Nothing
tests/testthat/_snaps/run_trials.md
In adaptr: Adaptive Trial Simulator
single trial simulation works
Code
run_trial(setup_equi_futil_only_first, seed = 12345)
Output
Single simulation result: generic binomially distributed outcome trial
* Undesirable outcome
* Initial/final common control arms: B/B
Final status: conclusive, stopped for equivalence
Final/maximum allowed sample sizes: 500/2000 (25.0%)
Available outcome data at last adaptive analysis: 500/500 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.20 equivalence 500 1 0.333
B 0.21 control 500 NA 0.333
C 0.70 inferior 500 0 0.333
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 39 195 0.200 0.202 0.0286 0.151
B 25 152 0.164 0.168 0.0294 0.115
C 114 153 0.745 0.743 0.0358 0.668
hi_cri_all
0.262
0.230
0.807
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 39 195 0.200 0.202 0.0282 0.149 0.261
B 25 152 0.164 0.167 0.0295 0.113 0.231
C 114 153 0.745 0.744 0.0346 0.669 0.807
Simulation details:
* Random seed: 12345
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
Code
run_trial(setup_equi_futil_only_first, seed = 12345)
Output
Single simulation result: generic binomially distributed outcome trial
* Undesirable outcome
* Initial/final common control arms: B/B
Final status: conclusive, stopped for equivalence
Final/maximum allowed sample sizes: 500/2000 (25.0%)
Available outcome data at last adaptive analysis: 500/500 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.20 equivalence 500 1 0.333
B 0.21 control 500 NA 0.333
C 0.70 inferior 500 0 0.333
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 39 195 0.200 0.202 0.0286 0.151
B 25 152 0.164 0.168 0.0294 0.115
C 114 153 0.745 0.743 0.0358 0.668
hi_cri_all
0.262
0.230
0.807
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 39 195 0.200 0.202 0.0282 0.149 0.261
B 25 152 0.164 0.167 0.0295 0.113 0.231
C 114 153 0.745 0.744 0.0346 0.669 0.807
Simulation details:
* Random seed: 12345
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
Code
run_trial(setup_rescale_probs, seed = 12345)
Output
Single simulation result: generic binomially distributed outcome trial
* Undesirable outcome
* Initial/final common control arms: B/B
Final status: conclusive, stopped for superiority
Final/maximum allowed sample sizes: 1500/2000 (75.0%)
Available outcome data at last adaptive analysis: 1500/1500 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.20 inferior 1500 0.0046 0.60
B 0.15 superior 1500 0.9954 0.40
C 0.30 inferior 1000 0.0010 0.15
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 143 701 0.204 0.205 0.0152 0.176
B 88 593 0.148 0.149 0.0151 0.122
C 56 206 0.272 0.273 0.0310 0.213
hi_cri_all
0.235
0.179
0.336
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 143 701 0.204 0.205 0.0151 0.176 0.235
B 88 593 0.148 0.149 0.0144 0.122 0.180
C 56 206 0.272 0.274 0.0303 0.216 0.334
Simulation details:
* Random seed: 12345
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
dispatch_trial_runs works
Code
dispatch_trial_runs(1:5, setup, seeds = seeds, sparse = FALSE, cores = 1)
Output
[[1]]
Single simulation result: generic binomially distributed outcome trial
* Desirable outcome
* Initial/final common control arms: B/C
Final status: conclusive, stopped for futility
Final/maximum allowed sample sizes: 500/2000 (25.0%)
Available outcome data at last adaptive analysis: 500/500 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 500 0.953 0.466
B 0.20 inferior 500 0.006 0.150
C 0.30 control 500 NA 0.384
