svycox.validate {SvyNom} | R Documentation |
Validating a nomogram for a survey-weighted Cox model
Description
Validates a nomogram for a survey-weighted Cox model using bootstrap.
Usage
svycox.validate(.boot.index, .nom, .data)
Arguments
.boot.index |
a matrix of bootstrap sample indicators with the number of rows the same as the number of rows in the data on which the nomogram was created and the number of columns being the number of bootstrap samples |
.nom |
a nomogram object returned from svycox.nomogram |
.data |
contains the dataset on which the validation will take place |
Details
Note that generating the bootstrap sample is design dependent and it is not part of the function. The user has to generate the bootstrap samples consistent with the design used. An example of how the bootstrap sample was generated for the dataset is presented in the reference below.
Value
prints the estimated optimism and returns the vector of optimism values for each bootstrap sample which can be used to summarize the validation with the measure of choice
References
Marinela Capanu, Mithat Gonen (2015). Building a Nomogram for Survey-Weighted Cox Models Using R. Journal of Statistical Software, Code Snippets, 64(1), 1-17. URL https://www.jstatsoft.org/v64/c01/.
Examples
bootit=200
library(survey)
library(rms)
data(noNA)
dd=datadist(noNA)
options(datadist="dd")
dstr2=svydesign(id=~1, strata=~group, prob=~inv_weight, fpc=~ssize, data=noNA)
mynom=svycox.nomogram(.design=dstr2, .model=Surv(survival,surv_cens)~ECOG+liver_only+Alb+Hb+Age+
Differentiation+Gt_1_m1site+lymph_only, .data=noNA, pred.at=24, fun.lab="Prob of 2 Yr OS")
cases=which(noNA$group=="long")
controls=which(noNA$group=="<24")
boot.index=matrix(NA,nrow(noNA),bootit)
for(i in 1:bootit){
boot.index[,i]=c(sample(cases,replace=TRUE),sample(controls,replace=TRUE))
}
myval=svycox.validate(boot.index,mynom,noNA)