R/get_potential_outcomes.R
get_potential_outcomes.RdAn instance of PatientSample, or one of its subclasses like
CorrelatedPatientSample, reflects one particular state of the
world, where patient i would reliably experience a toxicity or efficacy
event if treated at a particular dose. This function, given true toxicity and
efficacy probabilities at doses 1, ..., num_doses, calculates 0/1 matrices to
reflect whether the patients in those samples would have experienced toxicity
and efficacy at the doses, had they been dosed as such. Using the
vernacular of causal inference, these are _potential outcomes_. At any single
instant, a patient can only be dosed at one dose, so only one of the
outcomes for a patient would in reality have been observed; the rest are
counterfactual.
get_potential_outcomes(patient_samples, true_prob_tox, true_prob_eff)list of PatientSample objects, or
subclass thereof.
vector of probabilities of toxicity outcomes at doses
vector of probabilities of efficacy outcomes at doses
a list of lists, with names tox and eff, each mapping to a matrix of the potential outcomes.
num_sims <- 10
ps <- lapply(1:num_sims, function(x) PatientSample$new())
# Set tox_u and eff_u for each simulation
set.seed(2024)
lapply(1:num_sims, function(x) {
tox_u_new <- runif(n = 20)
eff_u_new <- runif(n = 20)
ps[[x]]$set_eff_and_tox(tox_u = tox_u_new, eff_u = eff_u_new)
})
#> [[1]]
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true_prob_tox <- c(0.05, 0.10, 0.15, 0.18, 0.45)
true_prob_eff <- c(0.40, 0.50, 0.52, 0.53, 0.53)
get_potential_outcomes(
patient_samples = ps,
true_prob_tox = true_prob_tox,
true_prob_eff = true_prob_eff
)
#> [[1]]
#> [[1]]$tox
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 1
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 0 0 0 0 0
#> [6,] 0 0 0 0 0
#> [7,] 0 0 0 0 1
#> [8,] 0 0 0 0 1
#> [9,] 0 0 0 0 0
#> [10,] 0 0 1 1 1
#> [11,] 0 0 0 0 0
#> [12,] 0 0 0 0 0
#> [13,] 0 0 0 0 0
#> [14,] 0 0 0 0 0
#> [15,] 0 0 0 0 1
#> [16,] 0 0 0 0 0
#> [17,] 0 0 1 1 1
#> [18,] 0 0 0 0 0
#> [19,] 0 0 1 1 1
#> [20,] 0 0 0 0 1
#>
#> [[1]]$eff
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 1
#> [2,] 1 1 1 1 1
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 0 0 0 0 0
#> [6,] 1 1 1 1 1
#> [7,] 0 0 0 0 0
#> [8,] 0 0 0 0 0
#> [9,] 1 1 1 1 1
#> [10,] 1 1 1 1 1
#> [11,] 0 1 1 1 1
#> [12,] 1 1 1 1 1
#> [13,] 1 1 1 1 1
#> [14,] 0 0 0 0 0
#> [15,] 0 0 0 0 0
#> [16,] 0 0 0 0 0
#> [17,] 1 1 1 1 1
#> [18,] 0 0 0 0 0
#> [19,] 1 1 1 1 1
#> [20,] 0 0 0 0 0
#>
#>
#> [[2]]
#> [[2]]$tox
