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# specificFirstRRR.R (Radiation Relative Risk variant of specificFirst.R)
rm(list=ls())
library(SEERaBomb)
library(reshape2)
system.time(load("~/Results/amlMDS/pm.RData")) # 4 secs to load.
system.time(load("~/Results/amlMDS/pf.RData")) # 4 secs to load.
.simpleCap <- function(s) paste(toupper(substring(s, 1, 1)), substring(s, 2),sep = "", collapse = " ")
names(pm$L)
hires=TRUE
hires=FALSE
if (hires) {
brks=c(0,0.25,0.5,0.75,1,1.5,2,2.5,3,4,5,6,8,10,12)
FirstS=c("prostate","breast") # first cancers to be plotted
} else { # intermediate level resolution
FirstS=c("NHL","lung")
brks=c(0,1,2,3,6,9,12)
}
dm=mkDF(pm,brks)
df=mkDF(pf,brks)
d=rbind(cbind(df,Sex="Female"),cbind(dm,Sex="Male"))
d=d%>%filter(cancer1%in%FirstS)%>%select(Sex,cancer1,cancer2,trt,O,E,t,int)
d=d%>%filter(!((cancer1=="breast")&(Sex=="Male"))) # remove male breast cancer cases
head(d)
tail(d)
mkRRR=function(d,first,Ncol=5000) {
# first="prostate"
d0=d%>%filter(cancer1==first,trt=="noRad")
di=d%>%filter(cancer1==first,trt=="rad")
O=d0$O
E=d0$E
Oi=di$O
Ei=di$E
Xi=matrix(0,ncol=Ncol,nrow=length(Oi))
X=matrix(0,ncol=Ncol,nrow=length(O))
for (i in 1:Ncol) Xi[,i]=rpois(n=length(Oi),lambda=Oi)
for (i in 1:Ncol) X[,i]=rpois(n=length(O),lambda=O)
X=(Xi/X)*(E/Ei)%*%t(rep(1,Ncol))
T=t(apply(X,1,function(x) quantile(x,probs=c(0.025,0.5,0.975),na.rm=TRUE)))
data.frame(Sex=d0$Sex,cancer1=d0$cancer1,cancer2=d0$cancer2,RR=T[,2],L=T[,1],U=T[,3],t=d0$t)
}
graphics.off()
quartz(width=7,height=4)
theme_set(theme_bw())
theme_update(legend.position = "none")
theme_update(axis.text=element_text(size=rel(1.2)),
axis.title=element_text(size=rel(1.3)),
legend.title=element_text(size=rel(0.9)),
legend.text=element_text(size=rel(0.9)),
strip.text = element_text(size = rel(1.5)))
for (First in FirstS) {
(D=mkRRR(d,First))
g=qplot(x=t,y=RR,data=D,geom=c("line","point"),#xlim=c(-.1,24),
xlab=paste("Years Since",.simpleCap(First),"First Cancer"),ylab="Radiation Relative Risk Ratio")
if (First=="breast"|First=="prostate") g=g+facet_grid(cancer2~.,scales="free")+geom_abline(intercept=1, slope=0) else
g=g+facet_grid(Sex~cancer2,scales="free")+geom_abline(intercept=1, slope=0) #g=g+scale_y_continuous(breaks=1:10)
g=g+geom_errorbar(aes(ymin=L,ymax=U,width=.15))
print(g)
ggsave(paste0("~/Results/amlMDS/",First,ifelse(hires,"hires",""),"RRR.png"))
ggsave(paste0("~/Results/amlMDS/",First,ifelse(hires,"hires",""),"RRR.eps"))
} # for loop on first types
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