curerate: Power Calculation for Weighted Log-Rank Tests in Cure Rate...
In CR: Power Calculation for Weighted Log-Rank Tests in Cure Rate Models

Description Usage Arguments Details Value Author(s) References See Also Examples

This R-function performs power calculation in a group sequential clinical trial with censored survival data and possibly unequal patient allocation between treatment and control groups. The function can also be used to determine the study duration in a clinical trial with censored survival data as the sum of the accrual duration, which determines the sample size in a traditional sense, and the follow-up duration, which more or less controls the number of events to be observed.

1 2	curerate(rho = 0, numreps, cureobs, curerx, medobs, medrx, acrate, probrx, actime, futime, info, crits, alpha = 0.025)

`rho`	numeric specifying the value of rho in the G-rho test (Harrington and Fleming, 1982), rho=0 (default) gives the log-rank test, rho=1 the Peto-Peto Wilcoxon test, and rho=-1 the test discuss by Gray and Tsiatis, 1989.
`numreps`	integer > 0 specifying the number of replications.
`cureobs`	numeric specifying the probability of cure on the observation arm of the study.
`curerx`	numeric specifying the probability of cure on the treatment arm of the study.
`medobs`	numeric > 0 specifying the median survival among the non-cured on observation.
`medrx`	numeric > 0 specifying the median survival among the non-cured on treatment.
`acrate`	numeric > 0 specifying the rate at which patients accrue, combined over both observation and treatment arms of the study.
`probrx`	numeric specifying the probability of assigment to the treatment arm, must be in [0,1].
`actime`	vector specifying the accrual durations.
`futime`	vector specifying the follow-up durations.
`info`	vector of information times for the interim looks; must be an increasing sequence in (0,1].
`crits`	vector of critical values corresponding to the interim analysis time points specified in `info`.
`alpha`	numeric specifying the one-sided level of significance; must be in (0,1); default value `0.025`; currently, it has no effect on the calculations, it is ignored in the current version of the software.

The function curerate is used to calculate the power of weighted log-rank tests in cure rate models.

An object of S4 class CureRate which has the following 22 components

`cureobs`	numeric
`medobs`	numeric
`curerx`	numeric
`medrx`	numeric
`actime`	numeric vector
`futime`	numeric vector
`info`	numeric vector
`crits`	numeric vector
`alpha`	numeric
`rho`	numeric
`acrate`	numeric
`probrx`	numeric
`numreps`	integer
`numobs`	numeric matrix
`timept`	numeric 3D array
`deaths`	numeric 3D array
`testname`	character
`power`	numeric 3D array
`numobs`	numeric matrix
`indac`	vector of integers
`indfu`	vector of integers
`printflag`	integer

Emil A. Cornea, Bahjat F. Qaqish, and Joseph G. Ibrahim

Maintainer: Emil A. Cornea <ecornea@live.unc.edu>

Ewell, M. and Ibrahim, J.G. (1997). The Large Sample Distribution of the Weighted Log Rank Statistic Under General Local Alternatives. Lifetime Data Analysis,3,5-12

Kim, K. (1992). Study Duration for Group Sequential Clinical Trials with Censored Survival Data Adjusting for Stratification. Statistics in Medicine, Vol. 11, 1477-1788

Harrington, D. P. and Fleming, T. R. (1982). A class of rank test procedures for censored survival data. Biometrika 69, 553-566.

Gray, R.J. and Tsiatis, A.A. (1989). A linear rank test for use when the main interest is in differences in cure rates. Biometrics 45, 899-904.

CR-package, CureRate-class, showcr, and show-methods

##---- Should be DIRECTLY executable !! ----
## Input Data
################
# rho - specifies the value of rho in the G-rho test (Harrington and Fleming, 1982). 
# rho = 0 gives the logrank test, and rho = 1 the Peto-Peto Wilcoxon test
#(and rho = -1 the test discussed by Gray and Tsiatis, 1989).
rho = 0 

numreps = 500
##cureobs - probability of cure on the observation arm of the study
cureobs = .359
##curerx - probability of cure on the treatment arm of the study
curerx = .459
##medobs - median survival among the non-cured on observation
medobs = .747
##medrx - median survival among the non-cured on treatment
medrx = .859
##acrate - rate at which patients accrue, combined over both 
##observation and treatment arms of the study
acrate = 232
##probrx - probability of assignment to the treatment arm
probrx = .5
##actime  - accrual duration
actime = c(3.3, 3.5, 3.8); 
##futime  - followup duration
futime = c(2.0,  2.5) 
##info - vector of information times for the interim looks
##must be an increasing sequence in (0,1]
info = c( .35, .61, .86, 1.0)
##crits - vector of critical values corresponding to the 
##interim analysis time points specified in info
crits = c(3.6128, 2.6506, 2.1894, 2.0536)


#############################################################


### Log-rank test: rho=0 (default)
mycr<-curerate(rho,numreps,cureobs,curerx,medobs,medrx,acrate,
          probrx,actime,futime,info,crits)
mycr       ### (*)

show(mycr)   ### same as above
showcr(mycr) ### same as above 
showcr(mycr,full.result=TRUE)
showcr(mycr,indac=2,indfu=1)
showcr(mycr,indac=2:3,indfu=2:1)
showcr(mycr,indac=c(1,3),indfu=2)

show(mycr)   ### same as (*) above
showcr(mycr) ### same as above
mycr         ### same as above

### Peto & Peto modification of the Gehan-Wilcoxon test: rho=1
rho=1
mycr<-curerate(rho,numreps,cureobs,curerx,medobs,medrx,acrate,
          probrx,actime,futime,info,crits)
mycr