Two-arm randomized trials

Design assumptions

The setting is a two-arm trial with equal randomization to control or treatment. The primary endpoint is overall survival (OS), measured from enrollment to death from any cause or last follow-up. The simulation treats enrollment and randomization as occurring at the same time. The assumed 12-month OS probability in the control arm is 30%. The minimum and maximum sample sizes are 100 and 300, respectively, and no loss to follow-up is assumed. Each participant is followed until death or 12 months, whichever comes first. After an expected-success stop or enrollment of 300 participants, the primary analysis is conducted once all enrolled participants’ required event or censoring outcomes are available. Its calendar time therefore depends on the last observed event or censoring time.

From this information, we have:

• Equal randomization: block = 2 and rand_ratio = c(control = 1, treatment = 1) (default parameters)
• Primary endpoint is at 12 months: end_of_study = 12
• 12-month event rate for control arm: hazard_control = prop_to_haz(1 - 0.30, endtime = 12) (note that the input argument is the failure proportion, not the survival proportion)
• No change points in hazard: cutpoints = NULL (default parameter)
• Maximum sample size: N_total = 300
• No attrition: prop_loss = 0

Named arms make unequal allocation unambiguous. For example, rand_ratio = c(control = 1, treatment = 2) specifies 1:2 randomization. Unnamed values are interpreted in control-treatment order for backward compatibility, but explicit arm names are recommended in a protocol simulation.

Sample-size selection analyses are planned after 100 participants have enrolled and after each additional 25 participants. Futility stopping is allowed from the first analysis, with \(F_n=0.10\). Stopping accrual for expected success is allowed from 125 participants onward, with \(S_n=0.90\). The assumed enrollment rate is constant at five participants per month.

Enrollment is stochastic even though the rate is constant. The package fixes the first patient at calendar time zero and generates each later inter-arrival gap from an exponential distribution with rate 5 per month. Consequently, the expected time from the first to the 300th enrollment is \((300 - 1) / 5 = 59.8\) months, but the realized completion time differs between simulated trials. lambda_time = NULL indicates that there are no enrollment-rate changes; zero is implicit and must not be supplied.

For comparison, a ramp-up specification such as lambda = c(2, 5) and lambda_time = 6 assigns positive realized enrollment times in \((0,6]\) to 2 expected enrollments per month and later times to 5 per month. The first participant at zero is the fixed calendar origin. Fractional changes such as lambda_time = 6.5 are also simulated exactly. Enrollment-rate knots use the trial calendar measured from first participant in, whereas hazard cutpoints use each participant’s follow-up time measured from that participant’s enrollment. The two schedules are independent and need not share their knots.

From this information, we have:

• Interim sample size looks: interim_look = seq(100, 275, 25)
• Futility probability thresholds: Fn = rep(0.10, 8)
• Predicted success probability thresholds: Sn = c(1, rep(0.9, 7))
• Immediate success is disabled: Qn = 1 (the default)
• lambda = 5 and lambda_time = NULL (default parameter)

Note that the first value of Sn is 1. This is because the trial is not allowed to stop for predicted success at the first interim analysis of \(n = 100\). The remaining elements of Sn are 0.9, corresponding to 90%.

Final analysis and hypotheses

The primary analysis is a two-sided log-rank test, with success declared at the \(\alpha = 0.05\) level.

From this information, we have:

• Two-sided log-rank test used: alternative = "two.sided" and method = "logrank"
• \(\alpha = 0.05\) level used to declare success: prob_ha = 0.95

For a frequentist analysis, goldilocks expresses evidence as \(1-p\), so prob_ha = 0.95 corresponds to a two-sided significance level of 0.05. A Bayesian analysis instead compares a posterior probability with prob_ha; the common numerical scale does not make the frequentist and Bayesian decision rules inferentially equivalent. The log-rank analysis requires h0 = 0, corresponding to equality of the survival distributions.

out_power_1sided <- update(
  out_power,
  alternative = "less",
  prob_ha = 0.975
)

Simulation settings

The operating characteristics will be determined using 500 simulated trials. At each interim analysis, we will use 100 imputations and assume independent weakly-informative \(\operatorname{Gamma}(0.1, 0.1)\) prior distributions for the treatment and control arm event time hazard rate parameters. As this is computationally expensive overall, we will exploit the option to parallelize the simulations over multiple cores.

