Format a phase 1 trial safety tabulation to show significant digits only
The essential insight of package precautionary is distilled into the safety tabulation which it generates from trial simulations, reporting the expected number of patients who will experience each grade of toxicity. To render this table for easy interpretation, these expectations are simply displayed with a number of significant digits appropriate to their Monte Carlo standard errors (MCSEs).
## S3 method for class 'safetytab' format(x, ...)
x |
A safety tabulation as found in the |
... |
Unused; included for compatibility with generic signature |
The MCSEs of safety tabulations remain available for inspection (see example), but are omitted from standard displays because they may lend themselves to misinterpretation as confidence bounds on the number of patients who will experience each toxicity grade in any given trial.
mtdi_gen <- hyper_mtdi_lognormal(CV = 1
,median_mtd = 5
,median_sdlog = 0.5
,units="mg/kg")
ordinalizer <- function(MTDi, r0 = 1.5)
MTDi * r0 ^ c(Gr1=-2, Gr2=-1, Gr3=0, Gr4=1, Gr5=2)
old <- options(dose_levels = c(0.5, 1, 2, 4, 6)
,ordinalizer = ordinalizer)
get_boin(num_doses = 5, target = 0.25) %>%
stop_at_n(n = 24) %>%
simulate_trials(
num_sims = 60
, true_prob_tox = mtdi_gen) -> boin_hsims
safety <- summary(boin_hsims)$safety
safety # The print method invokes 'format.safetytab' ..
# .. but we can also inspect the underlying matrix by indexing:
safety[,] # indexing strips 'safetytab' class, returning plain matrix
# Note that, by extend()ing the simulation we can increase precision:
if (interactive()) { # may run a bit too long for CRAN servers' taste
boin_hsims %>% extend(target_mcse = 0.1) -> boin_hsimsX
summary(boin_hsimsX)$safety
}
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