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 44 182 0.242 0.243 0.0309 0.1855
B 18 123 0.146 0.151 0.0321 0.0962
C 52 195 0.267 0.269 0.0312 0.2087
hi_cri_all
0.307
0.221
0.333
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 44 182 0.242 0.244 0.0308 0.1834 0.308
B 18 123 0.146 0.150 0.0314 0.0957 0.218
C 52 195 0.267 0.268 0.0318 0.2103 0.333
Simulation details:
* Random seed: none specified
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
[[2]]
Single simulation result: generic binomially distributed outcome trial
* Desirable outcome
* Initial/final common control arms: B/C
Final status: conclusive, stopped for superiority
Final/maximum allowed sample sizes: 500/2000 (25.0%)
Available outcome data at last adaptive analysis: 500/500 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 300 0.9534 0.333
B 0.20 inferior 500 0.0092 0.150
C 0.30 superior 500 0.9908 0.850
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 20 116 0.172 0.176 0.0351 0.115
B 26 119 0.218 0.221 0.0384 0.151
C 90 265 0.340 0.341 0.0289 0.285
hi_cri_all
0.251
0.302
0.400
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 20 116 0.172 0.175 0.0340 0.115 0.249
B 26 119 0.218 0.222 0.0387 0.155 0.303
C 90 265 0.340 0.340 0.0284 0.286 0.400
Simulation details:
* Random seed: none specified
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
[[3]]
Single simulation result: generic binomially distributed outcome trial
* Desirable outcome
* Initial/final common control arms: B/C
Final status: conclusive, stopped for futility
Final/maximum allowed sample sizes: 700/2000 (35.0%)
Available outcome data at last adaptive analysis: 700/700 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 700 0.9944 0.313
B 0.20 inferior 700 0.0094 0.150
C 0.30 control 700 NA 0.537
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 59 253 0.233 0.234 0.0266 0.185
B 27 152 0.178 0.180 0.0312 0.124
C 82 295 0.278 0.279 0.0265 0.229
hi_cri_all
0.290
0.249
0.333
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 59 253 0.233 0.235 0.0266 0.186 0.289
B 27 152 0.178 0.181 0.0308 0.125 0.245
C 82 295 0.278 0.279 0.0262 0.229 0.330
Simulation details:
* Random seed: none specified
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
[[4]]
Single simulation result: generic binomially distributed outcome trial
* Desirable outcome
* Initial/final common control arms: B/C
Final status: conclusive, stopped for futility
Final/maximum allowed sample sizes: 900/2000 (45.0%)
Available outcome data at last adaptive analysis: 900/900 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 900 0.991 0.328
B 0.20 inferior 900 0.008 0.150
C 0.30 control 900 NA 0.522
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 83 318 0.261 0.262 0.0246 0.216
B 38 191 0.199 0.201 0.0288 0.150
C 114 391 0.292 0.291 0.0229 0.250
hi_cri_all
0.312
0.261
0.339
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 83 318 0.261 0.262 0.0245 0.217 0.312
B 38 191 0.199 0.201 0.0296 0.146 0.259
C 114 391 0.292 0.293 0.0225 0.250 0.336
Simulation details:
* Random seed: none specified
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
[[5]]
Single simulation result: generic binomially distributed outcome trial
* Desirable outcome
* Initial/final common control arms: B/C
Final status: conclusive, stopped for superiority
Final/maximum allowed sample sizes: 1200/2000 (60.0%)
Available outcome data at last adaptive analysis: 1200/1200 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 300 0.9692 0.333
B 0.20 inferior 1200 0.0096 0.150
