tests/testthat/test-main.R

In graemeleehickey/bayesDP: Implementation of the Bayesian Discount Prior Approach for Clinical Trials

context("bayesDP")


################################################################################
# bdpnormal
################################################################################

# One-arm trial (OPC) example
fit <- bdpnormal(
  mu_t = 30, sigma_t = 10, N_t = 250,
  mu0_t = 50, sigma0_t = 5, N0_t = 250
)
summary(fit)
plot(fit)

# Two-arm (RCT) example
fit2 <- bdpnormal(
  mu_t = 30, sigma_t = 10, N_t = 250,
  mu0_t = 50, sigma0_t = 5, N0_t = 250,
  mu_c = 25, sigma_c = 10, N_c = 250,
  mu0_c = 50, sigma0_c = 5, N0_c = 250
)
summary(fit2)
plot(fit2)


################################################################################
# bdpbinomial
################################################################################


# One-arm trial (OPC) example
fit <- bdpbinomial(
  y_t = 10,
  N_t = 500,
  y0_t = 25,
  N0_t = 250
)
summary(fit)
print(fit)
plot(fit)

# Two-arm (RCT) example
fit2 <- bdpbinomial(
  y_t = 10,
  N_t = 500,
  y0_t = 25,
  N0_t = 250,
  y_c = 8,
  N_c = 500,
  y0_c = 20,
  N0_c = 250
)
summary(fit2)
print(fit2)
plot(fit2)


################################################################################
# bdpsurvival
################################################################################


# One-arm trial (OPC) example - survival probability at 5 years
# Simulate survival data for a single arm (OPC) trial
time <- c(rexp(50, rate = 1 / 20), rexp(50, rate = 1 / 10))
status <- c(rexp(50, rate = 1 / 30), rexp(50, rate = 1 / 30))
status <- ifelse(time < status, 1, 0)

# Collect data into a data frame
example_surv_1arm <- data.frame(
  status = status,
  time = time,
  historical = c(rep(1, 50), rep(0, 50)),
  treatment = 1
)

fit1 <- bdpsurvival(Surv(time, status) ~ historical + treatment,
  data = example_surv_1arm,
  surv_time = 5
)

print(fit1)

plot(fit1)


# Two-arm trial (OPC) example
# Simulate survival data for a two-arm trial
time <- c(
  rexp(50, rate = 1 / 20), # Current treatment
  rexp(50, rate = 1 / 10), # Current control
  rexp(50, rate = 1 / 30), # Historical treatment
  rexp(50, rate = 1 / 5)
) # Historical control
status <- rexp(200, rate = 1 / 40)
status <- ifelse(time < status, 1, 0)

# Collect data into a data frame
example_surv_2arm <- data.frame(
  status = status,
  time = time,
  historical = c(rep(0, 100), rep(1, 100)),
  treatment = c(rep(1, 50), rep(0, 50), rep(1, 50), rep(0, 50))
)

fit2 <- bdpsurvival(Surv(time, status) ~ historical + treatment,
  data = example_surv_2arm
)

summary(fit2)

### Fix alpha at 1
fit2_1 <- bdpsurvival(Surv(time, status) ~ historical + treatment,
  data = example_surv_2arm,
  fix_alpha = TRUE
)

summary(fit2_1)