Last updated on 2025-12-19 12:49:25 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.0.4.8 | 39.58 | 620.53 | 660.11 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.0.4.8 | 30.34 | 361.32 | 391.66 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.0.4.8 | 74.00 | 337.54 | 411.54 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.0.4.8 | 70.00 | 347.71 | 417.71 | ERROR | |
| r-devel-windows-x86_64 | 0.0.4.8 | 44.00 | 580.00 | 624.00 | OK | |
| r-patched-linux-x86_64 | 0.0.4.8 | 43.60 | 525.11 | 568.71 | OK | |
| r-release-linux-x86_64 | 0.0.4.8 | 40.60 | 530.64 | 571.24 | OK | |
| r-release-macos-arm64 | 0.0.4.8 | 11.00 | 124.00 | 135.00 | OK | |
| r-release-macos-x86_64 | 0.0.4.8 | 31.00 | 711.00 | 742.00 | OK | |
| r-release-windows-x86_64 | 0.0.4.8 | 28.00 | 583.00 | 611.00 | OK | |
| r-oldrel-macos-arm64 | 0.0.4.8 | 11.00 | 144.00 | 155.00 | OK | |
| r-oldrel-macos-x86_64 | 0.0.4.8 | 32.00 | 633.00 | 665.00 | OK | |
| r-oldrel-windows-x86_64 | 0.0.4.8 | 63.00 | 750.00 | 813.00 | OK |
Version: 0.0.4.8
Check: compiled code
Result: NOTE
File ‘TrialEmulation/libs/TrialEmulation.so’:
Found non-API call to R: ‘ATTRIB’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.0.4.8
Check: examples
Result: ERROR
Running examples in ‘TrialEmulation-Ex.R’ failed
The error most likely occurred in:
> ### Name: calculate_weights
> ### Title: Calculate Inverse Probability of Censoring Weights
> ### Aliases: calculate_weights calculate_weights,trial_sequence_ITT-method
> ### calculate_weights,trial_sequence_AT-method
> ### calculate_weights,trial_sequence_PP-method
>
> ### ** Examples
>
> ## Don't show:
> data.table::setDTthreads(2)
> ## End(Don't show)
> save_dir <- file.path(tempdir(), "switch_models")
> ts <- trial_sequence("PP") |>
+ set_data(
+ data = data_censored,
+ id = "id",
+ period = "period",
+ treatment = "treatment",
+ outcome = "outcome",
+ eligible = "eligible"
+ ) |>
+ set_switch_weight_model(
+ numerator = ~ age + x1 + x3,
+ denominator = ~age,
+ model_fitter = stats_glm_logit(save_path = save_dir)
+ ) |>
+ calculate_weights()
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_switch_weight_model': attempt access index 12/12 in VECTOR_ELT
Calls: calculate_weights ... [.data.table -> .handleSimpleError -> h -> .handleSimpleError -> h
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.0.4.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [159s/171s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(TrialEmulation)
>
> data.table::setDTthreads(2)
> test_check("TrialEmulation")
Saving _problems/test-data_extension-89.R
Saving _problems/test-data_extension-136.R
Saving _problems/test-data_extension-189.R
Saving _problems/test-data_manipulation-3.R
Saving _problems/test-data_manipulation-25.R
Saving _problems/test-data_manipulation-52.R
Saving _problems/test-data_manipulation-69.R
Starting data manipulation
Saving _problems/test-data_preparation-13.R
Saving _problems/test-data_preparation-94.R
Starting data manipulation
Saving _problems/test-data_preparation-121.R
Starting data manipulation
Saving _problems/test-data_preparation-144.R
Saving _problems/test-data_preparation-170.R
Saving _problems/test-generics-24.R
Saving _problems/test-generics-64.R
Saving _problems/test-generics-94.R
Saving _problems/test-modelling-404.R
Saving _problems/test-modelling-464.R
Saving _problems/test-predict-21.R
Saving _problems/test-predict-156.R
Saving _problems/test-sampling-83.R
Saving _problems/test-sampling-100.R
Saving _problems/test-sampling-119.R
Saving _problems/test-sampling-238.R
Saving _problems/test-te_datastore-5.R
Saving _problems/test-te_datastore_csv-73.R
Saving _problems/test-te_datastore_csv-179.R
Saving _problems/test-te_datastore_duckdb-22.R
Saving _problems/test-te_datastore_duckdb-63.R
Saving _problems/test-te_datastore_duckdb-147.R
Saving _problems/test-te_weights-16.R