C 0.30 superior 1200 0.9904 0.850
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 16 88 0.182 0.186 0.0398 0.114
B 70 292 0.240 0.241 0.0251 0.194
C 255 820 0.311 0.311 0.0161 0.280
hi_cri_all
0.273
0.293
0.344
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 16 88 0.182 0.187 0.0410 0.118 0.273
B 70 292 0.240 0.241 0.0243 0.193 0.292
C 255 820 0.311 0.311 0.0166 0.280 0.343
Simulation details:
* Random seed: none specified
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
Code
dispatch_trial_runs(1:5, setup, seeds = seeds, sparse = TRUE, cores = 2, cl = cl)
Output
[[1]]
Single simulation result [saved/printed with sparse details]
Final status: conclusive, stopped for futility
Final sample size: 500
Available outcome data at last adaptive analysis: 500/500 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 500 0.953 0.466
B 0.20 inferior 500 0.006 0.150
C 0.30 control 500 NA 0.384
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 44 182 0.242 0.243 0.0309 0.1855
B 18 123 0.146 0.151 0.0321 0.0962
C 52 195 0.267 0.269 0.0312 0.2087
hi_cri_all
0.307
0.221
0.333
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 44 182 0.242 0.244 0.0308 0.1834 0.308
B 18 123 0.146 0.150 0.0314 0.0957 0.218
C 52 195 0.267 0.268 0.0318 0.2103 0.333
Simulation details:
* Random seed: none specified
[[2]]
Single simulation result [saved/printed with sparse details]
Final status: conclusive, stopped for superiority
Final sample size: 500
Available outcome data at last adaptive analysis: 500/500 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 300 0.9534 0.333
B 0.20 inferior 500 0.0092 0.150
C 0.30 superior 500 0.9908 0.850
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 20 116 0.172 0.176 0.0351 0.115
B 26 119 0.218 0.221 0.0384 0.151
C 90 265 0.340 0.341 0.0289 0.285
hi_cri_all
0.251
0.302
0.400
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 20 116 0.172 0.175 0.0340 0.115 0.249
B 26 119 0.218 0.222 0.0387 0.155 0.303
C 90 265 0.340 0.340 0.0284 0.286 0.400
Simulation details:
* Random seed: none specified
[[3]]
Single simulation result [saved/printed with sparse details]
Final status: conclusive, stopped for futility
Final sample size: 700
Available outcome data at last adaptive analysis: 700/700 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 700 0.9944 0.313
B 0.20 inferior 700 0.0094 0.150
C 0.30 control 700 NA 0.537
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 59 253 0.233 0.234 0.0266 0.185
B 27 152 0.178 0.180 0.0312 0.124
C 82 295 0.278 0.279 0.0265 0.229
hi_cri_all
0.290
0.249
0.333
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 59 253 0.233 0.235 0.0266 0.186 0.289
B 27 152 0.178 0.181 0.0308 0.125 0.245
C 82 295 0.278 0.279 0.0262 0.229 0.330
Simulation details:
* Random seed: none specified
[[4]]
Single simulation result [saved/printed with sparse details]
Final status: conclusive, stopped for futility
Final sample size: 900
Available outcome data at last adaptive analysis: 900/900 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 900 0.991 0.328
B 0.20 inferior 900 0.008 0.150
C 0.30 control 900 NA 0.522
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 83 318 0.261 0.262 0.0246 0.216
B 38 191 0.199 0.201 0.0288 0.150
C 114 391 0.292 0.291 0.0229 0.250
hi_cri_all
0.312
0.261
0.339
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 83 318 0.261 0.262 0.0245 0.217 0.312
B 38 191 0.199 0.201 0.0296 0.146 0.259
C 114 391 0.292 0.293 0.0225 0.250 0.336
Simulation details:
* Random seed: none specified
[[5]]
