Post-proofing update

code_analysis.Rmd

@@ -185,7 +185,8 @@ graph <- graph +
   coord_cartesian(ylim = c(0, 300))
 setwd(fig.loc)
 svg(filename = "fig2timeseries.svg", width = (9*2/2.5), height = (6*2/2.5)) # Fig. 2
-graph
+graph + geom_vline(aes(xintercept = as.numeric(as.Date("2015-01-01"))),
+                   linetype = "dashed")
 dev.off()
 ```
 
@@ -347,6 +348,7 @@ while (counter < N.desired) {
 }
 hist(incub.distrib2)
 round(mean(incub.distrib2)) # 6mo (§2.3)
+round(sd(incub.distrib2)) # 4mo (SI §S6)
 
 p.data = c(0.01,0.05,0.1,0.2,0.25,0.3,0.4,0.5,0.6,0.7,0.75,0.8,0.9,0.95,0.99)
 q.data = c(0,5,10,15,18,21,28,31,36,47,57,61,92,145,246)+1 # add 1d so lnorm can fit
@@ -437,6 +439,7 @@ lines(x = 1:64, y = Vaishali.upper[9:72], lwd = 2, lty = 2, col = "#56B4E9")
 lines(x = 1:64, y = Vaishali.Re[9:72], lwd = 4, col = "#56B4E9")
 abline(h = 1)
 abline(v = (sliding.window+0.5), lty = 2)
+abline(v = 37, lty = "dotted")
 legend(x = c(14, 33), y = c(1.3, 1.67), text.width = 1, 
        legend = c('Vaishali district mean', '95%CI', 'Other 32 districts mean', '95%CI'), 
        col = c("#56B4E9", "#56B4E9", "black", "black"), 
@@ -455,6 +458,7 @@ for (district in 2:32) {
 lines(x = 1:64, y = alldistrict.Re[33,9:72], col = "#56B4E9", lwd = 4)
 abline(h = 1)
 abline(v = (sliding.window+0.5), lty = 2)
+abline(v = 37, lty = "dotted")
 axis(1, at = c(1,13,25,37,49,64), labels = c("Jan-12","Jan-13","Jan-14","Jan-15","Jan-16","Apr-17        "))
 axis(2, at = c(0.1,0.2,0.5,1,2,5,10,20), 
      labels = c("0·1","0·2","0·5","1","2","5","10","20"))