bdpsurvival: Bayesian Discount Prior: Survival Analysis
In bayesDP: Implementation of the Bayesian Discount Prior Approach for Clinical Trials

bdpsurvival

R Documentation

Bayesian Discount Prior: Survival Analysis

Description

bdpsurvival is used to estimate the survival probability (single arm trial; OPC) or hazard ratio (two-arm trial; RCT) for right-censored data using the survival analysis implementation of the Bayesian discount prior. In the current implementation, a two-arm analysis requires all of current treatment, current control, historical treatment, and historical control data. This code is modeled after the methodologies developed in Haddad et al. (2017).

Usage

bdpsurvival(
  formula = formula,
  data = data,
  data0 = NULL,
  breaks = NULL,
  a0 = 0.1,
  b0 = 0.1,
  surv_time = NULL,
  discount_function = "identity",
  alpha_max = 1,
  fix_alpha = FALSE,
  number_mcmc = 10000,
  weibull_scale = 0.135,
  weibull_shape = 3,
  method = "mc",
  compare = TRUE
)

Arguments

`formula`	an object of class "formula." Must have a survival object on the left side and at most one input on the right side, treatment. See "Details" for more information.
`data`	a data frame containing the current data variables in the model. Columns denoting 'time' and 'status' must be present. See "Details" for required structure.
`data0`	optional. A data frame containing the historical data variables in the model. If present, the column labels of data and data0 must match.
`breaks`	vector. Breaks (interval starts) used to compose the breaks of the piecewise exponential model. Do not include zero. Default breaks are the quantiles of the input times.
`a0`	scalar. Prior value for the gamma shape of the piecewise exponential hazards. Default is 0.1.
`b0`	scalar. Prior value for the gamma rate of the piecewise exponential hazards. Default is 0.1.
`surv_time`	scalar. Survival time of interest for computing the probability of survival for a single arm (OPC) trial. Default is overall, i.e., current+historical, median survival time.
`discount_function`	character. Specify the discount function to use. Currently supports `weibull`, `scaledweibull`, and `identity`. The discount function `scaledweibull` scales the output of the Weibull CDF to have a max value of 1. The `identity` discount function uses the posterior probability directly as the discount weight. Default value is "`identity`".
`alpha_max`	scalar. Maximum weight the discount function can apply. Default is 1. For a two-arm trial, users may specify a vector of two values where the first value is used to weight the historical treatment group and the second value is used to weight the historical control group.
`fix_alpha`	logical. Fix alpha at alpha_max? Default value is FALSE.
`number_mcmc`	scalar. Number of Monte Carlo simulations. Default is 10000.
`weibull_scale`	scalar. Scale parameter of the Weibull discount function used to compute alpha, the weight parameter of the historical data. Default value is 0.135. For a two-arm trial, users may specify a vector of two values where the first value is used to estimate the weight of the historical treatment group and the second value is used to estimate the weight of the historical control group.
`weibull_shape`	scalar. Shape parameter of the Weibull discount function used to compute alpha, the weight parameter of the historical data. Default value is 3. For a two-arm trial, users may specify a vector of two values where the first value is used to estimate the weight of the historical treatment group and the second value is used to estimate the weight of the historical control group.
`method`	character. Analysis method with respect to estimation of the weight parameter alpha. Default method "`mc`" estimates alpha for each Monte Carlo iteration. Alternate value "`fixed`" estimates alpha once and holds it fixed throughout the analysis. See the the `bdpsurvival` vignette `vignette("bdpsurvival-vignette", package="bayesDP")` for more details.
`compare`	logical. Should a comparison object be included in the fit? For a one-arm analysis, the comparison object is simply the posterior chain of the treatment group parameter. For a two-arm analysis, the comparison object is the posterior chain of the treatment effect that compares treatment and control. If `compare=TRUE`, the comparison object is accessible in the `final` slot, else the `final` slot is `NULL`. Default is `TRUE`.

Details

bdpsurvival uses a two-stage approach for determining the strength of historical data in estimation of a survival probability outcome. In the first stage, a discount function is used that that defines the maximum strength of the historical data and discounts based on disagreement with the current data. Disagreement between current and historical data is determined by stochastically comparing the respective posterior distributions under noninformative priors. With a single arm survival data analysis, the comparison is the probability (p) that the current survival is less than the historical survival. For a two-arm survival data, analysis the comparison is the probability that the hazard ratio comparing treatment and control is different from zero. The comparison metric p is then input into the discount function and the final strength of the historical data is returned (alpha).

In the second stage, posterior estimation is performed where the discount function parameter, alpha, is used incorporated in all posterior estimation procedures.