Saving _problems/test-te_weights-52.R
Saving _problems/test-te_weights-85.R
Saving _problems/test-trial_sequence-55.R
Saving _problems/test-trial_sequence-70.R
Saving _problems/test-trial_sequence-85.R
Saving _problems/test-trial_sequence-101.R
Saving _problems/test-trial_sequence-164.R
Saving _problems/test-trial_sequence-191.R
Saving _problems/test-trial_sequence-210.R
Saving _problems/test-trial_sequence-224.R
Saving _problems/test-trial_sequence-243.R
Saving _problems/test-trial_sequence-264.R
Saving _problems/test-trial_sequence-280.R
Saving _problems/test-trial_sequence-325.R
Saving _problems/test-trial_sequence-380.R
Saving _problems/test-trial_sequence-399.R
Saving _problems/test-trial_sequence-414.R
Saving _problems/test-trial_sequence-429.R
Saving _problems/test-trial_sequence-451.R
Saving _problems/test-trial_sequence-457.R
Saving _problems/test-trial_sequence-468.R
Saving _problems/test-trial_sequence-507.R
Saving _problems/test-trial_sequence-538.R
Saving _problems/test-trial_sequence-580.R
[ FAIL 55 | WARN 4 | SKIP 22 | PASS 181 ]
══ Skipped tests (22) ══════════════════════════════════════════════════════════
• On CRAN (22): 'test-data_utils.R:1:1', 'test-data_utils.R:100:1',
'test-data_utils.R:115:1', 'test-modelling.R:99:3', 'test-modelling.R:154:3',
'test-modelling.R:175:3', 'test-modelling.R:205:3', 'test-modelling.R:229:3',
'test-modelling.R:266:3', 'test-modelling.R:290:3', 'test-modelling.R:314:3',
'test-modelling.R:357:3', 'test-predict.R:34:1', 'test-predict.R:86:1',
'test-sampling.R:1:1', 'test-sampling.R:11:1', 'test-sampling.R:18:1',
'test-sampling.R:40:1', 'test-sampling.R:180:3',
'test-trial_sequence.R:40:1', 'test-trial_sequence.R:44:1',
'test-trial_sequence.R:48:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-data_extension.R:78:3'): expand works as expected ──────────────
Error in ``[.data.table`(temp_data, , `:=`(wtprod, 1), by = id)`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation:::expand(...) at test-data_extension.R:78:3
2. ├─temp_data[, `:=`(wtprod, 1), by = id]
3. └─data.table:::`[.data.table`(temp_data, , `:=`(wtprod, 1), by = id)
── Error ('test-data_extension.R:124:3'): data extensions works as expected with first and last periods ──
Error in ``[.data.table`(temp_data, , `:=`(wtprod, 1), by = id)`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation:::data_extension(...) at test-data_extension.R:124:3
2. └─TrialEmulation:::expand(...)
3. ├─temp_data[, `:=`(wtprod, 1), by = id]
4. └─data.table:::`[.data.table`(temp_data, , `:=`(wtprod, 1), by = id)
── Error ('test-data_extension.R:176:3'): data extensions works as expected with separate_files=TRUE ──
Error in ``[.data.table`(temp_data, , `:=`(wtprod, 1), by = id)`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation:::data_extension(...) at test-data_extension.R:176:3
2. └─TrialEmulation:::expand(...)
3. ├─temp_data[, `:=`(wtprod, 1), by = id]
4. └─data.table:::`[.data.table`(temp_data, , `:=`(wtprod, 1), by = id)
── Error ('test-data_manipulation.R:3:3'): data_manipulation works as expected with no censoring ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation:::data_manipulation(object, use_censor = FALSE) at test-data_manipulation.R:3:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-data_manipulation.R:25:3'): data_manipulation works as expected with censoring ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation:::data_manipulation(object, use_censor = TRUE) at test-data_manipulation.R:25:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-data_manipulation.R:49:3'): data_manipulation works as expected with observations before eligibilitiy ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-data_manipulation.R:49:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─TrialEmulation:::data_manipulation(object, use_censor = TRUE)
8. ├─...[]
9. └─data.table:::`[.data.table`(...)
