km_estimates | R Documentation |
km_estimates
Kaplan-Meier risk estimates for Net Reclassification Index analysis
for Cox Regression Models
km_estimates(data, p0, p1, time, status, t_risk, cutoff)
data |
Data frame with relevant predictors |
p0 |
risk outcome probabilities for reference model. |
p1 |
risk outcome probabilities for new model. |
time |
Character vector. Name of time variable. |
status |
Character vector. Name of status variable. |
t_risk |
Follow-up value to calculate cases, controls. See details. |
cutoff |
A numerical vector that defines the outcome probability cutoff values. |
Follow-up for which cases and controls are determined. For censored cases before this follow-up
the expected risk of being a case is calculated by using the Kaplan-Meier value to calculate
the expected number of cases. These expected numbers are used to calculate the NRI proportions.
(These are not shown by function nricens
).
An object from which the following objects can be extracted:
data
dataset.
prob_orig
outcome risk probabilities at t_risk for reference model.
prob_new
outcome risk probabilities at t_risk for new model.
time
name of time variable.
status
name of status variable.
cutoff
cutoff value for survival probability.
t_risk
follow-up time used to calculate outcome (risk) probabilities.
reclass_totals
table with total reclassification numbers.
reclass_cases
table with reclassification numbers for cases.
reclass_controls
table with reclassification numbers for controls.
totals
totals of controls, cases, censored cases.
km_est
totals of cases calculated using Kaplan-Meiers risk estimates.
nri_est
reclassification measures.
Martijn Heymans, 2023
Cook NR, Ridker PM. Advances in measuring the effect of individual predictors of cardiovascular risk: the role of reclassification measures. Ann Intern Med. 2009;150(11):795-802.
Steyerberg EW, Pencina MJ. Reclassification calculations for persons with incomplete follow-up. Ann Intern Med. 2010;152(3):195-6 (author reply 196-7).
Pencina MJ, D'Agostino RB Sr, Steyerberg EW. Extensions of net reclassification improvement calculations to measure usefulness of new biomarkers. Stat Med. 2011;30(1):11-21
Inoue E (2018). nricens: NRI for Risk Prediction Models with Time to Event and Binary Response Data. R package version 1.6, <https://CRAN.R-project.org/package=nricens>.
library(survival)
lbpmicox1 <- subset(psfmi::lbpmicox, Impnr==1) # extract dataset
fit_cox0 <-
coxph(Surv(Time, Status) ~ Duration + Pain, data=lbpmicox1, x=TRUE)
fit_cox1 <-
coxph(Surv(Time, Status) ~ Duration + Pain + Function + Radiation,
data=lbpmicox1, x=TRUE)
p0 <- risk_coxph(fit_cox0, t_risk=80)
p1 <- risk_coxph(fit_cox1, t_risk=80)
res_km <- km_estimates(data=lbpmicox1,
p0=p0,
p1=p1,
time = "Time",
status = "Status",
cutoff=0.45,
t_risk=80)
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