GenToxProb: Toxicity Probability Matrices Generation for Trial Simulation
In phase1RMD: Repeated Measurement Design for Phase I Clinical Trial

Description Usage Arguments Details Value Examples

A function to generate toxicity probability matrices employing proportional odds model, used as input for trial simulation. The generated matrices are a four-dimension array containing the probabilities of the occurrences of certain grades for certain types of toxicities, at each dose level and cycle under consideration. Dimension 1 refers to doses; dimension 2 corresponds to cycles of the treatment; dimension 3 regards the types of toxicities while dimenion 4 relates to grades.

GenToxProb(toxtype = c("Neurological", "Renal", "Hematological"), 
           intercept.alpha = c(2, 3, 4.2, 5.7), 
           coef.beta = c(-0.2, -0.4, -0.7), 
           cycle.gamma = 0, MaxCycle = 6, Numdose = 6)

`toxtype`	A character vector, specifying toxicity types considered in the trial.
`intercept.alpha`	A four element numeric vector specifying the intercepts for the cumulative probabilities of the occurrences of grades 0-4 of toxicities in proportional odds model. See Details below.
`coef.beta`	A n numeric vector specifying the slope for dose in proportional odds model for n types of toxicities. See Details below.
`cycle.gamma`	A scalar controlling the cycle effect in simulation in proportional odds model. See Details below.
`MaxCycle`	Maximum of number of cycles of the treatment.
`Numdose`	The number of doses under investigation.

The probability matrices of the occurrences of certain grades for certain types of toxicities, at each dose level and cycle are simulated from a proportional odds model that takes toxtype, intercept.alpha, coef.beta and cycle.gamma as the inputs. The model is as follows:

logit(c_j) = α_j + β * dose + γ * cycle, j=0,1,2,3

where given a dose and cycle, c_j is the cumulative probabilities of occurrences of toxicities grades up to j; α_0, α_1, α_2, α_3 are the intercepts, making up intercept.alpha; coef.beta stores β for different types of toxicities while cycle.gamma acts as γ, controlling the cycle effect. The probability for the occurrence of a certain grade of a certain toxicity type at a given dose and cycle is obtained from taking the corresponding differences between cumulative probabilities.

A four-dimension array where dimension 1 refers to doses; dimension 2 corresponds to cycles of the treatment; dimension 3 regards the types of toxicities while dimenion 4 relates to grades.