Code_PAPER/Simulations/Simulation_PAPER_PH_additionalresults.R
In MartaBofillRoig/SurvBin: Two-sample statistics for binary and time-to-event outcomes
################################################################
# SIMULATIONS Statistics Binary and Survival outcomes
# Marta Bofill and Guadalupe Gómez
################################################################
rm(list = ls())
# Working directory
setwd("C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Extension_Simulation")
# setwd("C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Extension_Simulation")
#####################################################################################
# PREAMBLE
#####################################################################################
library(copula)
library(pracma) # for using the function 'integral'
library(survival)
library(zoo) # 'rollmean' function
library(muhaz)
library(tidyr)
library(purrr) # 'possibly' function
#####################################################################################
# Functions for the binary and survival setting; for the covariance computation; and for simulating the binary and time-to-event data
source('C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Functions/binary-functions.R')
source('C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Functions/survival-functions.R')
source('C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Functions/cov-functions.R')
source('C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Functions/simulation-functions.R')
source('C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Functions/simulation-functions_H1.R')
source('C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Functions/lstats-functions.R')
source('C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Functions/lstats_boots.R')
# source('C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Functions/binary-functions.R')
# source('C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Functions/survival-functions.R')
# source('C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Functions/cov-functions.R')
# source('C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Functions/simulation-functions.R')
# source('C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Functions/simulation-functions_H1.R')
# source('C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Functions/lstats-functions.R')
# source('C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Functions/lstats_boots.R')
# Parameters
alpha=0.05;
z.alpha <- qnorm(1-alpha,0,1)
z.alphac <- qnorm(1-alpha/2,0,1)
# nsim: number of simulations
nsim=100
# simulation seed
set.seed(1939)
#####################################################################################
# Scenarios H0 FALSE -- case 1
#####################################################################################
a=c(1,2)
b=c(1)
tau=c(1)
taub= c(0.5,1)
r=c(3) #unif
p0=c(0.1, 0.3)
d=c(0.075)
HR=c(0.75)
theta=c(0.001,3)
n=c(500)
# test
eta=c(1)
rho=c(0,1)
gamma=c(0,1)
# omegab=c(0.5)
omegab=c(0.25,0.5,0.75)
data = tidyr::expand_grid(a,b,HR,tau,taub,r,p0,d,theta,n,eta,rho,gamma,omegab)
data$p1=data$d+data$p0
data$omegas=1-data$omegab
rm(a,b,taub,tau,r,p0,d,HR,omegab,theta,n,eta,rho,gamma)
#####################################################################################
#####################################################################################
t0=Sys.time()
data$Test_Power_pluginU=0
data$Test_Power_pluginP=0
data$Test_Power_Boots=0
data$Test_Power_Bonf=0
data$Test_Power_S=0
data$Test_Power_B=0
#####################################################################################
# Scenarios H0 FALSE -- case 2
#####################################################################################
a=c(1,2)
b=c(1)
tau=c(1)
taub= c(0.5,1)
r=c(3) #unif
p0=c(0.1, 0.3)
d=c(0.05)
HR=c(0.75)
theta=c(0.001,3)
n=c(500)
# test
eta=c(1)
rho=c(0,1)
gamma=c(0,1)
# omegab=c(0.5)
omegab=c(0.25,0.5,0.75)
data = tidyr::expand_grid(a,b,HR,tau,taub,r,p0,d,theta,n,eta,rho,gamma,omegab)
data$p1=data$d+data$p0
data$omegas=1-data$omegab
rm(a,b,taub,tau,r,p0,d,HR,omegab,theta,n,eta,rho,gamma)