Single simulation result [saved/printed with sparse details]
Final status: conclusive, stopped for superiority
Final sample size: 1200
Available outcome data at last adaptive analysis: 1200/1200 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 300 0.9692 0.333
B 0.20 inferior 1200 0.0096 0.150
C 0.30 superior 1200 0.9904 0.850
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 16 88 0.182 0.186 0.0398 0.114
B 70 292 0.240 0.241 0.0251 0.194
C 255 820 0.311 0.311 0.0161 0.280
hi_cri_all
0.273
0.293
0.344
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 16 88 0.182 0.187 0.0410 0.118 0.273
B 70 292 0.240 0.241 0.0243 0.193 0.292
C 255 820 0.311 0.311 0.0166 0.280 0.343
Simulation details:
* Random seed: none specified
prog_breaks
Code
prog_breaks(0.1, prev_n_rep = 10, n_rep_new = 20, cores = 1)
Output
$breaks
[1] 2 4 7 8 10 13 15 16 18 20
$start_mess
[1] "run_trials: 0/20 (0%) [starting]"
$prog_mess
[1] "run_trials: 2/20 (10%)" "run_trials: 4/20 (20%)"
[3] "run_trials: 7/20 (30%)" "run_trials: 8/20 (40%)"
[5] "run_trials: 10/20 (50%)" "run_trials: 13/20 (60%)"
[7] "run_trials: 15/20 (70%)" "run_trials: 16/20 (80%)"
[9] "run_trials: 18/20 (90%)" "run_trials: 20/20 (100%)"
$batches
$batches[[1]]
[1] 11 12
$batches[[2]]
[1] 13 14
$batches[[3]]
[1] 15 16 17
$batches[[4]]
[1] 18
$batches[[5]]
[1] 19 20
$batches[[6]]
[1] 21 22 23
$batches[[7]]
[1] 24 25
$batches[[8]]
[1] 26
$batches[[9]]
[1] 27 28
$batches[[10]]
[1] 29 30
Code
prog_breaks(0.1, prev_n_rep = 0, n_rep_new = 10, cores = 2)
Output
$breaks
[1] 2 4 6 8 10
$start_mess
[1] "run_trials: 0/10 (0%) [starting]"
$prog_mess
[1] "run_trials: 2/10 (20%)" "run_trials: 4/10 (40%)"
[3] "run_trials: 6/10 (60%)" "run_trials: 8/10 (80%)"
[5] "run_trials: 10/10 (100%)"
$batches
$batches[[1]]
[1] 1 2
$batches[[2]]
[1] 3 4
$batches[[3]]
[1] 5 6
$batches[[4]]
[1] 7 8
$batches[[5]]
[1] 9 10
Multiple trials simulation works on multiple cores
Code
extract_results(res)
Output
sim final_n sum_ys ratio_ys final_status superior_arm selected_arm
1 1 500 110 0.2200000 superiority B B
2 2 1200 273 0.2275000 superiority B B
3 3 1200 266 0.2216667 superiority B B
4 4 700 156 0.2228571 superiority B B
5 5 1300 295 0.2269231 superiority B B
6 6 600 131 0.2183333 superiority B B
7 7 1900 420 0.2210526 superiority B B
8 8 2000 433 0.2165000 max <NA> <NA>
9 9 1600 353 0.2206250 superiority B B
10 10 1000 220 0.2200000 equivalence <NA> <NA>
11 11 1200 264 0.2200000 superiority B B
12 12 400 94 0.2350000 superiority B B
13 13 2000 469 0.2345000 max <NA> <NA>
14 14 900 197 0.2188889 equivalence <NA> <NA>
15 15 1400 303 0.2164286 superiority B B
16 16 2000 462 0.2310000 max <NA> <NA>
17 17 1000 215 0.2150000 equivalence <NA> <NA>
18 18 2000 472 0.2360000 max <NA> <NA>
19 19 1600 372 0.2325000 superiority B B
20 20 500 135 0.2700000 superiority B B
err sq_err err_te sq_err_te
1 -0.037462579 1.403445e-03 NA NA
2 -0.008091122 6.546625e-05 NA NA
3 -0.009209925 8.482272e-05 NA NA
4 -0.025234966 6.368035e-04 NA NA
5 -0.003681956 1.355680e-05 NA NA
6 -0.032735518 1.071614e-03 NA NA
7 -0.001214794 1.475723e-06 NA NA
8 NA NA NA NA
9 -0.003254965 1.059480e-05 NA NA
10 NA NA NA NA
11 -0.011561899 1.336775e-04 NA NA
12 -0.035424899 1.254923e-03 NA NA
13 NA NA NA NA
14 NA NA NA NA
15 -0.017683969 3.127227e-04 NA NA
16 NA NA NA NA
17 NA NA NA NA
18 NA NA NA NA
19 0.004641866 2.154692e-05 NA NA
20 0.006639065 4.407718e-05 NA NA
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single trial simulation works
Code
run_trial(setup_equi_futil_only_first, seed = 12345)