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 1
#> [5,] 0 0 0 0 0
#> [6,] 0 0 0 0 1
#> [7,] 0 0 0 0 1
#> [8,] 0 0 0 0 1
#> [9,] 0 0 0 0 0
#> [10,] 0 0 0 0 0
#> [11,] 0 1 1 1 1
#> [12,] 0 0 0 0 0
#> [13,] 0 0 0 0 0
#> [14,] 0 0 0 0 0
#> [15,] 0 0 0 0 0
#> [16,] 0 0 0 0 0
#> [17,] 1 1 1 1 1
#> [18,] 0 0 0 0 1
#> [19,] 0 0 0 0 0
#> [20,] 0 0 0 0 1
#>
#> [[2]]$eff
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 1
#> [2,] 0 1 1 1 1
#> [3,] 1 1 1 1 1
#> [4,] 0 0 0 0 0
#> [5,] 1 1 1 1 1
#> [6,] 0 0 0 0 0
#> [7,] 0 0 0 0 0
#> [8,] 0 0 0 0 0
#> [9,] 1 1 1 1 1
#> [10,] 1 1 1 1 1
#> [11,] 0 0 0 0 0
#> [12,] 1 1 1 1 1
#> [13,] 0 0 0 0 0
#> [14,] 0 1 1 1 1
#> [15,] 1 1 1 1 1
#> [16,] 0 0 0 0 0
#> [17,] 1 1 1 1 1
#> [18,] 1 1 1 1 1
#> [19,] 0 0 0 0 0
#> [20,] 1 1 1 1 1
#>
#>
#> [[3]]
#> [[3]]$tox
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0 0 0 0 1
#> [2,] 0 0 0 0 1
#> [3,] 0 0 0 0 0
#> [4,] 1 1 1 1 1
#> [5,] 0 0 0 0 0
#> [6,] 0 0 0 0 0
#> [7,] 0 0 0 0 0
#> [8,] 0 0 0 0 1
#> [9,] 0 0 1 1 1
#> [10,] 0 0 0 0 0
#> [11,] 0 0 0 0 0
#> [12,] 0 0 0 0 0
#> [13,] 0 0 0 0 0
#> [14,] 1 1 1 1 1
#> [15,] 0 0 0 0 0
#> [16,] 0 0 0 0 1
#> [17,] 0 0 0 0 0
#> [18,] 0 0 0 0 0
#> [19,] 0 0 0 0 0
#> [20,] 0 0 0 0 0
#>
#> [[3]]$eff
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 1
#> [2,] 0 0 0 0 0
#> [3,] 1 1 1 1 1
#> [4,] 0 0 0 0 0
#> [5,] 1 1 1 1 1
#> [6,] 0 0 0 0 0
#> [7,] 1 1 1 1 1
#> [8,] 1 1 1 1 1
#> [9,] 1 1 1 1 1
#> [10,] 0 0 0 0 0
#> [11,] 1 1 1 1 1
#> [12,] 0 0 0 0 0
#> [13,] 0 0 0 0 0
#> [14,] 1 1 1 1 1
#> [15,] 0 1 1 1 1
#> [16,] 0 0 0 0 0
#> [17,] 0 0 0 0 0
#> [18,] 1 1 1 1 1
#> [19,] 0 1 1 1 1
#> [20,] 1 1 1 1 1
#>
#>
#> [[4]]
#> [[4]]$tox
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0 0 0 0 0
#> [2,] 0 1 1 1 1
#> [3,] 0 0 0 0 0
#> [4,] 0 0 1 1 1
#> [5,] 0 0 0 0 0
#> [6,] 1 1 1 1 1
#> [7,] 0 0 0 0 0
#> [8,] 0 0 0 0 0
#> [9,] 0 0 0 0 0
#> [10,] 0 0 0 0 0
#> [11,] 0 0 0 0 1
#> [12,] 1 1 1 1 1
#> [13,] 1 1 1 1 1
#> [14,] 0 0 0 0 1
#> [15,] 0 0 0 0 0
#> [16,] 0 0 0 0 0
#> [17,] 0 0 0 0 0
#> [18,] 0 1 1 1 1
#> [19,] 1 1 1 1 1
#> [20,] 0 0 0 0 0
#>
#> [[4]]$eff
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0 0 0 0 0
#> [2,] 1 1 1 1 1
#> [3,] 1 1 1 1 1
#> [4,] 0 1 1 1 1
#> [5,] 0 0 0 0 0
#> [6,] 0 0 0 0 0
#> [7,] 0 0 0 1 1
#> [8,] 1 1 1 1 1
#> [9,] 0 0 0 0 0
#> [10,] 1 1 1 1 1
#> [11,] 1 1 1 1 1
#> [12,] 0 1 1 1 1
#> [13,] 0 0 0 0 0
#> [14,] 1 1 1 1 1
#> [15,] 0 0 0 0 0
#> [16,] 0 1 1 1 1
#> [17,] 1 1 1 1 1
#> [18,] 1 1 1 1 1
#> [19,] 0 0 1 1 1
#> [20,] 1 1 1 1 1
#>
#>
#> [[5]]
#> [[5]]$tox