── Error ('test-data_manipulation.R:66:3'): data_manipulation works as expected with observations after outcome ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-data_manipulation.R:66:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─TrialEmulation:::data_manipulation(object, use_censor = TRUE)
8. ├─...[]
9. └─data.table:::`[.data.table`(...)
── Error ('test-data_preparation.R:4:3'): data_preparation works as expected ───
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-data_preparation.R:4:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-data_preparation.R:26:3'): data_preparation can be quiet ───────
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-data_preparation.R:26:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─TrialEmulation::data_preparation(...)
10. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
11. ├─...[]
12. └─data.table:::`[.data.table`(...)
── Error ('test-data_preparation.R:83:3'): data_preparation has correct values for 'treatment' ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-data_preparation.R:83:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-data_preparation.R:111:3'): data_preparation works with PP estimand type ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-data_preparation.R:111:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-data_preparation.R:133:3'): data_preparation works with As-Treated estimand type ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-data_preparation.R:133:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-data_preparation.R:156:3'): data_preparation works with ITT and censor weights ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-data_preparation.R:156:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-generics.R:5:3'): summary for data_preparation separate=TRUE ───
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-generics.R:5:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-generics.R:45:3'): summary for data_preparation separate=FALSE ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-generics.R:45:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-generics.R:75:3'): summary for initiators ──────────────────────
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-generics.R:75:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─TrialEmulation::initiators(...)
8. └─TrialEmulation::data_preparation(...)
9. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-modelling.R:383:3'): fit_msm works ─────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-modelling.R:383:3
2. ├─TrialEmulation::calculate_weights(...)
3. ├─TrialEmulation::set_censor_weight_model(...)
4. ├─TrialEmulation::set_data(...)
5. ├─TrialEmulation::set_data(...)
6. │ └─TrialEmulation (local) .local(object, data, ...)
7. │ ├─methods::callNextMethod(...)
8. │ │ └─base::eval(call, callEnv)
9. │ │ └─base::eval(call, callEnv)
10. │ └─TrialEmulation (local) .nextMethod(...)
11. │ └─TrialEmulation (local) .local(object, data, ...)
12. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
13. │ ├─...[]
14. │ └─data.table:::`[.data.table`(...)
15. ├─base::.handleSimpleError(...)
16. │ └─base (local) h(simpleError(msg, call))
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-modelling.R:443:3'): fit_msm works with weight functions ───────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-modelling.R:443:3
2. ├─TrialEmulation::calculate_weights(...)
3. ├─TrialEmulation::set_censor_weight_model(...)
4. ├─TrialEmulation::set_data(...)
5. ├─TrialEmulation::set_data(...)
6. │ └─TrialEmulation (local) .local(object, data, ...)
7. │ ├─methods::callNextMethod(...)
8. │ │ └─base::eval(call, callEnv)
9. │ │ └─base::eval(call, callEnv)
10. │ └─TrialEmulation (local) .nextMethod(...)
11. │ └─TrialEmulation (local) .local(object, data, ...)
12. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
13. │ ├─...[]
14. │ └─data.table:::`[.data.table`(...)
15. ├─base::.handleSimpleError(...)
16. │ └─base (local) h(simpleError(msg, call))
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-predict.R:7:3'): predict.TE_msm works as expected ──────────────
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::initiators(...) at test-predict.R:7:3
2. └─TrialEmulation::data_preparation(...)
3. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test-predict.R:146:3'): predict.TE_msm gives the same results as new predict ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'fit_msm': error in evaluating the argument 'object' in selecting a method for function 'load_expanded_data': error in evaluating the argument 'object' in selecting a method for function 'expand_trials': error in evaluating the argument 'object' in selecting a method for function 'set_expansion_options': error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::fit_msm(...) at test-predict.R:146:3
2. ├─TrialEmulation::load_expanded_data(...)
3. ├─TrialEmulation::expand_trials(...)
4. ├─TrialEmulation::set_expansion_options(...)
5. ├─TrialEmulation::set_outcome_model(...)
6. ├─TrialEmulation::set_data(trial_sequence("ITT"), trial_ex)
7. ├─TrialEmulation::set_data(trial_sequence("ITT"), trial_ex)
8. │ └─TrialEmulation (local) .local(object, data, ...)
9. │ ├─methods::callNextMethod(...)
10. │ │ └─base::eval(call, callEnv)
11. │ │ └─base::eval(call, callEnv)
12. │ └─TrialEmulation (local) .nextMethod(...)
