iAdapt (version 2.0.1)

get.thresh: Obtain average nTTP at each dose level

Description

Obtain average nTTP at each dose level

Usage

get.thresh(dose, ntox, W, TOX)

Arguments

dose

number of doses to be tested (scalar)

ntox

number (integer) of different toxicity types (e.g, hematological, neurological, GI)

W

matrix defines burden weight of each grade level for all toxicity types. The dimensions are ntox rows by 4 columns (for grades 0-4). See Ezzalfani et al. (2013) for details.

TOX

matrix array of toxicity probabilities. There should be ntox matrices. Each matrix represents one toxicity type, where probabilities of each toxicity grade are specified across each dose. Each matrix has the same dimensions: n rows, representing number of doses, and 5 columns (for grades 0-4). Probabilities across each dose (rows) must sum to 1. See Ezzalfani et al. (2013) for details.

Value

Vector of average nTTP for each dose level.

Examples

# NOT RUN {
# Number of test doses
dose = 6

# Number of toxicity types
ntox <- 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)
           

# Array of toxicity event probabilities
TOX = array(NA, c(dose, 5, ntox)) 

TOX[, , 1] = matrix(c(0.823, 0.152, 0.022, 0.002, 0.001,  #prob of tox for dose 1 and tox type 1
                      0.791, 0.172, 0.032, 0.004, 0.001,  #prob of tox for dose 2 and tox type 1
                      0.758, 0.180, 0.043, 0.010, 0.009,  #prob of tox for dose 3 and tox type 1
                      0.685, 0.190, 0.068, 0.044, 0.013,  #prob of tox for dose 4 and tox type 1
                      0.662, 0.200, 0.078, 0.046, 0.014,  #prob of tox for dose 5 and tox type 1
                      0.605, 0.223, 0.082, 0.070, 0.020), #prob of tox for dose 6 and tox type 1
                      nrow = 6, byrow = TRUE)
TOX[, , 2] = matrix(c(0.970, 0.027, 0.002, 0.001, 0.000,  #prob of tox for dose 1 and tox type 2
                      0.968, 0.029, 0.002, 0.001, 0.000,  #prob of tox for dose 2 and tox type 2
                      0.813, 0.172, 0.006, 0.009, 0.000,  #prob of tox for dose 3 and tox type 2
                      0.762, 0.183, 0.041, 0.010, 0.004,  #prob of tox for dose 4 and tox type 2
                      0.671, 0.205, 0.108, 0.011, 0.005,  #prob of tox for dose 5 and tox type 2
                      0.397, 0.258, 0.277, 0.060, 0.008), #prob of tox for dose 6 and tox type 2
                      nrow = 6, byrow = TRUE)
TOX[, , 3] = matrix(c(0.930, 0.060, 0.005, 0.001, 0.004,  #prob of tox for dose 1 and tox type 3
                      0.917, 0.070, 0.007, 0.001, 0.005,  #prob of tox for dose 2 and tox type 3
                      0.652, 0.280, 0.010, 0.021, 0.037,  #prob of tox for dose 3 and tox type 3
                      0.536, 0.209, 0.031, 0.090, 0.134,  #prob of tox for dose 4 and tox type 3
                      0.015, 0.134, 0.240, 0.335, 0.276,  #prob of tox for dose 5 and tox type 3
                      0.005, 0.052, 0.224, 0.372, 0.347), #prob of tox for dose 6 and tox type 3
                      nrow = 6, byrow = TRUE)
                      
get.thresh(dose = dose, ntox = ntox, W = W, TOX = TOX)
   
# }