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0 0 1 1 1
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 1 1
#> [5,] 0 0 0 0 0
#> [6,] 0 0 0 0 0
#> [7,] 1 1 1 1 1
#> [8,] 0 0 0 0 0
#> [9,] 0 0 0 0 0
#> [10,] 0 0 0 0 1
#> [11,] 0 0 0 0 0
#> [12,] 0 0 0 0 0
#> [13,] 0 0 0 0 1
#> [14,] 0 0 0 0 0
#> [15,] 0 0 0 0 1
#> [16,] 0 0 0 0 0
#> [17,] 0 0 0 0 1
#> [18,] 1 1 1 1 1
#> [19,] 0 0 0 0 0
#> [20,] 0 0 0 0 0
#>
#> [[5]]$eff
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 1
#> [2,] 0 0 0 0 0
#> [3,] 1 1 1 1 1
#> [4,] 0 0 0 0 0
#> [5,] 1 1 1 1 1
#> [6,] 0 0 0 0 0
#> [7,] 0 0 0 0 0
#> [8,] 0 0 0 0 0
#> [9,] 0 0 0 0 0
#> [10,] 1 1 1 1 1
#> [11,] 1 1 1 1 1
#> [12,] 1 1 1 1 1
#> [13,] 1 1 1 1 1
#> [14,] 1 1 1 1 1
#> [15,] 1 1 1 1 1
#> [16,] 1 1 1 1 1
#> [17,] 0 1 1 1 1
#> [18,] 0 1 1 1 1
#> [19,] 0 0 0 0 0
#> [20,] 0 0 0 0 0
#>
#>
#> [[6]]
#> [[6]]$tox
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0 0 0 0 0
#> [2,] 1 1 1 1 1
#> [3,] 0 0 0 0 0
#> [4,] 0 0 1 1 1
#> [5,] 0 0 0 0 0
#> [6,] 1 1 1 1 1
#> [7,] 0 0 0 0 0
#> [8,] 0 0 0 0 1
#> [9,] 0 0 1 1 1
#> [10,] 0 0 0 0 0
#> [11,] 0 0 0 0 0
#> [12,] 0 0 0 0 0
#> [13,] 0 0 0 0 1
#> [14,] 0 0 0 0 0
#> [15,] 0 0 0 0 0
#> [16,] 0 0 0 0 0
#> [17,] 0 0 0 0 1
#> [18,] 0 0 0 0 0
#> [19,] 0 0 1 1 1
#> [20,] 0 0 1 1 1
#>
#> [[6]]$eff
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 1
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 1 1 1 1
#> [5,] 1 1 1 1 1
#> [6,] 0 0 0 0 0
#> [7,] 0 1 1 1 1
#> [8,] 0 0 0 0 0
#> [9,] 1 1 1 1 1
#> [10,] 0 1 1 1 1
#> [11,] 1 1 1 1 1
#> [12,] 1 1 1 1 1
#> [13,] 0 0 0 0 0
#> [14,] 1 1 1 1 1
#> [15,] 0 0 0 0 0
#> [16,] 0 0 0 0 0
#> [17,] 1 1 1 1 1
#> [18,] 1 1 1 1 1
#> [19,] 0 0 0 0 0
#> [20,] 0 0 0 0 0
#>
#>
#> [[7]]
#> [[7]]$tox
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0 0 0 0 1
#> [2,] 1 1 1 1 1
#> [3,] 0 0 0 0 1
#> [4,] 0 0 0 0 1
#> [5,] 0 1 1 1 1
#> [6,] 0 0 1 1 1
#> [7,] 0 0 0 0 1
#> [8,] 0 0 0 0 0
#> [9,] 0 0 0 0 1
#> [10,] 0 0 0 0 0
#> [11,] 0 0 0 0 0
#> [12,] 0 0 1 1 1
#> [13,] 0 0 1 1 1
#> [14,] 0 0 0 0 0
#> [15,] 0 0 1 1 1
#> [16,] 0 0 0 0 1
#> [17,] 0 0 0 0 1
#> [18,] 0 0 0 0 1
#> [19,] 0 0 0 0 0
#> [20,] 1 1 1 1 1
#>
#> [[7]]$eff
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 1
#> [2,] 1 1 1 1 1
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 1 1 1 1 1
#> [6,] 0 0 0 0 0
#> [7,] 0 0 1 1 1
#> [8,] 1 1 1 1 1
#> [9,] 0 0 0 0 0
#> [10,] 0 0 0 0 0
#> [11,] 1 1 1 1 1
#> [12,] 1 1 1 1 1
#> [13,] 1 1 1 1 1
#> [14,] 1 1 1 1 1
#> [15,] 0 0 0 0 0
#> [16,] 0 1 1 1 1
#> [17,] 0 0 0 0 0
#> [18,] 1 1 1 1 1