• Number of simulated trials: N_trials = 500
• Number of imputations from predictive distribution: N_impute = 100
• Independent prior distribution for each hazard rate parameter: prior_surv = c(0.1, 0.1)
• Parallel computation using eight cores: ncores = 8
• Reproducible Monte Carlo study: seed = 123

The parameter N_mcmc is not used by the log-rank test. Here prop_loss = 0 means no dropout. A positive value would specify the CDF of an independent exponential dropout time at end_of_study; actual censoring by dropout can be less frequent because events can occur first. Log-rank, Cox, and RMST analyses retain right-censored follow-up with imputed_final = FALSE, including when dropout occurs. Imputed final analyses are not available for method = "logrank".

For methods accepting imputed_final = TRUE, complete final outcomes use the selected test directly. With missing outcomes, "cox", "rmst", and "riskdiff-wald" support final imputation and Rubin pooling, requiring at least two imputations and positive total variance. FM final imputation is unsupported; simulations with method = "riskdiff-fm" and imputed_final = TRUE require zero dropout in both arms. Binary analyses with imputed_final = FALSE exclude incomplete endpoint statuses; that complete-case analysis can be biased even under independent dropout, because early events can be observed before dropout. Binary designs with dropout should assess final imputation and its model assumptions.

Power and type I error

Initially, we want to determine the power to detect a significant treatment effect when the OS rate at 12-months for the treatment arm is 50%.

library(goldilocks)

hc <- prop_to_haz(0.7, endtime = 12)
ht <- prop_to_haz(0.5, endtime = 12)

out_power <- sim_trials(
  hazard_treatment = ht,
  hazard_control = hc,
  cutpoints = NULL,
  N_total = 300,
  lambda = 5,
  lambda_time = NULL,
  interim_look = seq(100, 275, 25),
  end_of_study = 12,
  prior_surv = c(0.1, 0.1),
  block = 2,
  rand_ratio = c(control = 1, treatment = 1),
  prop_loss = 0,
  alternative = "two.sided",
  Fn = rep(0.10, 8),
  Sn = c(1, rep(0.9, 7)),
  prob_ha = 0.95,
  N_impute = 100,
  N_trials = 500,
  method = "logrank",
  ncores = 8,
  seed = 123)

The 500 replicates used here are sufficient for illustration but not for a definitive design decision. A larger simulation should be used when greater precision is needed for type I error, power, or expected sample size.

To estimate type I error, we simulate under the null by setting the treatment hazard equal to the control hazard. update() retains the remaining design specification:

out_t1error <- update(out_power, hazard_treatment = hc, seed = 124)

initial_oc <- summarise_sims(list(out_power, out_t1error))
knitr::kable(
  initial_oc[c(
    "scenario",
    "n_requested",
    "n_used",
    "n_failed",
    "power",
    "stop_success",
    "stop_futility",
    "stop_max_N",
    "mean_N"
  )],
  digits = 3,
  col.names = c(
    "Scenario", "Requested", "Used", "Failed runs", "Power",
    "Expected success stop", "Futility stop", "Maximum N", "Mean N"
  ),
  caption = "Operating characteristics with a two-sided log-rank test at the 0.05 level. Scenario 1 is the alternative (treatment OS 50%); scenario 2 is the null (treatment OS 30%)."
)

The estimated type I error under this design is the power value for scenario 2: 6.2%. Its 95% Wilson Monte Carlo interval is 4.4% to 8.7%. The point estimate alone does not establish whether the design exceeds the intended 0.05 level; both Monte Carlo uncertainty and the complete adaptive decision rule matter.

