inst/docs/papers/attic/leukemia2016/mkExcelDemo.R

In SEERaBomb: SEER and Atomic Bomb Survivor Data Analysis Tools

# mkExcelDemo.R
rm(list=ls()) 
library(SEERaBomb) 
library(tidyverse)
library(magrittr)
if (1) {
  load("~/data/SEER/mrgd/cancDef.RData") 
  load("~/data/SEER/mrgd/popsae.RData") 
  canc=canc%>%select(-reg,-radiatn,-histo3,-ICD9)
  canc=canc%>%filter(cancer!="benign")
  canc%<>%separate(trt,c("trt","trtc"))
  canc$trt=factor(canc$trt)
  popsa=popsae%>%group_by(db,race,sex,age,year)%>%summarize(py=sum(py)) # sum on regs
  m=seerSet(canc,popsa,Sex="Male",ageStart=0,ageEnd=100) 
  f=seerSet(canc,popsa,Sex="Female",ageStart=0,ageEnd=100) 
  m=mk2D(m) 
  f=mk2D(f) 
  brks=c(0,0.5,1,2,3,10)
  m=tsd(m,brks=brks,trts=c("rad","noRad")) 
  f=tsd(f,brks=brks,trts=c("rad","noRad"))
  system.time(save(m,f,file="~/Results/amlMDS/mfExcel.RData")) #~10 seconds 
} else {
  load("~/Results/amlMDS/mfExcel.RData") 
}

mkExcelTsd(m,"b0_0.5_1_2_3_10",outDir="~/Results/amlMDS",outName="males") #out filenames are otherwise coded. 
mkExcelTsd(f,"b0_0.5_1_2_3_10",outDir="~/Results/amlMDS",outName="females")
mkExcelTsd(m,"b0_0.5_1_2_3_10",outDir="~/Results/amlMDS",outName="males",flip=T)
mkExcelTsd(f,"b0_0.5_1_2_3_10",outDir="~/Results/amlMDS",outName="females",flip=T)

# test using csd instead of tsd
if(1) {
  mc=csd(m,brkst=c(0,0.5,1,2,3,10),trts=c("rad","noRad")) 
  fc=csd(f,brkst=c(0,0.5,1,2,3,10),trts=c("rad","noRad")) 
  system.time(save(mc,fc,file="~/Results/amlMDS/mfExcelCSD.RData")) # 33 secs
} else {
  load("~/Results/amlMDS/mfExcelCSD.RData") 
}
mkExcelCsd(mc,"b0_0.5_1_2_3_10",biny="[1975,2017)",outDir="~/Results/amlMDS",outName="malesCsd") 
mkExcelCsd(fc,"b0_0.5_1_2_3_10",biny="[1975,2017)",outDir="~/Results/amlMDS",outName="femalesCsd") 
mkExcelCsd(mc,"b0_0.5_1_2_3_10",biny="[1975,2017)",outDir="~/Results/amlMDS",outName="malesCsd",flip=T) 
mkExcelCsd(fc,"b0_0.5_1_2_3_10",biny="[1975,2017)",outDir="~/Results/amlMDS",outName="femalesCsd",flip=T)