data and tutorial linked to manuscript

examples/Influenza_data/TempEst_analysis/Plot_root_tip_regression_Influenza.R

@@ -0,0 +1,29 @@
+# plot root-tip regression for several trees (Influenza dataset)
+#the original tree has 2063 leaves                                MRCA = 2010.9206    slope = 0.0027564
+#the 0.99 tree has 1729 leaves  83.8% of original n of leaves     MRCA = 2010.8562    slope = 0.0027231
+#the 0.9 tree has 1245 leaves  60.3% of original n of leaves      MRCA = 2010.7542    slope = 0.0026904
+#the 0.75 tree has 844 leaves 40.9% of original leaves            MRCA = 2010.6383    slope = 0.0026286
+#the 0.5 tree has 430 leaves 20.8% of original n of leaves        MRCA = 2010.6808    slope = 0.0027299
+
+library(ggplot2)
+
+
+ROOT1 = read.table("root_to_tip_1",head=T)
+ROOT0.99 = read.table("root_to_tip_0.99",head=T)
+ROOT0.9 = read.table("root_to_tip_0.9",head=T)
+ROOT0.75 = read.table("root_to_tip_0.75",head=T)
+ROOT0.5 = read.table("root_to_tip_0.5",head=T)
+
+pdf("root_tip_regr.pdf")
+
+ggplot(ROOT1,aes(x=date,y=distance)) + xlab("Time") + ylab("Distance from root") + 
+  scale_y_continuous(expand = c(0, 0)) +
+  theme(panel.background = element_rect(fill='white', colour='black')) +
+  scale_x_continuous(limits = c(2009, 2018)) +coord_cartesian(ylim = c(0, 0.03))+
+    geom_point(color='black', size = 2)+ 
+stat_smooth(method=lm, color ='black' ,fullrange = T,size = 0.3,level=0.99,fill='gray15')+
+    stat_smooth(method=lm,data=ROOT0.9, size = 0.3, aes(x=date,y=distance), color ='red',se=F, fullrange = T ) +
+  stat_smooth(method=lm,data=ROOT0.75, size = 0.3, aes(x=date,y=distance), color ='green',se=F, fullrange = T ) +
+stat_smooth(method=lm,data=ROOT0.5, size = 0.3, aes(x=date,y=distance), color ='blue',se=F, fullrange = T ) +
+  stat_smooth(method=lm,data=ROOT0.99, size = 0.3, aes(x=date,y=distance), color ='orange',se=F, fullrange = T )
+dev.off()

examples/Influenza_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL_res_100_LD

@@ -0,0 +1,26 @@
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examples/Influenza_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL_res_10_LD

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