13. │ └─TrialEmulation (local) .local(object, data, ...)
14. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
15. │ ├─...[]
16. │ └─data.table:::`[.data.table`(...)
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. ├─base::.handleSimpleError(...)
20. │ └─base (local) h(simpleError(msg, call))
21. ├─base::.handleSimpleError(...)
22. │ └─base (local) h(simpleError(msg, call))
23. ├─base::.handleSimpleError(...)
24. │ └─base (local) h(simpleError(msg, call))
25. └─base::.handleSimpleError(...)
26. └─base (local) h(simpleError(msg, call))
── Error ('test-sampling.R:74:3'): case_control_sampling_trials works with separate_files = TRUE ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-sampling.R:74:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-sampling.R:92:3'): case_control_sampling_trials works with separate_files = FALSE ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-sampling.R:92:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-sampling.R:110:3'): case_control_sampling_trials works with separate_files = TRUE is reproducible ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-sampling.R:110:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-sampling.R:221:3'): sample_controls works with trial_sequence objects containing te_datastore_datatable objects ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-sampling.R:221:3
2. ├─TrialEmulation::calculate_weights(...)
3. ├─TrialEmulation::set_censor_weight_model(...)
4. ├─TrialEmulation::set_data(...)
5. ├─TrialEmulation::set_data(...)
6. │ └─TrialEmulation (local) .local(object, data, ...)
7. │ ├─methods::callNextMethod(...)
8. │ │ └─base::eval(call, callEnv)
9. │ │ └─base::eval(call, callEnv)
10. │ └─TrialEmulation (local) .nextMethod(...)
11. │ └─TrialEmulation (local) .local(object, data, ...)
12. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
13. │ ├─...[]
14. │ └─data.table:::`[.data.table`(...)
15. ├─base::.handleSimpleError(...)
16. │ └─base (local) h(simpleError(msg, call))
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-te_datastore.R:2:3'): read_expanded_data can read te_datastore_datatable data ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_expansion_options': error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_expansion_options(...) at test-te_datastore.R:2:3
2. ├─TrialEmulation::set_outcome_model(...)
3. ├─TrialEmulation::set_data(trial_sequence("ITT"), data = data_censored)
4. ├─TrialEmulation::set_data(trial_sequence("ITT"), data = data_censored)
5. │ └─TrialEmulation (local) .local(object, data, ...)
6. │ ├─methods::callNextMethod(...)
7. │ │ └─base::eval(call, callEnv)
8. │ │ └─base::eval(call, callEnv)
9. │ └─TrialEmulation (local) .nextMethod(...)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
12. │ ├─...[]
13. │ └─data.table:::`[.data.table`(...)
14. ├─base::.handleSimpleError(...)
15. │ └─base (local) h(simpleError(msg, call))
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-te_datastore_csv.R:56:3'): sample_controls works with trial_sequence objects containing te_datastore_csv objects ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-te_datastore_csv.R:56:3
2. ├─TrialEmulation::calculate_weights(...)
3. ├─TrialEmulation::set_censor_weight_model(...)
4. ├─TrialEmulation::set_data(...)
5. ├─TrialEmulation::set_data(...)
6. │ └─TrialEmulation (local) .local(object, data, ...)
7. │ ├─methods::callNextMethod(...)
8. │ │ └─base::eval(call, callEnv)
9. │ │ └─base::eval(call, callEnv)
10. │ └─TrialEmulation (local) .nextMethod(...)
11. │ └─TrialEmulation (local) .local(object, data, ...)
12. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
13. │ ├─...[]
14. │ └─data.table:::`[.data.table`(...)
15. ├─base::.handleSimpleError(...)
16. │ └─base (local) h(simpleError(msg, call))
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-te_datastore_csv.R:162:3'): load_expanded_data works with trial_sequence objects containing te_datastore_csv objects ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-te_datastore_csv.R:162:3
2. ├─TrialEmulation::calculate_weights(...)
3. ├─TrialEmulation::set_censor_weight_model(...)
4. ├─TrialEmulation::set_data(...)
5. ├─TrialEmulation::set_data(...)
6. │ └─TrialEmulation (local) .local(object, data, ...)
7. │ ├─methods::callNextMethod(...)
8. │ │ └─base::eval(call, callEnv)
9. │ │ └─base::eval(call, callEnv)
10. │ └─TrialEmulation (local) .nextMethod(...)
