require(rms)
create <- FALSE
if(create) {
d <- csv.get("hongLiData.csv", lowernames=TRUE, charfactor=TRUE)
d <-
upData(d,
labels=c(surg.discharge.days="Discharge Days",
primarysite="Primary Site",
facilitytype="Facility Type",
insurance1="Insurance",
race1="Race",
region="Region",
samefacility="Same Facility",
port.nccn.fail="outcome"))
d <- d[Cs(port.nccn.fail, surg.discharge.days, primarysite, facilitytype,
insurance1, race1, samefacility, region)]
save(d, file='nomogram2.rda', compress=TRUE)
} else load('nomogram2.rda')
ddist <- datadist(d); options(datadist='ddist')
f <- lrm(port.nccn.fail ~ surg.discharge.days + primarysite +
facilitytype + insurance1 + race1 + samefacility + region,
data=d)
for(abbrev in c(FALSE, TRUE)) {
n <- nomogram(f, lp.at=seq(-2, 5, by=0.5), fun=plogis,
fun.at=c(seq(.1, .9, by=.1), .95, .99, .999),
funlabel="Risk of Delayed PORT Initiation",
abbrev=abbrev, minlength=1, lp=FALSE)
if(! abbrev) n1 <- n else n2 <- n
}
plot(n1)
plot(n2)
attr(n2, 'info')$Abbrev
# Hong Li <liho@musc.edu>
# The variable samefacility has two categories and region has 4 categories. But in the nomogram, the variable samefacility and region are switched, i.e. samefacility has 4 categories and region has 2 categories. All other variables are correct.
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