pdf", width=2.7, height=2.2) par(mar=c(1,1,1,1)) plot(Fig12_sil_mult_S$tbins_mid[!is.na(Fig12_sil_mult_S$gamma)],Fig12_sil_mult_S$gamma[!is.na(Fig12_sil_mult_S$gamma)], cex=0.6, pch=21, col="black", bg="black", type="o", xlim=c(-471,-420), ylim= c(0,max(na.omit(Fig12_sil_mult_S$gamma+Fig12_sil_mult_S$gamma_CI)))) arrows(Fig12_sil_mult_S$tbins_mid[!is.na(Fig12_sil_mult_S$gamma)], Fig12_sil_mult_S$gamma[!is.na(Fig12_sil_mult_S$gamma)]-Fig12_sil_mult_S$gamma_CI[!is.na(!is.na(Fig12_sil_mult_S$gamma_CI))], Fig12_sil_mult_S$tbins_mid[!is.na(Fig12_sil_mult_S$gamma)], Fig12_sil_mult_S$gamma[!is.na(Fig12_sil_mult_S$gamma)]+Fig12_sil_mult_S$gamma_CI[!is.na(!is.na(Fig12_sil_mult_S$gamma_CI))], col="black",length=0.01, angle=90, code=3) arrows(Fig12_sil_mult_S$tbins_mid[!is.na(Fig12_sil_mult_S$beta_CI_1)], Fig12_sil_mult_S$beta1[!is.na(Fig12_sil_mult_S$beta1)]-Fig12_sil_mult_S$beta_CI_1[!is.na(!is.na(Fig12_sil_mult_S$beta_CI_1))], Fig12_sil_mult_S$tbins_mid[!is.na(Fig12_sil_mult_S$beta1)], Fig12_sil_mult_S$beta1[!is.na(Fig12_sil_mult_S$beta1)]+Fig12_sil_mult_S$beta_CI_1[!is.na(!is.na(Fig12_sil_mult_S$beta_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig12_sil_mult_S$tbins_mid[!is.na(Fig12_sil_mult_S$beta1)], Fig12_sil_mult_S$beta1[!is.na(Fig12_sil_mult_S$beta1)], col="black") points(Fig12_sil_mult_S$tbins_mid[!is.na(Fig12_sil_mult_S$beta1)], Fig12_sil_mult_S$beta1[!is.na(Fig12_sil_mult_S$beta1)], cex=0.6, pch=22, col="black", bg="grey50") arrows(Fig12_sil_mult_S$tbins_mid[!is.na(Fig12_sil_mult_S$alpha1)], Fig12_sil_mult_S$alpha1[!is.na(Fig12_sil_mult_S$alpha1)]-Fig12_sil_mult_S$alpha_CI_1[!is.na(!is.na(Fig12_sil_mult_S$alpha_CI_1))], Fig12_sil_mult_S$tbins_mid[!is.na(Fig12_sil_mult_S$alpha1)], Fig12_sil_mult_S$alpha1[!is.na(Fig12_sil_mult_S$alpha1)]+Fig12_sil_mult_S$alpha_CI_1[!is.na(!is.na(Fig12_sil_mult_S$alpha_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig12_sil_mult_S$tbins_mid[!is.na(Fig12_sil_mult_S$alpha1)], Fig12_sil_mult_S$alpha1[!is.na(Fig12_sil_mult_S$alpha1)], col="black") points(Fig12_sil_mult_S$tbins_mid[!is.na(Fig12_sil_mult_S$alpha1)], Fig12_sil_mult_S$alpha1[!is.na(Fig12_sil_mult_S$alpha1)], cex=0.6, pch=23, col="black", bg="grey50") dev.off() pdf(file="Rplot_afig12b.pdf", width=2.7, height=2.2) par(mar=c(1,1,1,1)) plot(Fig12_sil_mult_shan$tbins_mid[!is.na(Fig12_sil_mult_shan$gamma)],Fig12_sil_mult_shan$gamma[!is.na(Fig12_sil_mult_shan$gamma)], cex=0.6, pch=21, col="black", bg="black", type="o", xlim=c(-471,-420), ylim= c(0,max(na.omit(Fig12_sil_mult_shan$gamma+Fig