inst/docs/papers/tutorial/common.R

In SEERaBomb: SEER and Atomic Bomb Survivor Data Analysis Tools

###common.R
graphics.off();rm(list=ls())#clear plots and environment
library(tidyverse);library(SEERaBomb);library(ggsci)#load packages          
library(survival);library(survminer);library(bbmle)
load("~/data/SEER/mrgd/cancDef.RData")#load SEER cancer data
load("~/data/SEER/mrgd/popsae.RData")#load SEER population data
load("~/data/abomb/abomb.RData")#load A-bomb data
load("~/data/usMort/mrt.RData")#loads US mortality data
canc$cancer=fct_collapse(canc$cancer,AML=c("AML","AMLti","APL"))
secs=c("AML","ALL","CML")#second cancers of interest
gp=geom_point();gl=geom_line()
geRR=geom_errorbar(aes(ymin=rrL,ymax=rrU),width=.2)
ge=geom_errorbar(aes(ymin=LL,ymax=UL),width=0.2)#for absolute risks
gh=geom_hline(yintercept=1)
svts=scale_x_continuous(breaks=c(0,5,10))#surv times
agts=scale_x_continuous(breaks=c(25,50,75))#age times
sbb=theme(strip.background=element_blank())
ltb=theme(legend.margin=margin(0,0,0,0),legend.title=element_blank())
ltp=theme(legend.position="top")
lh=theme(legend.direction="horizontal")
sy=scale_y_log10()
jco=scale_color_jco()
tc=function(sz) theme_classic(base_size=sz);
gxi=xlab("Age (Years)")
gyi=ylab(quote(paste("Cases per ",10^5," Person Years")))