Calibrating the final threshold

The final-analysis threshold should therefore be calibrated jointly with the interim rules. As a preliminary candidate, consider \(P < 0.04\), specified as prob_ha = 0.96. The calibration vignette gives a systematic grid-search and independent-validation procedure. The candidate below illustrates a stricter threshold; it is not a validated calibration.

out_power2 <- update(out_power, prob_ha = 0.96, return_trace = TRUE)
out_t1error2 <- update(
  out_power2,
  hazard_treatment = hc,
  return_trace = FALSE,
  seed = 125
)

oc_calibrated <- summarise_sims(list(
  "target: treatment OS 50%" = out_power2,
  "null: treatment OS 30%" = out_t1error2
), max_mcse = c(power = 0.02, mean_N = 3))

target_oc <- oc_calibrated[
  oc_calibrated$scenario == "target: treatment OS 50%",
]
null_oc <- oc_calibrated[
  oc_calibrated$scenario == "null: treatment OS 30%",
]

format_mc_interval <- function(estimate, lower, upper, digits = 3) {
  format_string <- paste0(
    "%.", digits, "f [%.", digits, "f-%.", digits, "f]"
  )
  sprintf(format_string, estimate, lower, upper)
}
oc_calibrated_display <- data.frame(
  scenario = oc_calibrated$scenario,
  simulations = sprintf(
    "%d/%d (%d)",
    oc_calibrated$n_used,
    oc_calibrated$n_requested,
    oc_calibrated$n_failed
  ),
  power = format_mc_interval(
    oc_calibrated$power,
    oc_calibrated$power_mc_lower,
    oc_calibrated$power_mc_upper
  ),
  expected_success = format_mc_interval(
    oc_calibrated$stop_success,
    oc_calibrated$stop_success_mc_lower,
    oc_calibrated$stop_success_mc_upper
  ),
  futility = format_mc_interval(
    oc_calibrated$stop_futility,
    oc_calibrated$stop_futility_mc_lower,
    oc_calibrated$stop_futility_mc_upper
  ),
  maximum_N = format_mc_interval(
    oc_calibrated$stop_max_N,
    oc_calibrated$stop_max_N_mc_lower,
    oc_calibrated$stop_max_N_mc_upper
  ),
  mean_N = format_mc_interval(
    oc_calibrated$mean_N,
    oc_calibrated$mean_N_mc_lower,
    oc_calibrated$mean_N_mc_upper,
    digits = 1
  )
)
knitr::kable(
  oc_calibrated_display,
  col.names = c(
    "Scenario",
    "Used/requested (failed)",
    "Power [95% MC CI]",
    "Expected success [95% MC CI]",
    "Futility [95% MC CI]",
    "Maximum N [95% MC CI]",
    "Mean N [95% MC CI]"
  ),
  caption = "Operating characteristics with the more stringent P < 0.04 threshold (`prob_ha = 0.96`)."
)

Here, “95% MC CI” means a Monte Carlo confidence interval: it describes how precisely this finite batch estimates the operating characteristic under the fixed simulation assumptions. It is not a clinical confidence interval for the treatment effect and does not represent uncertainty in the assumed event, accrual, or loss-to-follow-up models. Probability intervals use the Wilson method, while mean sample size uses a t interval based on its Monte Carlo standard error. The optional max_mcse argument warns when a named precision target is not met; it does not change the simulations or estimates.

In this illustrative 500-trial simulation, assuming a 50% 12-month OS probability in the treatment arm, 84.4% of trials stopped accrual for expected success, 4.8% stopped for futility, and the mean sample size was 184.6. Estimated power was 91.8%. Under the null scenario, in which treatment and control had the same 12-month OS probability, 81.4% stopped for futility. Larger simulation studies are appropriate when the displayed Monte Carlo precision is insufficient for a final design decision.

Calendar time and follow-up

The same simulation can be summarized on the calendar-time scale without adding any design arguments. Time zero is first patient enrolled, and the time unit is months in this example. “Analysis ready” is when the last observed event or censoring required for the final analysis becomes available; it does not include an external allowance for data cleaning or database lock. The percentage in the trials column uses all requested simulations as its denominator, so failed and excluded simulations cannot silently disappear.