#####################################################################################
#####################################################################################
t0=Sys.time()
data$Test_Power_pluginU=0
data$Test_Power_pluginP=0
data$Test_Power_Boots=0
data$Test_Power_Bonf=0
data$Test_Power_S=0
data$Test_Power_B=0
#####################################################################################
#####################################################################################
# for(i in 1:3){ # just for testing
for(i in 1:dim(data)[1]){
data$Test_Power_pluginU[i] <- sum(replicate(nsim,fCS.TEST_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i], ws=data$omegas[i],
var_est='Unpooled')) > z.alpha)/nsim
data$Test_Power_pluginP[i] <- sum(replicate(nsim,fCS.TEST_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i], ws=data$omegas[i],
var_est='Pooled')) > z.alpha)/nsim
data$Test_Power_Boots[i] <- sum(replicate(nsim,fCS.TEST_boots_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i],
ws=data$omegas[i],
Boot=50)) > z.alpha)/nsim
data$Test_Power_Bonf[i] <- sum(replicate(nsim,(sum(fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])>z.alphac)>=1)))/nsim
data$Test_Power_S[i] <- sum(replicate(nsim,fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])[2]) > z.alpha)/nsim
data$Test_Power_B[i] <- sum(replicate(nsim,fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])[1]) > z.alpha)/nsim
t1=Sys.time()-t0
cat(i, "\t", t1, "\n", file="LOG_Results_H1_add.txt", append=TRUE)
save.image("C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Extension_Simulation/results/RESULTS_PAPER_add.RData")
}
t1=Sys.time()-t0
cat(t1, "\n", file="LOG_Results_H1_add.txt", append=TRUE)
(t1)
rm(i)
save.image("C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Extension_Simulation/results/RESULTS_PAPER_add.RData")
#####################################################################################
# Scenarios H0 FALSE -- case 3
#####################################################################################
a=c(0.5,1,2)
b=c(1)
tau=c(1)
taub= c(0.5,1)
r=c(3) #unif
p0=c(0.1, 0.3)
d=c(0.075)
HR=c(0.85)
theta=c(0.001,2,3)
n=c(500)
# test
eta=c(1)
rho=c(0,1)
gamma=c(0,1)
# omegab=c(0.5)
omegab=c(0.25,0.5,0.75)
data = tidyr::expand_grid(a,b,HR,tau,taub,r,p0,d,theta,n,eta,rho,gamma,omegab)
data$p1=data$d+data$p0
data$omegas=1-data$omegab
rm(a,b,taub,tau,r,p0,d,HR,omegab,theta,n,eta,rho,gamma)
#####################################################################################
#####################################################################################
t0=Sys.time()
data$Test_Power_pluginU=0
data$Test_Power_pluginP=0
data$Test_Power_Boots=0
data$Test_Power_Bonf=0
data$Test_Power_S=0
data$Test_Power_B=0
#####################################################################################
#####################################################################################
# for(i in 1:3){ # just for testing
for(i in 1:dim(data)[1]){
data$Test_Power_pluginU[i] <- sum(replicate(nsim,fCS.TEST_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i], ws=data$omegas[i],
var_est='Unpooled')) > z.alpha)/nsim
data$Test_Power_pluginP[i] <- sum(replicate(nsim,fCS.TEST_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i], ws=data$omegas[i],
var_est='Pooled')) > z.alpha)/nsim
data$Test_Power_Boots[i] <- sum(replicate(nsim,fCS.TEST_boots_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i],
ws=data$omegas[i],
Boot=50)) > z.alpha)/nsim
data$Test_Power_Bonf[i] <- sum(replicate(nsim,(sum(fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])>z.alphac)>=1)))/nsim
data$Test_Power_S[i] <- sum(replicate(nsim,fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])[2]) > z.alpha)/nsim
data$Test_Power_B[i] <- sum(replicate(nsim,fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])[1]) > z.alpha)/nsim
t1=Sys.time()-t0
cat(i, "\t", t1, "\n", file="LOG_Results_H1_add2.txt", append=TRUE)
save.image("C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Extension_Simulation/results/RESULTS_PAPER_add2.RData")
}
t1=Sys.time()-t0