11. │ └─TrialEmulation (local) .local(object, data, ...)
12. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
13. │ ├─...[]
14. │ └─data.table:::`[.data.table`(...)
15. ├─base::.handleSimpleError(...)
16. │ └─base (local) h(simpleError(msg, call))
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-te_datastore_duckdb.R:19:3'): read_expanded_data can read te_datastore_duckdb data ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_expansion_options': error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_expansion_options(...) at test-te_datastore_duckdb.R:19:3
2. ├─TrialEmulation::set_outcome_model(...)
3. ├─TrialEmulation::set_data(trial_sequence("ITT"), data = data)
4. ├─TrialEmulation::set_data(trial_sequence("ITT"), data = data)
5. │ └─TrialEmulation (local) .local(object, data, ...)
6. │ ├─methods::callNextMethod(...)
7. │ │ └─base::eval(call, callEnv)
8. │ │ └─base::eval(call, callEnv)
9. │ └─TrialEmulation (local) .nextMethod(...)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
12. │ ├─...[]
13. │ └─data.table:::`[.data.table`(...)
14. ├─base::.handleSimpleError(...)
15. │ └─base (local) h(simpleError(msg, call))
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-te_datastore_duckdb.R:61:3'): sample_controls works with trial_sequence objects containing te_datastore_duckdb objects ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-te_datastore_duckdb.R:61:3
2. ├─TrialEmulation::set_data(trial_sequence(estimand = "ITT"), data = data_censored)
3. ├─TrialEmulation::set_data(trial_sequence(estimand = "ITT"), data = data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-te_datastore_duckdb.R:145:3'): load_expanded_data works with trial_sequence objects containing te_datastore_duckdb objects ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-te_datastore_duckdb.R:145:3
2. ├─TrialEmulation::set_data(trial_sequence(estimand = "ITT"), data = data_censored)
3. ├─TrialEmulation::set_data(trial_sequence(estimand = "ITT"), data = data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-te_weights.R:3:3'): show works for te_weights_spec objects ─────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_switch_weight_model': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_switch_weight_model(...) at test-te_weights.R:3:3
2. ├─TrialEmulation::set_censor_weight_model(...)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
5. │ └─TrialEmulation (local) .local(object, data, ...)
6. │ ├─methods::callNextMethod(...)
7. │ │ └─base::eval(call, callEnv)
8. │ │ └─base::eval(call, callEnv)
9. │ └─TrialEmulation (local) .nextMethod(...)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
12. │ ├─...[]
13. │ └─data.table:::`[.data.table`(...)
14. ├─base::.handleSimpleError(...)
15. │ └─base (local) h(simpleError(msg, call))
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-te_weights.R:45:3'): weight_model_data_indices works ───────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_switch_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::calculate_weights(...) at test-te_weights.R:45:3
2. ├─TrialEmulation::set_switch_weight_model(...)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
5. │ └─TrialEmulation (local) .local(object, data, ...)
6. │ ├─methods::callNextMethod(...)
7. │ │ └─base::eval(call, callEnv)
8. │ │ └─base::eval(call, callEnv)
9. │ └─TrialEmulation (local) .nextMethod(...)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
12. │ ├─...[]
13. │ └─data.table:::`[.data.table`(...)
14. ├─base::.handleSimpleError(...)
15. │ └─base (local) h(simpleError(msg, call))
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-te_weights.R:78:3'): weight_model_data_indices catches bad input ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_switch_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::calculate_weights(...) at test-te_weights.R:78:3
2. ├─TrialEmulation::set_switch_weight_model(...)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
5. │ └─TrialEmulation (local) .local(object, data, ...)
6. │ ├─methods::callNextMethod(...)
7. │ │ └─base::eval(call, callEnv)
8. │ │ └─base::eval(call, callEnv)
9. │ └─TrialEmulation (local) .nextMethod(...)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
12. │ ├─...[]
13. │ └─data.table:::`[.data.table`(...)
14. ├─base::.handleSimpleError(...)
15. │ └─base (local) h(simpleError(msg, call))
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:53:3'): show works for trial_sequence_PP with data and outcome_model set ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:53:3
2. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:63:3'): set_data works for trial_sequence_ITT ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_data(...) at test-trial_sequence.R:63:3
2. └─TrialEmulation::set_data(...)
3. └─TrialEmulation (local) .local(object, data, ...)
4. ├─methods::callNextMethod(...)
