Description Usage Arguments Value Examples
(nTTP) Function LRtox.nTTP()
calculates the likelihood of safety for a single dose
and designates whether to escalate to the next dose (safe) or stop dose escalation and move onto stage 2 (unsafe).
1 | LRtox.nTTP(tox_grades, ntox, coh.size, W, p1, p2, K = 2, std.nTTP = 0.15)
|
tox_grades |
data frame of observed AE grades for each patient (rows) across all toxicity types (columns). e.g. for one patient, grades for 3 toxicity types might be c(3, 2, 4), where they experienced a grade 3 AE for tox type 1, grade 2 AE for tox type 2, etc. |
ntox |
number (integer) of different toxicity types |
coh.size |
cohort size (number of patients) per dose (Stage 1) |
W |
matrix defining burden weight of each grade level for all toxicity types. The dimensions are ntox rows by 5 columns (for grades 0-4). See Ezzalfani et al. (2013) for details. |
p1 |
toxicity under null (unsafe DLT rate). Values range from 0 - 1. |
p2 |
toxicity under alternative (safe DLT rate). Values range from 0 - 1; p1 > p2 |
K |
threshold for LR. Takes integer values: 1,2,...(recommended K=2) |
std.nTTP |
the standard deviation of nTTP scores at each dose level (constant across doses) |
List object that gives the likelihood ratio of safety and indicates whether to escalate to the next highest dose level, or stop dose escalation and move onto stage 2.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ntox = 3 # three different types of toxicity
coh.size = 3 # number of patients enrolled per dose
# Observed AE grades for each patient on tested dose
obs = data.frame(tox1 = c(3, 2, 4),
tox2 = c(1, 1, 2),
tox3 = c(2, 3, 3))
# Toxicity burden weight matrix
W = matrix(c(0, 0.5, 0.75, 1.0, 1.5, # Burden weight for grades 0-4 for toxicity 1
0, 0.5, 0.75, 1.0, 1.5, # Burden weight for grades 0-4 for toxicity 2
0, 0.00, 0.00, 0.5, 1), # Burden weight for grades 0-4 for toxicity 3
nrow = ntox, byrow = TRUE)
# Acceptable (p2) and unacceptable nTTP values
p1 <- 0.35
p2 <- 0.10
LRtox.nTTP(obs, ntox, coh.size, W, p1, p2, K = 2, std.nTTP = 0.15)
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