cat(t1, "\n", file="LOG_Results_H1_add2.txt", append=TRUE)
(t1)
rm(i)
save.image("C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Extension_Simulation/results/RESULTS_PAPER_add2.RData")
#####################################################################################
#####################################################################################
set.seed(421)
# for(i in 1:3){ # just for testing
for(i in 201:dim(data)[1]){
data$Test_Power_pluginU[i] <- sum(replicate(nsim,fCS.TEST_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i], ws=data$omegas[i],
var_est='Unpooled')) > z.alpha)/nsim
data$Test_Power_pluginP[i] <- sum(replicate(nsim,fCS.TEST_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i], ws=data$omegas[i],
var_est='Pooled')) > z.alpha)/nsim
data$Test_Power_Boots[i] <- sum(replicate(nsim,fCS.TEST_boots_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i],
ws=data$omegas[i],
Boot=50)) > z.alpha)/nsim
data$Test_Power_Bonf[i] <- sum(replicate(nsim,(sum(fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])>z.alphac)>=1)))/nsim
data$Test_Power_S[i] <- sum(replicate(nsim,fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])[2]) > z.alpha)/nsim
data$Test_Power_B[i] <- sum(replicate(nsim,fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])[1]) > z.alpha)/nsim
t1=Sys.time()-t0
cat(i, "\t", t1, "\n", file="LOG_Results_H1_add2.txt", append=TRUE)
# save.image("C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Extension_Simulation/results/RESULTS_PAPER_add2.RData")
}
t1=Sys.time()-t0
cat(t1, "\n", file="LOG_Results_H1_add2.txt", append=TRUE)
(t1)
rm(i)
save.image("C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Extension_Simulation/results/RESULTS_PAPER_add2.RData")
#####################################################################################
#####################################################################################
MartaBofillRoig/SurvBin documentation built on Sept. 29, 2021, 5:18 p.m.
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################################################################
# SIMULATIONS Statistics Binary and Survival outcomes
# Marta Bofill and Guadalupe Gómez
################################################################
rm(list = ls())
# Working directory
setwd("C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Extension_Simulation")
# setwd("C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Extension_Simulation")
#####################################################################################
# PREAMBLE
#####################################################################################
library(copula)
library(pracma) # for using the function 'integral'
library(survival)
library(zoo) # 'rollmean' function
library(muhaz)
library(tidyr)
library(purrr) # 'possibly' function
#####################################################################################
# Functions for the binary and survival setting; for the covariance computation; and for simulating the binary and time-to-event data
source('C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Functions/binary-functions.R')
source('C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Functions/survival-functions.R')
source('C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Functions/cov-functions.R')
source('C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Functions/simulation-functions.R')
source('C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Functions/simulation-functions_H1.R')
source('C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Functions/lstats-functions.R')
source('C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Functions/lstats_boots.R')
# source('C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Functions/binary-functions.R')
# source('C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Functions/survival-functions.R')
# source('C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Functions/cov-functions.R')
# source('C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Functions/simulation-functions.R')
# source('C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Functions/simulation-functions_H1.R')
# source('C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Functions/lstats-functions.R')
# source('C:/Users/Marta/Nextcloud/Gitkraken/SurvBin/Code_PAPER/Functions/lstats_boots.R')
# Parameters
alpha=0.05;