Output
Single simulation result: generic binomially distributed outcome trial
* Undesirable outcome
* Initial/final common control arms: B/B
Final status: conclusive, stopped for equivalence
Final/maximum allowed sample sizes: 500/2000 (25.0%)
Available outcome data at last adaptive analysis: 500/500 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.20 equivalence 500 1 0.333
B 0.21 control 500 NA 0.333
C 0.70 inferior 500 0 0.333
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 39 195 0.200 0.202 0.0286 0.151
B 25 152 0.164 0.168 0.0294 0.115
C 114 153 0.745 0.743 0.0358 0.668
hi_cri_all
0.262
0.230
0.807
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 39 195 0.200 0.202 0.0282 0.149 0.261
B 25 152 0.164 0.167 0.0295 0.113 0.231
C 114 153 0.745 0.744 0.0346 0.669 0.807
Simulation details:
* Random seed: 12345
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
Code
run_trial(setup_equi_futil_only_first, seed = 12345)
Output
Single simulation result: generic binomially distributed outcome trial
* Undesirable outcome
* Initial/final common control arms: B/B
Final status: conclusive, stopped for equivalence
Final/maximum allowed sample sizes: 500/2000 (25.0%)
Available outcome data at last adaptive analysis: 500/500 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.20 equivalence 500 1 0.333
B 0.21 control 500 NA 0.333
C 0.70 inferior 500 0 0.333
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 39 195 0.200 0.202 0.0286 0.151
B 25 152 0.164 0.168 0.0294 0.115
C 114 153 0.745 0.743 0.0358 0.668
hi_cri_all
0.262
0.230
0.807
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 39 195 0.200 0.202 0.0282 0.149 0.261
B 25 152 0.164 0.167 0.0295 0.113 0.231
C 114 153 0.745 0.744 0.0346 0.669 0.807
Simulation details:
* Random seed: 12345
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
Code
run_trial(setup_rescale_probs, seed = 12345)
Output
Single simulation result: generic binomially distributed outcome trial
* Undesirable outcome
* Initial/final common control arms: B/B
Final status: conclusive, stopped for superiority
Final/maximum allowed sample sizes: 1500/2000 (75.0%)
Available outcome data at last adaptive analysis: 1500/1500 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.20 inferior 1500 0.0046 0.60
B 0.15 superior 1500 0.9954 0.40
C 0.30 inferior 1000 0.0010 0.15
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 143 701 0.204 0.205 0.0152 0.176
B 88 593 0.148 0.149 0.0151 0.122
C 56 206 0.272 0.273 0.0310 0.213
hi_cri_all
0.235
0.179
0.336
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 143 701 0.204 0.205 0.0151 0.176 0.235
B 88 593 0.148 0.149 0.0144 0.122 0.180
C 56 206 0.272 0.274 0.0303 0.216 0.334
Simulation details:
* Random seed: 12345
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
dispatch_trial_runs works
Code
dispatch_trial_runs(1:5, setup, seeds = seeds, sparse = FALSE, cores = 1)
Output
[[1]]
Single simulation result: generic binomially distributed outcome trial
* Desirable outcome
* Initial/final common control arms: B/C
Final status: conclusive, stopped for futility
Final/maximum allowed sample sizes: 500/2000 (25.0%)
Available outcome data at last adaptive analysis: 500/500 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 500 0.953 0.466
B 0.20 inferior 500 0.006 0.150
C 0.30 control 500 NA 0.384
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 44 182 0.242 0.243 0.0309 0.1855
B 18 123 0.146 0.151 0.0321 0.0962
C 52 195 0.267 0.269 0.0312 0.2087
hi_cri_all
0.307
0.221
0.333