#> [19,] 1 1 1 1 1
#> [20,] 0 0 0 0 0
#>
#>
#> [[8]]
#> [[8]]$tox
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 1 1 1
#> [4,] 0 0 0 0 0
#> [5,] 0 0 0 0 1
#> [6,] 0 0 0 0 1
#> [7,] 0 0 0 0 0
#> [8,] 0 0 0 0 0
#> [9,] 0 0 0 0 0
#> [10,] 1 1 1 1 1
#> [11,] 0 0 0 0 0
#> [12,] 0 0 0 0 0
#> [13,] 0 0 0 0 0
#> [14,] 0 0 0 0 0
#> [15,] 0 0 0 0 0
#> [16,] 0 0 0 0 1
#> [17,] 0 0 0 0 0
#> [18,] 0 0 0 0 0
#> [19,] 0 0 0 0 0
#> [20,] 0 0 0 0 1
#>
#> [[8]]$eff
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 1
#> [2,] 0 0 0 0 0
#> [3,] 0 1 1 1 1
#> [4,] 0 0 0 0 0
#> [5,] 0 0 0 0 0
#> [6,] 1 1 1 1 1
#> [7,] 0 0 0 0 0
#> [8,] 0 0 0 0 0
#> [9,] 1 1 1 1 1
#> [10,] 0 0 0 0 0
#> [11,] 1 1 1 1 1
#> [12,] 1 1 1 1 1
#> [13,] 0 0 0 0 0
#> [14,] 1 1 1 1 1
#> [15,] 1 1 1 1 1
#> [16,] 1 1 1 1 1
#> [17,] 1 1 1 1 1
#> [18,] 0 0 0 0 0
#> [19,] 0 0 0 0 0
#> [20,] 1 1 1 1 1
#>
#>
#> [[9]]
#> [[9]]$tox
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 0 0 0 0 0
#> [6,] 0 0 0 0 1
#> [7,] 0 0 0 0 0
#> [8,] 0 0 0 0 0
#> [9,] 0 0 0 0 1
#> [10,] 0 0 0 0 1
#> [11,] 0 0 0 0 1
#> [12,] 0 0 0 0 0
#> [13,] 0 0 0 0 0
#> [14,] 0 0 0 0 0
#> [15,] 1 1 1 1 1
#> [16,] 0 0 0 0 0
#> [17,] 0 0 0 0 0
#> [18,] 0 0 0 0 0
#> [19,] 0 0 0 0 0
#> [20,] 0 0 0 0 0
#>
#> [[9]]$eff
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 1
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 1 1 1 1 1
#> [6,] 1 1 1 1 1
#> [7,] 0 0 0 0 0
#> [8,] 1 1 1 1 1
#> [9,] 0 0 0 0 0
#> [10,] 0 0 0 0 0
#> [11,] 0 0 0 0 0
#> [12,] 0 0 0 1 1
#> [13,] 0 0 0 0 0
#> [14,] 0 0 0 0 0
#> [15,] 0 0 0 0 0
#> [16,] 1 1 1 1 1
#> [17,] 0 0 0 0 0
#> [18,] 0 0 0 0 0
#> [19,] 1 1 1 1 1
#> [20,] 0 0 0 0 0
#>
#>
#> [[10]]
#> [[10]]$tox
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0 0 0 0 0
#> [2,] 0 1 1 1 1
#> [3,] 0 0 0 0 0
#> [4,] 0 0 0 0 0
#> [5,] 0 0 0 0 0
#> [6,] 0 0 0 0 0
#> [7,] 0 0 0 0 1
#> [8,] 0 0 0 0 0
#> [9,] 0 0 0 0 1
#> [10,] 0 0 0 0 0
#> [11,] 0 0 0 0 0
#> [12,] 0 0 0 0 0
#> [13,] 0 0 0 0 0
#> [14,] 1 1 1 1 1
#> [15,] 0 0 0 0 1
#> [16,] 0 0 0 0 0
#> [17,] 0 0 0 0 1
#> [18,] 0 1 1 1 1
#> [19,] 0 0 0 0 0
#> [20,] 0 0 1 1 1
#>
#> [[10]]$eff
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 1 1 1 1 1
#> [2,] 1 1 1 1 1
#> [3,] 1 1 1 1 1
#> [4,] 0 0 0 0 0
#> [5,] 0 0 0 0 0
#> [6,] 0 1 1 1 1
#> [7,] 0 0 0 0 0
#> [8,] 0 0 0 0 0
#> [9,] 0 0 0 0 0
#> [10,] 1 1 1 1 1
#> [11,] 0 0 0 0 0
#> [12,] 1 1 1 1 1
#> [13,] 0 0 0 0 0
#> [14,] 1 1 1 1 1
#> [15,] 0 0 0 0 0
#> [16,] 0 0 0 0 0
#> [17,] 0 0 0 0 0
#> [18,] 0 0 0 0 0
#> [19,] 1 1 1 1 1
#> [20,] 0 0 0 0 0
#>
#>