z.alpha <- qnorm(1-alpha,0,1)
z.alphac <- qnorm(1-alpha/2,0,1)
# nsim: number of simulations
nsim=100
# simulation seed
set.seed(1939)
#####################################################################################
# Scenarios H0 FALSE -- case 1
#####################################################################################
a=c(1,2)
b=c(1)
tau=c(1)
taub= c(0.5,1)
r=c(3) #unif
p0=c(0.1, 0.3)
d=c(0.075)
HR=c(0.75)
theta=c(0.001,3)
n=c(500)
# test
eta=c(1)
rho=c(0,1)
gamma=c(0,1)
# omegab=c(0.5)
omegab=c(0.25,0.5,0.75)
data = tidyr::expand_grid(a,b,HR,tau,taub,r,p0,d,theta,n,eta,rho,gamma,omegab)
data$p1=data$d+data$p0
data$omegas=1-data$omegab
rm(a,b,taub,tau,r,p0,d,HR,omegab,theta,n,eta,rho,gamma)
#####################################################################################
#####################################################################################
t0=Sys.time()
data$Test_Power_pluginU=0
data$Test_Power_pluginP=0
data$Test_Power_Boots=0
data$Test_Power_Bonf=0
data$Test_Power_S=0
data$Test_Power_B=0
#####################################################################################
# Scenarios H0 FALSE -- case 2
#####################################################################################
a=c(1,2)
b=c(1)
tau=c(1)
taub= c(0.5,1)
r=c(3) #unif
p0=c(0.1, 0.3)
d=c(0.05)
HR=c(0.75)
theta=c(0.001,3)
n=c(500)
# test
eta=c(1)
rho=c(0,1)
gamma=c(0,1)
# omegab=c(0.5)
omegab=c(0.25,0.5,0.75)
data = tidyr::expand_grid(a,b,HR,tau,taub,r,p0,d,theta,n,eta,rho,gamma,omegab)
data$p1=data$d+data$p0
data$omegas=1-data$omegab
rm(a,b,taub,tau,r,p0,d,HR,omegab,theta,n,eta,rho,gamma)
#####################################################################################
#####################################################################################
t0=Sys.time()
data$Test_Power_pluginU=0
data$Test_Power_pluginP=0
data$Test_Power_Boots=0
data$Test_Power_Bonf=0
data$Test_Power_S=0
data$Test_Power_B=0
#####################################################################################
#####################################################################################
# for(i in 1:3){ # just for testing
for(i in 1:dim(data)[1]){
data$Test_Power_pluginU[i] <- sum(replicate(nsim,fCS.TEST_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i], ws=data$omegas[i],
var_est='Unpooled')) > z.alpha)/nsim
data$Test_Power_pluginP[i] <- sum(replicate(nsim,fCS.TEST_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i], ws=data$omegas[i],
var_est='Pooled')) > z.alpha)/nsim
data$Test_Power_Boots[i] <- sum(replicate(nsim,fCS.TEST_boots_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i],
ws=data$omegas[i],
Boot=50)) > z.alpha)/nsim
data$Test_Power_Bonf[i] <- sum(replicate(nsim,(sum(fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])>z.alphac)>=1)))/nsim
data$Test_Power_S[i] <- sum(replicate(nsim,fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])[2]) > z.alpha)/nsim
data$Test_Power_B[i] <- sum(replicate(nsim,fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])[1]) > z.alpha)/nsim
t1=Sys.time()-t0
cat(i, "\t", t1, "\n", file="LOG_Results_H1_add.txt", append=TRUE)
save.image("C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Extension_Simulation/results/RESULTS_PAPER_add.RData")
}
t1=Sys.time()-t0
cat(t1, "\n", file="LOG_Results_H1_add.txt", append=TRUE)
(t1)
rm(i)
save.image("C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Extension_Simulation/results/RESULTS_PAPER_add.RData")
#####################################################################################
# Scenarios H0 FALSE -- case 3
#####################################################################################
a=c(0.5,1,2)
b=c(1)
tau=c(1)
taub= c(0.5,1)
r=c(3) #unif
p0=c(0.1, 0.3)
d=c(0.075)
HR=c(0.85)
theta=c(0.001,2,3)
n=c(500)
# test
eta=c(1)
rho=c(0,1)
gamma=c(0,1)