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 44 182 0.242 0.244 0.0308 0.1834 0.308
B 18 123 0.146 0.150 0.0314 0.0957 0.218
C 52 195 0.267 0.268 0.0318 0.2103 0.333
Simulation details:
* Random seed: none specified
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
[[2]]
Single simulation result: generic binomially distributed outcome trial
* Desirable outcome
* Initial/final common control arms: B/C
Final status: conclusive, stopped for superiority
Final/maximum allowed sample sizes: 500/2000 (25.0%)
Available outcome data at last adaptive analysis: 500/500 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 300 0.9534 0.333
B 0.20 inferior 500 0.0092 0.150
C 0.30 superior 500 0.9908 0.850
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 20 116 0.172 0.176 0.0351 0.115
B 26 119 0.218 0.221 0.0384 0.151
C 90 265 0.340 0.341 0.0289 0.285
hi_cri_all
0.251
0.302
0.400
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 20 116 0.172 0.175 0.0340 0.115 0.249
B 26 119 0.218 0.222 0.0387 0.155 0.303
C 90 265 0.340 0.340 0.0284 0.286 0.400
Simulation details:
* Random seed: none specified
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
[[3]]
Single simulation result: generic binomially distributed outcome trial
* Desirable outcome
* Initial/final common control arms: B/C
Final status: conclusive, stopped for futility
Final/maximum allowed sample sizes: 700/2000 (35.0%)
Available outcome data at last adaptive analysis: 700/700 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 700 0.9944 0.313
B 0.20 inferior 700 0.0094 0.150
C 0.30 control 700 NA 0.537
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 59 253 0.233 0.234 0.0266 0.185
B 27 152 0.178 0.180 0.0312 0.124
C 82 295 0.278 0.279 0.0265 0.229
hi_cri_all
0.290
0.249
0.333
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 59 253 0.233 0.235 0.0266 0.186 0.289
B 27 152 0.178 0.181 0.0308 0.125 0.245
C 82 295 0.278 0.279 0.0262 0.229 0.330
Simulation details:
* Random seed: none specified
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
[[4]]
Single simulation result: generic binomially distributed outcome trial
* Desirable outcome
* Initial/final common control arms: B/C
Final status: conclusive, stopped for futility
Final/maximum allowed sample sizes: 900/2000 (45.0%)
Available outcome data at last adaptive analysis: 900/900 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 900 0.991 0.328
B 0.20 inferior 900 0.008 0.150
C 0.30 control 900 NA 0.522
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 83 318 0.261 0.262 0.0246 0.216
B 38 191 0.199 0.201 0.0288 0.150
C 114 391 0.292 0.291 0.0229 0.250
hi_cri_all
0.312
0.261
0.339
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 83 318 0.261 0.262 0.0245 0.217 0.312
B 38 191 0.199 0.201 0.0296 0.146 0.259
C 114 391 0.292 0.293 0.0225 0.250 0.336
Simulation details:
* Random seed: none specified
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
[[5]]
Single simulation result: generic binomially distributed outcome trial
* Desirable outcome
* Initial/final common control arms: B/C
Final status: conclusive, stopped for superiority
Final/maximum allowed sample sizes: 1200/2000 (60.0%)
Available outcome data at last adaptive analysis: 1200/1200 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 300 0.9692 0.333
B 0.20 inferior 1200 0.0096 0.150
C 0.30 superior 1200 0.9904 0.850
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 16 88 0.182 0.186 0.0398 0.114
B 70 292 0.240 0.241 0.0251 0.194
C 255 820 0.311 0.311 0.0161 0.280
