smoothHR {smoothHR}

Smooth Hazard Ratio Curves Taking a Reference Value

Description

Provides flexible hazard ratio curves allowing non-linear relationships between continuous predictors and survival. To better understand the effects that each continuous covariate has on the outcome, results are expressed in terms of hazard ratio curves, taking a specific covariate value as reference. Confidence bands for these curves are also derived.

Usage

smoothHR(data, time=NULL, time2=NULL, status=NULL, formula=NULL, coxfit,
status.event=NULL)

Arguments

data

A data.frame in which to interpret the variables named in the formula or in the arguments time, time2, status and coxfit.

time

For right censored data, this is the follow up time. For interval data, the first argument is the starting time for the interval.

time2

Ending time of the interval for interval censored or counting process data only. Intervals are assumed to be open on the left and closed on the right, (start, end]. For counting process data, event indicates whether an event occurred at the end of the interval.

status

The status indicator, normally 0=alive, 1=dead. Other choices are TRUE/FALSE (TRUE = death) or 1/2 (2=death). For interval censored data, the status indicator is 0=right censored, 1=event at time, 2=left censored, 3=interval censored. Although unusual, the event indicator can be omitted, in which case all subjects are assumed to have an event.

formula

A formula object, with the terms on the right after the ~ operator.

coxfit

An object of class coxph. This argument is optional, being an alternative to the arguments time, time2, status and formula.

status.event

The status indicator is a qualitative variable where usually the highest value is left for the event of interest (usually 0=alive, 1=dead). If that is not the case the status.event indicates which value denotes the event of interest.

Value

An object of class HR. There are methods for print, predict and plot. HR objects are implemented as a list with elements:

dataset

Dataset used.

coxfit

The object of class 'coxph' used.

phtest

Result from testing the proportional hazards assumption.

Author(s)

Artur Araújo and Luís Meira-Machado

References

Cadarso-Suarez, C. and Meira-Machado, L. and Kneib, T. and Gude, F. (2010). Flexible hazard ratio curves for continuous predictors in multi-state models: an application to breast cancer data. Statistical Modelling, 10(3), 291-314. doi:10.1177/1471082X0801000303

Meira-Machado, L. and Cadarso-Suárez, C. and Gude, F. and Araújo, A. (2013). smoothHR: An R Package for Pointwise Nonparametric Estimation of Hazard Ratio Curves of Continuous Predictors. Computational and Mathematical Methods in Medicine, 2013, 11 pages. doi:10.1155/2013/745742

Examples

# Example 1
library(survival)
data(whas500)
fit <- coxph(Surv(lenfol, fstat)~age+hr+gender+diasbp+pspline(bmi)+pspline(los), data=whas500,
x=TRUE)
hr1 <- smoothHR(data=whas500, coxfit=fit)
print(hr1)

# Example 2
hr2 <- smoothHR( data=whas500, time="lenfol", status="fstat", formula=~age+hr+gender+diasbp+
pspline(bmi)+pspline(los) )
print(hr2)