# omegab=c(0.5)
omegab=c(0.25,0.5,0.75)
data = tidyr::expand_grid(a,b,HR,tau,taub,r,p0,d,theta,n,eta,rho,gamma,omegab)
data$p1=data$d+data$p0
data$omegas=1-data$omegab
rm(a,b,taub,tau,r,p0,d,HR,omegab,theta,n,eta,rho,gamma)
#####################################################################################
#####################################################################################
t0=Sys.time()
data$Test_Power_pluginU=0
data$Test_Power_pluginP=0
data$Test_Power_Boots=0
data$Test_Power_Bonf=0
data$Test_Power_S=0
data$Test_Power_B=0
#####################################################################################
#####################################################################################
# for(i in 1:3){ # just for testing
for(i in 1:dim(data)[1]){
data$Test_Power_pluginU[i] <- sum(replicate(nsim,fCS.TEST_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i], ws=data$omegas[i],
var_est='Unpooled')) > z.alpha)/nsim
data$Test_Power_pluginP[i] <- sum(replicate(nsim,fCS.TEST_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i], ws=data$omegas[i],
var_est='Pooled')) > z.alpha)/nsim
data$Test_Power_Boots[i] <- sum(replicate(nsim,fCS.TEST_boots_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i],
ws=data$omegas[i],
Boot=50)) > z.alpha)/nsim
data$Test_Power_Bonf[i] <- sum(replicate(nsim,(sum(fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])>z.alphac)>=1)))/nsim
data$Test_Power_S[i] <- sum(replicate(nsim,fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])[2]) > z.alpha)/nsim
data$Test_Power_B[i] <- sum(replicate(nsim,fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])[1]) > z.alpha)/nsim
t1=Sys.time()-t0
cat(i, "\t", t1, "\n", file="LOG_Results_H1_add2.txt", append=TRUE)
save.image("C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Extension_Simulation/results/RESULTS_PAPER_add2.RData")
}
t1=Sys.time()-t0
cat(t1, "\n", file="LOG_Results_H1_add2.txt", append=TRUE)
(t1)
rm(i)
save.image("C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Extension_Simulation/results/RESULTS_PAPER_add2.RData")
#####################################################################################
#####################################################################################
set.seed(421)
# for(i in 1:3){ # just for testing
for(i in 201:dim(data)[1]){
data$Test_Power_pluginU[i] <- sum(replicate(nsim,fCS.TEST_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i], ws=data$omegas[i],
var_est='Unpooled')) > z.alpha)/nsim
data$Test_Power_pluginP[i] <- sum(replicate(nsim,fCS.TEST_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i], ws=data$omegas[i],
var_est='Pooled')) > z.alpha)/nsim
data$Test_Power_Boots[i] <- sum(replicate(nsim,fCS.TEST_boots_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i], eta=data$eta[i],
wb=data$omegab[i],
ws=data$omegas[i],
Boot=50)) > z.alpha)/nsim
data$Test_Power_Bonf[i] <- sum(replicate(nsim,(sum(fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])>z.alphac)>=1)))/nsim
data$Test_Power_S[i] <- sum(replicate(nsim,fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])[2]) > z.alpha)/nsim
data$Test_Power_B[i] <- sum(replicate(nsim,fCS.TEST_Bonf_H1(a.shape=data$a[i], b.scale=data$b[i], HR=data$HR[i],
rate.param=data$r[i], p0=data$p0[i], p1=data$p1[i],
ass.par=data$theta[i],
n0=data$n[i]/2, n1=data$n[i]/2,
censoring="Unif",
tau=data$tau[i],
taub=data$taub[i],
rho=data$rho[i], gam=data$gamma[i],
eta=data$eta[i])[1]) > z.alpha)/nsim
t1=Sys.time()-t0
cat(i, "\t", t1, "\n", file="LOG_Results_H1_add2.txt", append=TRUE)
# save.image("C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Extension_Simulation/results/RESULTS_PAPER_add2.RData")
}
t1=Sys.time()-t0
cat(t1, "\n", file="LOG_Results_H1_add2.txt", append=TRUE)
(t1)
rm(i)
save.image("C:/Users/mbofi/Dropbox/C5/Scripts/GitKraken/survivalbinary/Code_PAPER/Extension_Simulation/results/RESULTS_PAPER_add2.RData")
#####################################################################################
#####################################################################################
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