inst/docs/papers/tutorial/attic/breast2leu.R

In SEERaBomb: SEER and Atomic Bomb Survivor Data Analysis Tools

rm(list=ls());library(tidyverse);library(SEERaBomb)
load("~/data/SEER/mrgd/popsae.RData") 
(p=popsae%>%count(race,sex,age,year,wt=py)%>%rename(py=n))
load("~/data/SEER/mrgd/cancDef.RData") 
canc$cancer=fct_collapse(canc$cancer,AML=c("AML","AMLti","APL"))
secs=c("CML","AML","ALL") 
(d=canc%>%filter(sex=="Female",cancer%in%c("breast",secs)))
pf=seerSet(d,p,Sex="Female")#pooled (races) females 
pf=mk2D(pf,secondS=secs)#adds secs background rates to pf
trts=c("rad.chemo","rad.noChemo","noRad.chemo","noRad.noChemo")
pf=csd(pf,brkst=c(0,1,2,3,5,10),brksa=c(0,60),trts=trts,firstS="breast")
(D=pf$DF%>%filter(ageG=="(0,60]")) 
D=D%>%mutate(cancer2=fct_relevel(cancer2,"AML"))#make AML 1st
D$t=D$t+c(0,0.075,0.15)#shift times to separate error bars
myt=theme(legend.title=element_blank(),legend.margin=margin(0,0,0,0))
myth=theme(legend.direction="horizontal",legend.key.height=unit(.25,'lines'))
myth=myt+myth+theme(legend.position=c(.25,.95))
g=ggplot(aes(x=t,y=RR,col=cancer2),data=D)+geom_point()+geom_line()+myth+
  labs(x="Years Since Breast Cancer Diagnosis",y="Relative Risk of Leukemia")
g=g+facet_grid(rad~chemo)+geom_abline(intercept=1,slope=0) 
g+geom_errorbar(aes(ymin=rrL,ymax=rrU),width=0.05)+coord_cartesian(ylim=c(0,25)) 
ggsave("~/Results/tutorial/breast2leu.pdf",width=4,height=2.5) 

# D%>%filter(cancer2=="CML",rad=="Rad") # see values of CML RR CI at peaks
# D%>%group_by(rad,chemo)%>%summarize(O=sum(O),E=sum(E),meanPYage=weighted.mean(age,w=py)) 
# pf=csd(pf, brkst=c(0,1,2,3,5,10),brksy=c(1973,2000), brksa=c(0,60), trts=trts, firstS="breast")
# (D=pf$DF%>%filter(ageG=="(0,60]",yearG=="[2000,2016)")) #no diff in CML (0,1] of noRad.chemo