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Uncertainty for the classical two-stage TDT quantities

Source: R/two_stage.R
ts_ci.Rd

Two propagation methods on the Stage-2 fit:

  • "delta" — delta-method standard errors for z and CTmax, with both Normal and t quantiles (the t-quantile is the small-sample correction for the few Stage-2 residual degrees of freedom). This is the method the bias simulation reports.

  • "mvn" — slope-CI inversion for z (defined only when the slope CI is wholly negative) plus MVN simulation of the Stage-2 coefficients for CTmax and T_crit, and a predict.lm confidence band for the LT-vs-T line over temp_grid. This is the method the case studies report.

Usage

ts_ci(
  stage2,
  method = c("delta", "mvn"),
  level = 0.95,
  t_ref = NULL,
  time_multiplier = NULL,
  TC_rate_range = NULL,
  temp_grid = NULL,
  n_sim = 1000,
  seed = 123
)

Arguments

stage2

Output of ts_stage2().

method

"delta" or "mvn".

level

Confidence level. Default 0.95.

t_ref, time_multiplier, TC_rate_range

Optional explicit checks against the settings recorded by ts_stage2(). By default they are inherited. A value that disagrees with the Stage-2 fit errors rather than silently changing the CTmax convention.

temp_grid

Temperatures for the line band ("mvn" only).

n_sim

MVN draws ("mvn" only). Default 1000.

seed

RNG seed ("mvn" only). Default 123.

Value

For "delta", a list with z and CTmax, each list(point, lower, upper, lower_t, upper_t, se), plus df_resid. When the recorded t_ref is exactly 60 minutes, the list also contains the compatibility alias CTmax_1hr, identical to CTmax; it is absent for other reference durations. For "mvn", a list with summary_ci (z/CTmax/T_crit bounds) and curve_ci (per-temp_grid line band).

Examples

d <- simulate_tls(
  family = "binomial", temps = seq(30, 42, by = 2),
  times = c(0.01, 0.03, 0.1, 0.3, 1, 3, 10, 30, 100),
  reps = 4, n = 50, CTmax = 36, z = 4, seed = 42
)
s2 <- ts_stage2(ts_stage1(d, "temp", "duration", "survived", "total"),
                t_ref = 60, time_multiplier = 60)
ts_ci(s2, method = "delta")$z
#> $point
#> [1] 4.083895
#> 
#> $lower
#> [1] 4.002786
#> 
#> $upper
#> [1] 4.165004
#> 
#> $lower_t
#> [1] 3.977516
#> 
#> $upper_t
#> [1] 4.190274
#> 
#> $se
#> [1] 0.04138309
#>