12_sil_mult_shan$gamma_CI)))) arrows(Fig12_sil_mult_shan$tbins_mid[!is.na(Fig12_sil_mult_shan$gamma)], Fig12_sil_mult_shan$gamma[!is.na(Fig12_sil_mult_shan$gamma)]-Fig12_sil_mult_shan$gamma_CI[!is.na(!is.na(Fig12_sil_mult_shan$gamma_CI))], Fig12_sil_mult_shan$tbins_mid[!is.na(Fig12_sil_mult_shan$gamma)], Fig12_sil_mult_shan$gamma[!is.na(Fig12_sil_mult_shan$gamma)]+Fig12_sil_mult_shan$gamma_CI[!is.na(!is.na(Fig12_sil_mult_shan$gamma_CI))], col="black",length=0.01, angle=90, code=3) arrows(Fig12_sil_mult_shan$tbins_mid[!is.na(Fig12_sil_mult_shan$beta_CI_1)], Fig12_sil_mult_shan$beta1[!is.na(Fig12_sil_mult_shan$beta1)]-Fig12_sil_mult_shan$beta_CI_1[!is.na(!is.na(Fig12_sil_mult_shan$beta_CI_1))], Fig12_sil_mult_shan$tbins_mid[!is.na(Fig12_sil_mult_shan$beta1)], Fig12_sil_mult_shan$beta1[!is.na(Fig12_sil_mult_shan$beta1)]+Fig12_sil_mult_shan$beta_CI_1[!is.na(!is.na(Fig12_sil_mult_shan$beta_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig12_sil_mult_shan$tbins_mid[!is.na(Fig12_sil_mult_shan$beta1)], Fig12_sil_mult_shan$beta1[!is.na(Fig12_sil_mult_shan$beta1)], col="black") points(Fig12_sil_mult_shan$tbins_mid[!is.na(Fig12_sil_mult_shan$beta1)], Fig12_sil_mult_shan$beta1[!is.na(Fig12_sil_mult_shan$beta1)], cex=0.6, pch=22, col="black", bg="grey50") arrows(Fig12_sil_mult_shan$tbins_mid[!is.na(Fig12_sil_mult_shan$alpha1)], Fig12_sil_mult_shan$alpha1[!is.na(Fig12_sil_mult_shan$alpha1)]-Fig12_sil_mult_shan$alpha_CI_1[!is.na(!is.na(Fig12_sil_mult_shan$alpha_CI_1))], Fig12_sil_mult_shan$tbins_mid[!is.na(Fig12_sil_mult_shan$alpha1)], Fig12_sil_mult_shan$alpha1[!is.na(Fig12_sil_mult_shan$alpha1)]+Fig12_sil_mult_shan$alpha_CI_1[!is.na(!is.na(Fig12_sil_mult_shan$alpha_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig12_sil_mult_shan$tbins_mid[!is.na(Fig12_sil_mult_shan$alpha1)], Fig12_sil_mult_shan$alpha1[!is.na(Fig12_sil_mult_shan$alpha1)], col="black") points(Fig12_sil_mult_shan$tbins_mid[!is.na(Fig12_sil_mult_shan$alpha1)], Fig12_sil_mult_shan$alpha1[!is.na(Fig12_sil_mult_shan$alpha1)], cex=0.6, pch=23, col="black", bg="grey50") dev.off() pdf(file="Rplot_afig12c.pdf", width=2.7, height=2.2) par(mar=c(1,1,1,1)) plot(Fig12_sil_mult_sim$tbins_mid[!is.na(Fig12_sil_mult_sim$gamma)],Fig12_sil_mult_sim$gamma[!is.na(Fig12_sil_mult_sim$gamma)], cex=0.6, pch=21, col="black", bg="black", type="o", xlim=c(-471,-420), ylim= c(0,max(na.omit(Fig12_sil_mult_sim$gamma+Fig12_sil_mult_sim$gamma_CI)))) arrows(Fig12_sil_mult_sim$tbins_mid[!is.na(Fig12_sil_mult_sim$gamma)], Fig12_sil_mult_sim$gamma[!is.na(Fig12_sil_mult_sim$gamma)]-Fig12_sil_mult_sim$gamma_CI[!is.na(!is.na(Fig12_sil_mult_sim$gamma_CI))], Fig12_sil_mult_sim$tbins_mid[!is.na(Fig12_sil_mult_sim$gamma)], Fig12_sil_mult_sim$gamma[!is.na(Fig12_sil_mult_sim$gamma)]+Fig12_sil_mult_sim$gamma_CI[!is.na(!is.na(Fig12_sil_mult_sim$gamma_CI))], col="black",length=0.01, angle=90, code=3) arrows(Fig12_sil_mult_sim$tbins_mid[!is.na(Fig12_sil_mult_sim$beta_CI_1)], Fig12_sil_mult_sim$beta1[!is.na(Fig12_sil_mult_sim$beta1)]-Fig12_sil_mult_sim$beta_CI_1[!is.na(!is.na(Fig12_sil_mult_sim$beta_CI_1))], Fig12_sil_mult_sim$tbins_mid[!is.na(Fig12_sil_mult_sim$beta1)], Fig12_sil_mult_sim$beta1[!is.na(Fig12_sil_mult_sim$beta1)]+Fig12_sil_mult_sim$beta_CI_1[!is.na(!is.na(Fig12_sil_mult_sim$beta_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig12_sil_mult_sim$tbins_mid[!is.na(Fig12_sil_mult_sim$beta1)], Fig12_sil_mult_sim$beta1[!is.na(Fig12_sil_mult_sim$beta1)], col="black") points(Fig12_sil_mult_sim$tbins_mid[!is.na(Fig12_sil_mult_sim$beta1)], Fig12_sil_mult_sim$beta1[!is.na(Fig12_sil_mult_sim$beta1)], cex=0.6, pch=22, col="black", bg="grey50") arrows(Fig12_sil_mult_sim$tbins_mid[!is.na(Fig12_sil_mult_sim$alpha1)], Fig12_sil_mult_sim$alpha1[!is.na(Fig12_sil_mult_sim$alpha1)]-Fig12_sil_mult_sim$alpha_CI_1[!is.na(!is.na(Fig12_sil_mult_sim$alpha_CI_1))], Fig12_sil_mult_sim$tbins_mid[!is.na(Fig12_sil_mult_sim$alpha1)], Fig12_sil_mult_sim$alpha1[!is.na(Fig12_sil_mult_sim$alpha1)]+Fig12_sil_mult_sim$alpha_CI_1[!is.na(!is.na(Fig12_sil_mult_sim$alpha_CI_1))], col="black",length=0.01, angle=90, code=3) lines(Fig12_sil_mult_sim$tbins_mid[!is.na(Fig12_sil_mult_sim$alpha1)], Fig12_sil_mult_sim$alpha1[!is.na(Fig12_sil_mult_sim$alpha1)], col="black") points(Fig12_sil_mult_sim$tbins_mid[!is.na(Fig12_sil_mult_sim$alpha1)], Fig12_sil_mult_sim$alpha1[!is.na(Fig12_sil_mult_sim$alpha1)], cex=0.6, pch=23, col="black", bg="grey50") dev.off() ########################################### ########################################## # sitemaps library(ggplot2) library(ggmap) library(maps) library(mapdata) library(vegan) bbu = unique(brachs_binned_es[,2:4]) for (i in 2:length(tbins)) { cns <- tbins[i] sub_ee <- brachs_binned_es[brachs_binned_es$bb1 == cns,] myfile <- file.path(getwd(), paste0("site_plot_", cns, ".tiff")) tiff(myfile, width = 4, height = 4, units = 'in', res = 300) baltic.map <- map(col = "grey80", border = "grey40", fill = TRUE, xlim = c(20, 29), ylim = c(54, 60), mar = rep(0.1, 4)) points(sub_ee$longitude, sub_ee$latitude, cex =0.3, pch = 19) dev.off() }