calendar_oc <- summarise_calendar_time(out_power2)
calendar_duration <- calendar_oc$trial_duration
calendar_duration$trials <- sprintf(
  "%d (%.1f%%)",
  calendar_duration$n_trials,
  calendar_duration$percent_trials
)
calendar_duration$accrual <- sprintf(
  "%.1f [%.1f-%.1f]",
  calendar_duration$accrual_stop_median,
  calendar_duration$accrual_stop_p10,
  calendar_duration$accrual_stop_p90
)
calendar_duration$analysis_ready <- sprintf(
  "%.1f [%.1f-%.1f]",
  calendar_duration$analysis_ready_median,
  calendar_duration$analysis_ready_p10,
  calendar_duration$analysis_ready_p90
)
knitr::kable(
  calendar_duration[c(
    "stopping_reason",
    "trials",
    "mean_N",
    "accrual",
    "analysis_ready",
    "followup_person_time_mean",
    "peak_active_followup_mean"
  )],
  digits = 1,
  col.names = c(
    "Stopping reason",
    "Trials, n (%)",
    "Mean enrolled",
    "Accrual stopped, median [P10-P90]",
    "Analysis ready, median [P10-P90]",
    "Mean person-months",
    "Mean peak under follow-up"
  ),
  caption = "Calendar-time duration and follow-up burden under the treatment-effect scenario."
)

Because out_power2 was simulated with return_trace = TRUE, a second wide table describes when each interim look was reached and how many subjects were actively under follow-up at that time. A trial that stops before a later look remains in the requested denominator but does not contribute a timing value at that look.

calendar_interim <- calendar_oc$interim_timing
calendar_interim$reached <- sprintf(
  "%d (%.1f%%)",
  calendar_interim$n_reached,
  calendar_interim$percent_reached
)
calendar_interim$calendar_time <- sprintf(
  "%.1f [%.1f-%.1f]",
  calendar_interim$calendar_time_median,
  calendar_interim$calendar_time_p10,
  calendar_interim$calendar_time_p90
)
calendar_interim$active_followup <- sprintf(
  "%.0f [%.0f-%.0f]",
  calendar_interim$active_followup_median,
  calendar_interim$active_followup_p10,
  calendar_interim$active_followup_p90
)
knitr::kable(
  calendar_interim[c(
    "look",
    "planned_N",
    "reached",
    "calendar_time",
    "active_followup"
  )],
  col.names = c(
    "Look",
    "Planned N",
    "Reached, n (%)",
    "Calendar month, median [P10-P90]",
    "Active follow-up, median [P10-P90]"
  ),
  caption = "Calendar timing and concurrent follow-up at each interim look."
)

Graphical assessment

The same results can be viewed graphically. plot_sim_ocs() compares final success, stopping behavior, and expected sample size across the treatment-effect scenarios. Because the meaning and direction of an effect depends on the chosen analysis, the effect scale is supplied explicitly; here it is the true 12-month treatment survival probability. Match values by scenario name so that they remain aligned when summarise_sims() sorts the rows.

effect_by_scenario <- c(
  "target: treatment OS 50%" = 0.50,
  "null: treatment OS 30%" = 0.30
)
oc_calibrated$true_treatment_survival <- unname(
  effect_by_scenario[oc_calibrated$scenario]
)
plot_sim_ocs(
  oc_calibrated,
  effect = "true_treatment_survival",
  xlab = "True 12-month treatment survival probability"
)

For a single scenario, plot_sim_stopping() can show four complementary views. The default marginal view gives each outcome as a percentage of all simulated trials. The conditional view uses only trials still active when each look begins as its denominator, while the cumulative view shows the status of all trials after every look and includes those continuing to the next look. A flowchart view displays counts moving from the total simulation set through futility, continued enrollment, and early success at successive looks. Because out_power2 retains simulation traces, the latter three views include reached looks even when no trial stopped at that look. Percentage labels use a compact size so values at adjacent looks remain visually distinct.

plot_sim_stopping(out_power2)

plot_sim_stopping(out_power2, type = "conditional")

plot_sim_stopping(out_power2, type = "cumulative")

plot_sim_stopping(out_power2, type = "flowchart")

The predictive-probability decision map requires traces from every simulated trial. These are opt-in because they increase the size of the simulation result:

plot_sim_decisions(out_power2)

Each decision-map panel represents an interim look. The horizontal coordinate is the predictive probability of success after continuing to the maximum sample size; the vertical coordinate is the predictive probability if enrollment stops now. Shading and dashed lines show the continuation, futility, and expected-success regions.

Once we have identified a suitable design, we would typically re-run the simulations using a larger number of simulations and, perhaps, imputations.

References

Broglio KR, Connor JT, Berry SM. Not too big, not too small: a Goldilocks approach to sample size selection. Journal of Biopharmaceutical Statistics, 2014; 24(3): 685–705.