hi_cri_all
0.273
0.293
0.344
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 16 88 0.182 0.187 0.0410 0.118 0.273
B 70 292 0.240 0.241 0.0243 0.193 0.292
C 255 820 0.311 0.311 0.0166 0.280 0.343
Simulation details:
* Random seed: none specified
* Credible interval width: 95%
* Number of posterior draws: 5000
* Posterior estimation method: medians with MAD-SDs
Code
dispatch_trial_runs(1:5, setup, seeds = seeds, sparse = TRUE, cores = 2, cl = cl)
Output
[[1]]
Single simulation result [saved/printed with sparse details]
Final status: conclusive, stopped for futility
Final sample size: 500
Available outcome data at last adaptive analysis: 500/500 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 500 0.953 0.466
B 0.20 inferior 500 0.006 0.150
C 0.30 control 500 NA 0.384
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 44 182 0.242 0.243 0.0309 0.1855
B 18 123 0.146 0.151 0.0321 0.0962
C 52 195 0.267 0.269 0.0312 0.2087
hi_cri_all
0.307
0.221
0.333
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 44 182 0.242 0.244 0.0308 0.1834 0.308
B 18 123 0.146 0.150 0.0314 0.0957 0.218
C 52 195 0.267 0.268 0.0318 0.2103 0.333
Simulation details:
* Random seed: none specified
[[2]]
Single simulation result [saved/printed with sparse details]
Final status: conclusive, stopped for superiority
Final sample size: 500
Available outcome data at last adaptive analysis: 500/500 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 300 0.9534 0.333
B 0.20 inferior 500 0.0092 0.150
C 0.30 superior 500 0.9908 0.850
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 20 116 0.172 0.176 0.0351 0.115
B 26 119 0.218 0.221 0.0384 0.151
C 90 265 0.340 0.341 0.0289 0.285
hi_cri_all
0.251
0.302
0.400
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 20 116 0.172 0.175 0.0340 0.115 0.249
B 26 119 0.218 0.222 0.0387 0.155 0.303
C 90 265 0.340 0.340 0.0284 0.286 0.400
Simulation details:
* Random seed: none specified
[[3]]
Single simulation result [saved/printed with sparse details]
Final status: conclusive, stopped for futility
Final sample size: 700
Available outcome data at last adaptive analysis: 700/700 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 700 0.9944 0.313
B 0.20 inferior 700 0.0094 0.150
C 0.30 control 700 NA 0.537
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 59 253 0.233 0.234 0.0266 0.185
B 27 152 0.178 0.180 0.0312 0.124
C 82 295 0.278 0.279 0.0265 0.229
hi_cri_all
0.290
0.249
0.333
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 59 253 0.233 0.235 0.0266 0.186 0.289
B 27 152 0.178 0.181 0.0308 0.125 0.245
C 82 295 0.278 0.279 0.0262 0.229 0.330
Simulation details:
* Random seed: none specified
[[4]]
Single simulation result [saved/printed with sparse details]
Final status: conclusive, stopped for futility
Final sample size: 900
Available outcome data at last adaptive analysis: 900/900 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 900 0.991 0.328
B 0.20 inferior 900 0.008 0.150
C 0.30 control 900 NA 0.522
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 83 318 0.261 0.262 0.0246 0.216
B 38 191 0.199 0.201 0.0288 0.150
C 114 391 0.292 0.291 0.0229 0.250
hi_cri_all
0.312
0.261
0.339
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 83 318 0.261 0.262 0.0245 0.217 0.312
B 38 191 0.199 0.201 0.0296 0.146 0.259
C 114 391 0.292 0.293 0.0225 0.250 0.336
Simulation details:
* Random seed: none specified
[[5]]
Single simulation result [saved/printed with sparse details]
Final status: conclusive, stopped for superiority