To carry out a single arm (OPC) analysis, data for the current and historical treatments are specified in separate data frames, data and data0, respectively. The data frames must have matching columns denoting time and status. The 'time' column is the survival (censor) time of the event and the 'status' column is the event indicator. The results are then based on the posterior probability of survival at surv_time for the current data augmented by the historical data.

Two-arm (RCT) analyses are specified similarly to a single arm trial. Again the input data frames must have columns denoting time and status, but now an additional column named 'treatment' is required to denote treatment and control data. The 'treatment' column must use 0 to indicate the control group. The current data are augmented by historical data (if present) and the results are then based on the posterior distribution of the hazard ratio between the treatment and control groups.

For more details, see the bdpsurvival vignette:
vignette("bdpsurvival-vignette", package="bayesDP")

Value

bdpsurvival returns an object of class "bdpsurvival". The functions summary and print are used to obtain and print a summary of the results, including user inputs. The plot function displays visual outputs as well.

An object of class "bdpsurvival" is a list containing at least the following components:

posterior_treatment

list. Entries contain values related to the treatment group:

alpha_discount numeric. Alpha value, the weighting parameter of the historical data.
p_hat numeric. The posterior probability of the stochastic comparison between the current and historical data.
posterior_survival vector. If one-arm trial, a vector of length number_mcmc containing the posterior probability draws of survival at surv_time.
posterior_flat_survival vector. If one-arm trial, a vector of length number_mcmc containing the probability draws of survival at surv_time for the current treatment not augmented by historical treatment.
prior_survival vector. If one-arm trial, a vector of length number_mcmc containing the probability draws of survival at surv_time for the historical treatment.
posterior_hazard matrix. A matrix with number_mcmc rows and length(breaks) columns containing the posterior draws of the piecewise hazards for each interval break point.
posterior_flat_hazard matrix. A matrix with number_mcmc rows and length(breaks) columns containing the draws of piecewise hazards for each interval break point for current treatment not augmented by historical treatment.
prior_hazard matrix. A matrix with number_mcmc rows and length(breaks) columns containing the draws of piecewise hazards for each interval break point for historical treatment.

posterior_control

list. If two-arm trial, contains values related to the control group analogous to the posterior_treatment output.

final

list. Contains the final comparison object, dependent on the analysis type:

One-arm analysis: vector. Posterior chain of survival probability at requested time.
Two-arm analysis: vector. Posterior chain of log-hazard rate comparing treatment and control groups.

args1

list. Entries contain user inputs. In addition, the following elements are output:

S_t, S_c, S0_t, S0_c survival objects. Used internally to pass survival data between functions.
arm2 logical. Used internally to indicate one-arm or two-arm analysis.

References

Haddad, T., Himes, A., Thompson, L., Irony, T., Nair, R. MDIC Computer Modeling and Simulation working group.(2017) Incorporation of stochastic engineering models as prior information in Bayesian medical device trials. Journal of Biopharmaceutical Statistics, 1-15.

Examples

# One-arm trial (OPC) example - survival probability at 5 years

# Collect data into data frames
df_ <- data.frame(
  status = rexp(50, rate = 1 / 30),
  time = rexp(50, rate = 1 / 20)
)
df_$status <- ifelse(df_$time < df_$status, 1, 0)

df0 <- data.frame(
  status = rexp(50, rate = 1 / 30),
  time = rexp(50, rate = 1 / 10)
)
df0$status <- ifelse(df0$time < df0$status, 1, 0)


fit1 <- bdpsurvival(Surv(time, status) ~ 1,
  data = df_,
  data0 = df0,
  surv_time = 5,
  method = "fixed"
)

print(fit1)
## Not run: 
plot(fit1)

## End(Not run)

# Two-arm trial example
# Collect data into data frames
df_ <- data.frame(
  time = c(
    rexp(50, rate = 1 / 20), # Current treatment
    rexp(50, rate = 1 / 10)
  ), # Current control
  status = rexp(100, rate = 1 / 40),
  treatment = c(rep(1, 50), rep(0, 50))
)
df_$status <- ifelse(df_$time < df_$status, 1, 0)

df0 <- data.frame(
  time = c(
    rexp(50, rate = 1 / 30), # Historical treatment
    rexp(50, rate = 1 / 5)
  ), # Historical control
  status = rexp(100, rate = 1 / 40),
  treatment = c(rep(1, 50), rep(0, 50))
)
df0$status <- ifelse(df0$time < df0$status, 1, 0)

fit2 <- bdpsurvival(Surv(time, status) ~ treatment,
  data = df_,
  data0 = df0,
  method = "fixed"
)
summary(fit2)

### Fix alpha at 1
fit2_1 <- bdpsurvival(Surv(time, status) ~ treatment,
  data = df_,
  data0 = df0,
  fix_alpha = TRUE,
  method = "fixed"
)
summary(fit2_1)

bayesDP documentation built on April 4, 2025, 4:01 a.m.