# R/estimatelogHR.R In carolinewei/apsurvival: Total sample size and its allocation for the MRCT

#### Documented in estimatelogHR

```#’ Estimate log hazard ratio based on logrank test statisitic and
#' simulating survival data under model hazard_1(t)=hazard_0(t)*e^r.
#'
#' @param r True log hazard ratio
#' @param lamda The event hazard rate for placebo
#' @param lamda_cen The discontinuation hazard rate
#' @param L The whole study duration of fixed study duration
#' design
#' @param E Event number of two groups combined
#'
#' @return A single value.
#' @export
#'
#' @examples
#' r0=log(0.7)
#' E0=Eventnum(alpha=0.05, beta=0.2, r=r0)
#' set.seed(123)
#' estimatelogHR(r=r0, lamda=1, lamda_cen=1, L=2, E=E0)
#'
estimatelogHR <- function(r, lamda=1, lamda_cen=1, L=2, E){
lamda1 = lamda*exp(r)
H0 = lamda/(lamda+lamda_cen)*(1-exp(-L*(lamda+lamda_cen)))
H1 = lamda1/(lamda1+lamda_cen)*(1-exp(-L*(lamda1+lamda_cen)))
N = round(2*E/(H0+H1))
if (N %% 2 == 1) N = N+1
ratio = 0.5
n = N*ratio

T0 <- round(rexp(n,lamda),2)
T1 <- round(rexp(n,lamda*exp(r)),2)
T_sur <- c(T0,T1)
cen <- round(rexp(N,lamda_cen),2)
T_cen <- pmin(cen, L)
y <- pmin(T_sur, T_cen)
status <- as.numeric(T_sur > T_cen)
ifdeath <- 1-status
eventnum <- N-sum(status)

g0 <- as.data.frame( cbind(y[1:n],status[1:n],ifdeath[1:n]) )
colnames(g0) <- c("survTime", "ifcensor", "ifdeath")
g1 <- as.data.frame( cbind(y[(n+1):N],status[(n+1):N],ifdeath[(n+1):N]) )
colnames(g1) <- c("survTime", "ifcensor", "ifdeath")
combine <- rbind(g0,g1)

event <- combine[which(combine[,2]==0),1]
event <- sort(event)
event <- unique(event)

o <- rep(NA,length(event))
e <- rep(NA,length(event))
v <- rep(NA,length(event))

for(i in 1: length(event)){
tao = event[i]
d0 = sum(g0\$ifdeath[which(g0\$survTime==tao)])
d1 = sum(g1\$ifdeath[which(g1\$survTime==tao)])
y0 = n-sum(g0\$ifdeath[which(g0\$survTime<tao)])-sum(g0\$ifcensor[which(g0\$survTime<tao)])
y1 = n-sum(g1\$ifdeath[which(g1\$survTime<tao)])-sum(g1\$ifcensor[which(g1\$survTime<tao)])

o[i] = d1
e[i] = y1/(y0+y1)*(d0+d1)
v[i] = y0*y1*(d0+d1)*(y0+y1-d1-d0)/(y0+y1)^2/(y0+y1-1)
}

v <- v[!is.nan(v)]
z <- sum(o-e)/sqrt(sum(v))
loghr <- 2*z/sqrt(eventnum)
return(loghr)
}
```
carolinewei/apsurvival documentation built on Nov. 4, 2019, 8:44 a.m.