1 files changed, 53 insertions, 6 deletions
diff --git a/R Scripts/plot-data-prep.R b/R Scripts/plot-data-prep.R
index b56ca1f..d577b5d 100644
--- a/R Scripts/plot-data-prep.R
+++ b/R Scripts/plot-data-prep.R
@@ -1,7 +1,10 @@
 library(igraph)
 library(grid)
+library(gridBase)
 library(gridExtra)
 
+############
+###### Data Prep Diagram
 # create bipartite graph
 edges = c(1,6,
           1,7,
@@ -15,15 +18,15 @@ edges = c(1,6,
           5,9)
 g = graph.bipartite(c(rep(T,5),rep(F,5)),edges)
 
-# need to plot table separately from graphs and combine outside R
-par(mfrow=c(1,2))
-
+par(mfrow=c(1,3))
 # (A) data table
 data = data.frame(get.edgelist(g))
 data$X2 = toupper(letters[data$X2-5])
 colnames(data) = c('Event Code (EC)','Identity Code (IC)')
-grid.newpage(F)
-plot(graph(1:2),layout=matrix(c(1,1,1,1),ncol=2))
+plot.new()
+vps <- baseViewports()
+pushViewport(vps$figure)
+vp1 <-plotViewport()
 grid.table(data)
 
 # (B) bipartite person-event graph
@@ -36,7 +39,51 @@ plot(g, layout=layout[,2:1], vertex.color=cols,edge.color='black',
 
 # (C) unipartite person-person graph
 g2 = bipartite.projection(g)$proj1
-plot(g2, vertex.color='#1f78b4', edge.color='black',
+layout.g2 = layout.auto(g2)
+plot(g2, vertex.color='#1f78b4', edge.color='black',layout=layout.g2,
+     vertex.frame.color=NA,vertex.size=30,vertex.label=toupper(letters[1:5]),
+     vertex.label.color='white',vertex.label.family='sans')
+
+#############
+#### Hawkes Process Diagram
+par(mfrow=c(1,3))
+
+vics = data.frame(IC = toupper(letters[1:5]), 
+                  Victim = c(T,F,F,F,T),
+                  Day = c(3,NA,NA,NA,5))
+colnames(vics) = c('Identity Code (IC)','Victim','Infection Date')
+
+plot.new()
+vps <- baseViewports()
+pushViewport(vps$figure)
+vp1 <-plotViewport()
+grid.table(vics)
+
+cols = rep('#1f78b4',vcount(g2))
+cols[vics$Victim==T] = '#e41a1c'
+
+plot(g2, vertex.color=cols, edge.color='black',layout=layout.g2,
      vertex.frame.color=NA,vertex.size=30,vertex.label=toupper(letters[1:5]),
      vertex.label.color='white',vertex.label.family='sans')
 
+
+rate = function(x){
+  print(x)
+  r = rep(.3,length(x))
+  times = c(1,4)
+  for (time in times){
+    r[x>=time] = r[x>=time] + 1.5*exp((time-x[x>=time])/4)
+  }
+  return(r)
+}
+plot(rate,from=0,to=10,ylim=c(0,3),lwd=0,bty='l',
+     yaxt='n',xlab='Date',ylab='Infection Rate')
+mtext("Date", line = 3, side = 1)
+n = 1000
+xs = c(0,seq(0,10,length.out=n),10)
+ys = rate(xs)
+ys[c(1,n+2)] = 0
+polygon(xs,ys,col='#1f78b4',border=NA)
+
+
+