R/phase1_outcomes_to_cohorts.R
phase1_outcomes_to_cohorts.RdBreak a phase I outcome string into a list of cohort parts.
Break a phase I outcome string into a list of cohort parts.
The outcome string describes the doses given, outcomes observed and the timing of analyses that recommend a dose. The format of the string is described in Brock (2019), and that itself is the phase I analogue of the similar idea described in Brock _et al_. (2017).
The letters T and N are used to represents patients that experienced
(T)oxicity and (N)o toxicity. These letters are concatenated after numerical
dose-levels to convey the outcomes of cohorts of patients.
For instance, 2NNT represents a cohort of three patients that were
treated at dose-level 2, one of whom experienced toxicity, and two that did
not. The results of cohorts are separated by spaces and it is assumed that a
dose-finding decision takes place at the end of a cohort. Thus,
2NNT 1NN builds on our previous example, where the next cohort of two
were treated at dose-level 1 and neither of these patients experienced
toxicity. See examples.
phase1_outcomes_to_cohorts(outcomes)character string representing the doses given, outcomes observed, and timing of analyses. See Description.
a list with a slot for each cohort. Each cohort slot is itself a
list, containing elements:
* dose, the integer dose delivered to the cohort;
* outcomes, a character string representing the T or N
outcomes for the patients in this cohort.
Brock, K. (2019). trialr: Bayesian Clinical Trial Designs in R and Stan. arXiv:1907.00161 [stat.CO]
Brock, K., Billingham, L., Copland, M., Siddique, S., Sirovica, M., & Yap, C. (2017). Implementing the EffTox dose-finding design in the Matchpoint trial. BMC Medical Research Methodology, 17(1), 112. https://doi.org/10.1186/s12874-017-0381-x
x = phase1_outcomes_to_cohorts('1NNN 2NNT 3TT')
length(x)
#> [1] 3
x[[1]]$dose
#> [1] 1
x[[1]]$outcomes
#> [1] "NNN"
x[[2]]$dose
#> [1] 2
x[[2]]$outcomes
#> [1] "NNT"
x[[3]]$dose
#> [1] 3
x[[3]]$outcomes
#> [1] "TT"