Code_PAPER/Functions/simulation-functions.R

In MartaBofillRoig/SurvBin: Two-sample statistics for binary and time-to-event outcomes

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

# cop2 : conditional transformation for copula FRANK
# simsurvbin : simulates binary and survival data; returns the database
# fCS.TEST : simulates binary and survival data; returns the L-statistic
# fCS.TEST_Bonf : simulates binary and survival data; returns the surv and bin tests

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

# Table A1 conditional transformation for copula FRANK
cop2 <- function(v1,v2,theta){
  u2 = -(1/theta)*log(1+(v2*(1-exp(-theta)))/(v2*(exp(-theta*v1)-1)-exp(-theta*v1)))
}

##################################################################################
simsurvbin <- function(a.shape, b.scale, rate.param, prob0, ass.par, ss, censoring="Exp"){

  # CENSORING
  ######################################
  if(censoring=="Exp"){
    TC1 = rexp(n= ss, rate = rate.param)
    TC0 = rexp(n= ss, rate = rate.param)
  }
  if(censoring=="Unif"){
    TC1 = runif(n= ss, min=0,max=rate.param)
    TC0 = runif(n= ss, min=0,max=rate.param)
  }


  # TREATMENT GROUP
  ######################################
  v1 <- runif(n=ss)
  v2 <- runif(n=ss)
  u1 <- v1
  u2 <- cop2(v1,v2,ass.par)

  v = cbind(u1,u2)

  # without latent variable
  BE1 = ifelse(v[,2]<prob0, 1, 0)

  # time-to-event (survival)
  TE1 = b.scale*(-log(1-v[,1]))^(1/a.shape)
  time1= ifelse(TE1<=TC1, TE1,TC1)
  status1 = ifelse(TE1<=TC1,1,0)
  treat1 = rep(1,ss)

  # CONTROL GROUP
  ######################################
  v1 <- runif(n=ss)
  v2 <- runif(n=ss)
  u1 <- v1
  u2 <- cop2(v1,v2,ass.par)

  v = cbind(u1,u2)

  # without latent variable
  BE0 = ifelse(v[,2]<prob0, 1, 0)

  # time-to-event (survival)
  TE0 = b.scale*(-log(1-v[,1]))^(1/a.shape)
  time0= ifelse(TE0<=TC0, TE0,TC0)
  status0 = ifelse(TE0<=TC0,1,0)
  treat0 = rep(0,ss)

  # TWO-SAMPLE db
  ######################################
  treat0=as.vector(treat0)
  treat1=as.vector(treat1)
  db = data.frame(binary=c(BE1, BE0), time=c(time1,time0), status=c(status1,status0),treat=c(treat1,treat0))


  return(db)
}


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

fCS.TEST <- function(a.shape, b.scale, rate.param, prob0, ass.par, ss, censoring="Exp", tau, taub, rho, gam, eta, wb, ws, var_est){

  # TWO-SAMPLE db
  ######################################
  db = simsurvbin(a.shape, b.scale, rate.param, prob0, ass.par, ss, censoring)

  # STATISTICS
  ######################################
  TestBS = lstats(db$time,db$status, db$binary, db$treat, tau0=0, tau, taub, rho, gam, eta, wb, ws, var_est)

  return(TestBS[1])
}


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

fCS.TEST_Bonf <- function(a.shape, b.scale, rate.param, prob0, ass.par, ss, censoring="Exp", tau, taub, rho, gam, eta){

  # TWO-SAMPLE db
  ######################################
  db = simsurvbin(a.shape, b.scale, rate.param, prob0, ass.par, ss, censoring)

  # STATISTICS
  ######################################
  B <- bintest(db$binary, db$treat, var_est="Unpooled")
  test_b <- B[1]

  S <- survtest(db$time, db$status, db$treat, tau, rho, gam, eta)
  test_s <- S[1]

  return(c(test_b,test_s))
}


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

fCS.TEST_s <- function(a.shape, b.scale, rate.param, prob0, ass.par, ss, censoring="Exp", tau, taub, rho, gam, eta, wb, ws, var_est='Unpooled'){

  # TWO-SAMPLE db
  ######################################
  db = simsurvbin(a.shape, b.scale, rate.param, prob0, ass.par, ss, censoring)

  # STATISTICS
  ######################################
  S <- survtest(db$time, db$status, db$treat, tau, rho, gam, eta, var_est)

  return(S[1])
}


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

fCS.TEST_b <- function(a.shape, b.scale, rate.param, prob0, ass.par, ss, censoring="Exp", tau, taub, rho, gam, eta, wb, ws, var_est="Unpooled"){

  # TWO-SAMPLE db
  ######################################
  db = simsurvbin(a.shape, b.scale, rate.param, prob0, ass.par, ss, censoring)

  # STATISTICS
  ######################################
  B <- bintest(db$binary, db$treat, var_est)

  return(B[1])
}