diff options
Diffstat (limited to 'R Scripts/plot-data-prep.R')
| -rw-r--r-- | R Scripts/plot-data-prep.R | 20 |
1 files changed, 11 insertions, 9 deletions
diff --git a/R Scripts/plot-data-prep.R b/R Scripts/plot-data-prep.R index 937512a..27c2416 100644 --- a/R Scripts/plot-data-prep.R +++ b/R Scripts/plot-data-prep.R @@ -8,15 +8,15 @@ library(gridExtra) # create bipartite graph edges = c(1,6, 1,7, - 1,10, + 1,9, 2,8, 3,7, 3,8, - 3,10, + 3,9, 4,7, 4,8, 5,6, - 5,9) + 5,10) g = graph.bipartite(c(rep(T,5),rep(F,5)),edges) par(mfrow=c(1,3), mar=c(1,1,1,1)) @@ -41,7 +41,7 @@ plot(g, layout=layout[,2:1], vertex.color=cols,edge.color='black', # (C) unipartite person-person graph par(mar=rep(1,4)) g2 = bipartite.projection(g)$proj1 -layout.g2 = matrix(c(0,.33,-.75,-.33,0,-1,0,1,.75,-.33),ncol=2,byrow=T) +layout.g2 = matrix(c(0,.33,-.75,-.33,0,-1,.75,-.33,0,1),ncol=2,byrow=T) plot(g2, vertex.color='#1f78b4', edge.color='black',layout=layout.g2,rescale=F, vertex.frame.color=NA,vertex.size=30,vertex.label=toupper(letters[1:5]), vertex.label.color='white',vertex.label.family='sans') @@ -50,10 +50,11 @@ plot(g2, vertex.color='#1f78b4', edge.color='black',layout=layout.g2,rescale=F, ############################################################################## #### Hawkes Process Diagram layout(matrix(c(1,2,3,3,3,3), ncol=2, byrow = TRUE)) +par(mar=c(1,1,1,1)) vics = data.frame(IC = toupper(letters[1:5]), - Victim = c(T,F,F,F,T), - Day = c(2,NA,NA,NA,4)) + Victim = c('TRUE','FALSE','FALSE','TRUE','FALSE'), + Day = c(2,NA,NA,4,NA)) colnames(vics) = c('Identity Code (IC)','Victim','Infection Date') # A @@ -78,7 +79,7 @@ rate = function(x){ print(x) r = rep(base+0.3,length(x)) for (time in times){ - r[x>=time] = r[x>=time] + 1.5*exp((time-x[x>=time])/2) + r[x>=time] = r[x>=time] + 1.5*exp((time-x[x>=time])/2.5) } return(r) } @@ -86,7 +87,7 @@ rate = function(x){ tmin = 1 tmax = 6 n = 1000 -plot(rate,from=tmin,to=tmax,ylim=c(0,15),lwd=0,bty='l',col='white', +plot(rate,from=tmin,to=tmax,ylim=c(0,13),lwd=0,bty='l',col='white', yaxt='n',xlab='Date',ylab='Infection Rate') for(i in 1:vcount(g2)){ base <<- 3*(5-i) @@ -98,5 +99,6 @@ for(i in 1:vcount(g2)){ polygon(xs,ys,col='#1f78b4',border=NA) } axis(2, at=seq(0.3,12.3,3), lab=toupper(letters[seq(5,1,-1)]), tick=F, las=T,lwd=0) - +polygon(c(1.98,1.98,2.02,2.02),c(12,14,14,12),col='#e41a1c',border=NA) +polygon(c(3.98,3.98,4.02,4.02),c(3,5,5,3),col='#e41a1c',border=NA) |