Final sample size: 1200
Available outcome data at last adaptive analysis: 1200/1200 (100.0%)
Trial results overview:
arms true_ys final_status status_look status_probs final_alloc
A 0.25 futile 300 0.9692 0.333
B 0.20 inferior 1200 0.0096 0.150
C 0.30 superior 1200 0.9904 0.850
Esimates from final analysis (all patients):
arms sum_ys_all ns_all raw_ests_all post_ests_all post_errs_all lo_cri_all
A 16 88 0.182 0.186 0.0398 0.114
B 70 292 0.240 0.241 0.0251 0.194
C 255 820 0.311 0.311 0.0161 0.280
hi_cri_all
0.273
0.293
0.344
Estimates from last adaptive analysis including each arm:
arms sum_ys ns raw_ests post_ests post_errs lo_cri hi_cri
A 16 88 0.182 0.187 0.0410 0.118 0.273
B 70 292 0.240 0.241 0.0243 0.193 0.292
C 255 820 0.311 0.311 0.0166 0.280 0.343
Simulation details:
* Random seed: none specified
prog_breaks
Code
prog_breaks(0.1, prev_n_rep = 10, n_rep_new = 20, cores = 1)
Output
$breaks
[1] 2 4 7 8 10 13 15 16 18 20
$start_mess
[1] "run_trials: 0/20 (0%) [starting]"
$prog_mess
[1] "run_trials: 2/20 (10%)" "run_trials: 4/20 (20%)"
[3] "run_trials: 7/20 (30%)" "run_trials: 8/20 (40%)"
[5] "run_trials: 10/20 (50%)" "run_trials: 13/20 (60%)"
[7] "run_trials: 15/20 (70%)" "run_trials: 16/20 (80%)"
[9] "run_trials: 18/20 (90%)" "run_trials: 20/20 (100%)"
$batches
$batches[[1]]
[1] 11 12
$batches[[2]]
[1] 13 14
$batches[[3]]
[1] 15 16 17
$batches[[4]]
[1] 18
$batches[[5]]
[1] 19 20
$batches[[6]]
[1] 21 22 23
$batches[[7]]
[1] 24 25
$batches[[8]]
[1] 26
$batches[[9]]
[1] 27 28
$batches[[10]]
[1] 29 30
Code
prog_breaks(0.1, prev_n_rep = 0, n_rep_new = 10, cores = 2)
Output
$breaks
[1] 2 4 6 8 10
$start_mess
[1] "run_trials: 0/10 (0%) [starting]"
$prog_mess
[1] "run_trials: 2/10 (20%)" "run_trials: 4/10 (40%)"
[3] "run_trials: 6/10 (60%)" "run_trials: 8/10 (80%)"
[5] "run_trials: 10/10 (100%)"
$batches
$batches[[1]]
[1] 1 2
$batches[[2]]
[1] 3 4
$batches[[3]]
[1] 5 6
$batches[[4]]
[1] 7 8
$batches[[5]]
[1] 9 10
Multiple trials simulation works on multiple cores
Code
extract_results(res)
Output
sim final_n sum_ys ratio_ys final_status superior_arm selected_arm
1 1 500 110 0.2200000 superiority B B
2 2 1200 273 0.2275000 superiority B B
3 3 1200 266 0.2216667 superiority B B
4 4 700 156 0.2228571 superiority B B
5 5 1300 295 0.2269231 superiority B B
6 6 600 131 0.2183333 superiority B B
7 7 1900 420 0.2210526 superiority B B
8 8 2000 433 0.2165000 max <NA> <NA>
9 9 1600 353 0.2206250 superiority B B
10 10 1000 220 0.2200000 equivalence <NA> <NA>
11 11 1200 264 0.2200000 superiority B B
12 12 400 94 0.2350000 superiority B B
13 13 2000 469 0.2345000 max <NA> <NA>
14 14 900 197 0.2188889 equivalence <NA> <NA>
15 15 1400 303 0.2164286 superiority B B
16 16 2000 462 0.2310000 max <NA> <NA>
17 17 1000 215 0.2150000 equivalence <NA> <NA>
18 18 2000 472 0.2360000 max <NA> <NA>
19 19 1600 372 0.2325000 superiority B B
20 20 500 135 0.2700000 superiority B B
err sq_err err_te sq_err_te
1 -0.037462579 1.403445e-03 NA NA
2 -0.008091122 6.546625e-05 NA NA
3 -0.009209925 8.482272e-05 NA NA
4 -0.025234966 6.368035e-04 NA NA
5 -0.003681956 1.355680e-05 NA NA
6 -0.032735518 1.071614e-03 NA NA
7 -0.001214794 1.475723e-06 NA NA
8 NA NA NA NA
9 -0.003254965 1.059480e-05 NA NA
10 NA NA NA NA
11 -0.011561899 1.336775e-04 NA NA
12 -0.035424899 1.254923e-03 NA NA
13 NA NA NA NA
14 NA NA NA NA
15 -0.017683969 3.127227e-04 NA NA
16 NA NA NA NA
17 NA NA NA NA
18 NA NA NA NA
19 0.004641866 2.154692e-05 NA NA
20 0.006639065 4.407718e-05 NA NA
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