updates for manuscript revision

Influenza_data/TempEst_analysis/Plot_root_tip_regression_Influenza.R

+# 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()

Influenza_data/TempEst_analysis/nextstrain_flu_h3n2_ha_12y_tree.new_trimmed_tree_RTL_0.5

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\ No newline at end of file

Influenza_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL_res_100_LD

+0.998865940013	1980
+0.992223203581	1880
+0.980093768618	1780
+0.964594528542	1680
+0.942983503011	1580
+0.919368390287	1480
+0.892779410875	1380
+0.865211597491	1280
+0.833444024677	1180
+0.796632323731	1080
+0.761630151885	980
+0.717102387953	880
+0.669364209884	780
+0.618294535771	680
+0.559647792692	580
+0.493484449775	480
+0.415247560698	380
+0.337576210292	280
+0.237918528053	180
+0.140643743423	99
+0.0854739189395	56
+0.0574035115182	30
+0.0393586342788	16
+0.0313735141439	9
+0.0213840212255	5
+0.0164555128084	3
\ No newline at end of file

Influenza_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL_res_10_LD

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MTB_data/MTB_tree_res_1000_LD

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