Nothing
mkDF<-function(seerSet,srs=NULL) {
age=trt=race=surv=year=py=popsa=cancer1=nO=O=E=ageE=ageEci=ageO=int=sig2O=ageOci=NULL
if (is.null(seerSet$L)) stop("seerSet L field is empty. Please run tsd on your seerSet object!") else {
nms=names(seerSet$L)
indx=seerSet$active
cat("Current active series:",indx,"\n",sep="")
print(seerSet$series)
if (is.null(srs)) {indx=seerSet$active #grab most recent
cat(paste0("Using (active) series ",indx,", i.e. ", nms[indx],".\n"))
# cat(paste0("Using active time series in L. Index:",indx,"\n"))
}
if (length(srs)>1) {
cat("... collapsing brks vector to a single string.\n")
srs=paste0("b",paste(srs,collapse="_"))
}
if (is.character(srs)){ indx=srs #grab ith most recent
cat(paste0("Using series ",which(indx==nms),", i.e. ", indx,".\n"))
}
if (is.numeric(srs)){ indx=srs #grab ith most recent
cat("Using series ",indx,", i.e. ", nms[indx],".\n",sep="")
}
L=seerSet$L[[indx]]
}
# library(reshape2);library(plyr);library(SEERaBomb)
# load("~/Results/amlMDS/aveAgeFull.RData")
# seerSet=pm
# L=seerSet$L[[seerSet$active]]
secondS=seerSet$secondS
firstS=L$firstS
# options(stringsAsFactors=FALSE)
f=data.frame(cancer1=firstS)
# f$cancer1
fs=merge(f,data.frame(cancer2=secondS))%>%arrange(cancer1)
# fs$cancer1
funf=function(x){
y=left_join(f,x,by=c("cancer1"))
y[is.na(y)]=0
y
}
funfs=function(x,by){
y=left_join(fs,x,by=by)
y[is.na(y[,"n"]),"n"]=0
y
}
funOE=function(x,by,out="O"){
x=melt(x)
names(x)=c("cancer1","cancer2",out)
left_join(fs,x,by=by)
# y=left_join(fs,x,by=by)
# y[is.na(y[,"n"]),"n"]=0
# y
}
trts=L$trtS
# ae=NULL
ao=NULL
pya=NULL
o=NULL
e=NULL
options(warn=-1)
for (i in trts){
# i=trts[1]
# ae=rbind(ae,cbind(ldply(lapply(L[[i]]$AgeE,funfs,by=c("cancer1"))),trt=i))
pya=rbind(pya,cbind(ldply(lapply(L[[i]]$PYA,funfs,by=c("cancer1"))),trt=i))
ao=rbind(ao,cbind(ldply(lapply(L[[i]]$AgeO,funfs,by=c("cancer1","cancer2"))),trt=i))
# py=rbind(py,cbind(ldply(lapply(L[[i]]$PY1,funf)),trt=i))
o=rbind(o,cbind(ldply(lapply(L[[i]]$O,funOE,by=c("cancer1","cancer2"),out="O")),trt=i))
e=rbind(e,cbind(ldply(lapply(L[[i]]$E,funOE,by=c("cancer1","cancer2"),out="E")),trt=i))
}
# melt(L[[i]]$O[[1]])
# lapply(L[[i]]$O,dim)
# lapply(L[[i]]$E,dim)
options(warn=0)
# head(ae,2)
head(pya,2)
head(ao,2)
head(o,2)
head(e,2)
names(ao)[4:5]=c("ageO","sig2O")
# names(ae)[1]=c("int")
names(pya)[1]=c("int")
# d=cbind(ae,ao%>%select(ageO:nO))
# d=ao%>%select(ageO:nO)
# py=as.data.frame(lapply(pya,rep,each=2))
# py=as.data.frame(lapply(py,rep,each=2))
# head(py,2)
# d=cbind(d,py%>%select(py1:midPnt))
# d=cbind(d,py%>%select(py:t))
d=cbind(pya%>%select(int:trt),ao%>%select(ageO:sig2O))
d=cbind(d,O=o$O,E=e$E)
d$int=factor(d$int,levels=unique(d$int))
head(d)
d=d%>%mutate(RR=O/E,
rrL=qchisq(.025,2*O)/(2*E),
rrU=qchisq(.975,2*O+2)/(2*E))
# glimpse(d)
sem=sqrt(d$sig2/d$n)
options(warn=-1) # expect warnings on t df of 0 and -1
ci95=qt(0.975,d$n-1)*sem
d$aeL=d$age-ci95
d$aeU=d$age+ci95
sem=sqrt(d$sig2O/d$O)
ci95=qt(0.975,d$O-1)*sem
options(warn=0) # turn off expect warnings on t df of 0 and -1
d$aoL=d$ageO-ci95
d$aoU=d$ageO+ci95
i=sapply(d,is.numeric)
d[i]=round(d[i],2)
# glimpse(d)
d
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.