# NOT RUN {
old <- options(dose_levels = c(0.5, 1, 2, 4, 6, 8))
mtdi_gen <- hyper_mtdi_lognormal(CV = 1
, median_mtd = 6, median_sdlog = 0.5
, units="mg/kg")
num_sims <- ifelse(interactive()
, 300
, 15 # avoid taxing CRAN servers
)
hsims <- get_three_plus_three(num_doses = 6) %>%
simulate_trials(
num_sims = num_sims
, true_prob_tox = mtdi_gen)
summary(hsims, ordinalizer=NULL) # vanilla summary with binary toxicity
summary(hsims, ordinalizer = function(dose, r0 = sqrt(2))
c(Gr1=dose/r0^2, Gr2=dose/r0, Gr3=dose, Gr4=dose*r0, Gr5=dose*r0^2)
)
hsims <- hsims %>% extend(num_sims = num_sims)
summary(hsims, ordinalizer = function(dose, r0 = sqrt(2))
c(Gr1=dose/r0^2, Gr2=dose/r0, Gr3=dose, Gr4=dose*r0, Gr5=dose*r0^2)
)$safety
# Set a CRM skeleton from the average probs in above simulation
num_sims <- ifelse(interactive()
, 16
, 4 # avoid taxing CRAN servers
)
get_dfcrm(skeleton = hsims$avg_prob_tox
,target = 0.25
) %>% stop_at_n(n = 24) %>%
simulate_trials(
num_sims = num_sims
, true_prob_tox = mtdi_gen
) -> crm_hsims
summary(crm_hsims
, ordinalizer = function(MTDi, r0 = sqrt(2))
MTDi * r0^c(Gr1=-2, Gr2=-1, Gr3=0, Gr4=1, Gr5=2)
)
options(old)
old <- options(dose_levels = c(2, 6, 20, 60, 180, 400))
mtdi_dist <- mtdi_lognormal(CV = 0.5
,median = 140
,units = "ng/kg/week")
num_sims <- ifelse(interactive()
, 100
, 10 # avoid taxing CRAN servers
)
sims <- get_three_plus_three(num_doses = 6) %>%
simulate_trials(
num_sims = num_sims
, true_prob_tox = mtdi_dist)
# Now set a proper ordinalizer via options():
options(ordinalizer = function(dose, r0) {
c(Gr1=dose/r0^2, Gr2=dose/r0, Gr3=dose, Gr4=dose*r0, Gr5=dose*r0^2)
})
summary(sims, r0=2)
# Set a CRM skeleton from the average probs in above simulation
get_dfcrm(skeleton = sims$true_prob_tox
,target = 0.25
) %>% stop_at_n(n = 24) %>%
simulate_trials(
num_sims = 20
, true_prob_tox = mtdi_dist
) -> crm_sims
summary(crm_sims
, ordinalizer = function(MTDi, r0 = sqrt(2))
MTDi * r0^c(Gr1=-2, Gr2=-1, Gr3=0, Gr4=1, Gr5=2)
)
if (interactive()) { # don't overtax CRAN servers
crm_sims <- crm_sims %>% extend(target_mcse = 0.1)
summary(crm_sims
, ordinalizer = function(MTDi, r0 = sqrt(2))
MTDi * r0^c(Gr1=-2, Gr2=-1, Gr3=0, Gr4=1, Gr5=2)
)$safety
}
options(old)
# }
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