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Stage 2 of the classical two-stage TDT pipeline

Source: R/two_stage.R
ts_stage2.Rd

Regresses the valid Stage-1 log10(LT50) estimates on assay temperature by ordinary least squares and derives the classical quantities. z = -1/slope; CTmax(t_ref) = (log10(t_ref) - intercept) / slope; T_crit follows the rate-multiplier definition, CTmax + z * mean(log10(TC_rate_range/100)). t_ref is expressed in minutes and is recorded in the returned $settings. Thus summary$CTmax is always CTmax at the explicitly recorded reference duration, not necessarily CTmax at one hour. Stage 2 retains only rows chosen by rows; if fewer than three valid Stage-1 temperatures remain, it returns a NULL fit and an NA summary rather than extrapolating a TDT line.

Usage

ts_stage2(
  stage1,
  t_ref = 60,
  time_multiplier = 1,
  TC_rate_range = c(0.1, 1),
  rows = c("stage1_ok", "finite_ok")
)

Arguments

stage1

Output of ts_stage1().

t_ref

Reference exposure duration for CTmax (minutes). Default 60.

time_multiplier

Multiplier from the Stage-1 duration unit to minutes (e.g. 60 if durations are in hours). Default 1.

TC_rate_range

Length-2 HI-rate range (% per hour) for T_crit.

rows

Which Stage-1 rows to keep: "stage1_ok" (bracketing validation, the case-study default) or "finite_ok" (finite/negative slope only, the simulation's looser rule).

Value

list(fit, summary, settings); fit is NULL if fewer than 3 valid Stage-1 estimates remain. summary has intercept, slope_T, z, CTmax, T_crit, r_squared, n_stage1, n_excluded. $settings records t_ref, time_multiplier, and TC_rate_range; downstream ts_ci() and ts_curve() inherit these settings by default. For compatibility, when t_ref = 60 exactly, summary also contains a truthful CTmax_1hr alias for CTmax; it is absent at every other reference duration.

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
)
s1 <- ts_stage1(d, "temp", "duration", "survived", "total")
ts_stage2(s1, t_ref = 60, time_multiplier = 60)$summary
#> # A tibble: 1 × 9
#>   intercept slope_T     z CTmax T_crit r_squared n_stage1 n_excluded CTmax_1hr
#>       <dbl>   <dbl> <dbl> <dbl>  <dbl>     <dbl>    <int>      <int>     <dbl>
#> 1      10.6  -0.245  4.08  36.0   25.8     0.999        7          0      36.0