5. │ └─base::eval(call, callEnv)
6. │ └─base::eval(call, callEnv)
7. └─TrialEmulation (local) .nextMethod(...)
8. └─TrialEmulation (local) .local(object, data, ...)
9. └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-trial_sequence.R:78:3'): set_data works for trial_sequence_PP ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_data(...) at test-trial_sequence.R:78:3
2. └─TrialEmulation::set_data(...)
3. └─TrialEmulation (local) .local(object, data, ...)
4. ├─methods::callNextMethod(...)
5. │ └─base::eval(call, callEnv)
6. │ └─base::eval(call, callEnv)
7. └─TrialEmulation (local) .nextMethod(...)
8. └─TrialEmulation (local) .local(object, data, ...)
9. └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-trial_sequence.R:94:3'): set_data works for trial_sequence_AT ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_data(...) at test-trial_sequence.R:94:3
2. └─TrialEmulation::set_data(...)
3. └─TrialEmulation (local) .local(object, data, ...)
4. ├─methods::callNextMethod(...)
5. │ └─base::eval(call, callEnv)
6. │ └─base::eval(call, callEnv)
7. └─TrialEmulation (local) .nextMethod(...)
8. └─TrialEmulation (local) .local(object, data, ...)
9. └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-trial_sequence.R:157:3'): ipw_data works as expected ───────────
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_data(...) at test-trial_sequence.R:157:3
2. └─TrialEmulation::set_data(...)
3. └─TrialEmulation (local) .local(object, data, ...)
4. ├─methods::callNextMethod(...)
5. │ └─base::eval(call, callEnv)
6. │ └─base::eval(call, callEnv)
7. └─TrialEmulation (local) .nextMethod(...)
8. └─TrialEmulation (local) .local(object, data, ...)
9. └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-trial_sequence.R:185:3'): set_switch_weight_model works for PP ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_switch_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_switch_weight_model(...) at test-trial_sequence.R:185:3
2. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:201:3'): time_on_sequence doesn't get included in numerator ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_switch_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-trial_sequence.R:201:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─TrialEmulation::set_switch_weight_model(...)
8. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
9. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ ├─methods::callNextMethod(...)
12. │ │ └─base::eval(call, callEnv)
13. │ │ └─base::eval(call, callEnv)
14. │ └─TrialEmulation (local) .nextMethod(...)
15. │ └─TrialEmulation (local) .local(object, data, ...)
16. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
17. │ ├─...[]
18. │ └─data.table:::`[.data.table`(...)
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:216:3'): set_censor_weight_model works for ITT ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_censor_weight_model(...) at test-trial_sequence.R:216:3
2. ├─TrialEmulation::set_data(trial_sequence("ITT"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("ITT"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:235:3'): set_censor_weight_model works for PP ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_censor_weight_model(...) at test-trial_sequence.R:235:3
2. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:253:3'): time_on_sequence doesn't get included in numerator ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-trial_sequence.R:253:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─TrialEmulation::set_censor_weight_model(...)
8. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
9. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ ├─methods::callNextMethod(...)
12. │ │ └─base::eval(call, callEnv)
13. │ │ └─base::eval(call, callEnv)
14. │ └─TrialEmulation (local) .nextMethod(...)
15. │ └─TrialEmulation (local) .local(object, data, ...)
16. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
17. │ ├─...[]
18. │ └─data.table:::`[.data.table`(...)
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:271:3'): calculate_weights works for ITT with censor weights ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::calculate_weights(...) at test-trial_sequence.R:271:3
2. ├─TrialEmulation::set_censor_weight_model(...)
3. ├─TrialEmulation::set_data(trial_sequence("ITT"), data_censored)
4. ├─TrialEmulation::set_data(trial_sequence("ITT"), data_censored)
5. │ └─TrialEmulation (local) .local(object, data, ...)
6. │ ├─methods::callNextMethod(...)
7. │ │ └─base::eval(call, callEnv)
8. │ │ └─base::eval(call, callEnv)
9. │ └─TrialEmulation (local) .nextMethod(...)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
12. │ ├─...[]
13. │ └─data.table:::`[.data.table`(...)
14. ├─base::.handleSimpleError(...)
15. │ └─base (local) h(simpleError(msg, call))
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:318:3'): calculate_weights works for PP with switch_weights ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_switch_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::calculate_weights(...) at test-trial_sequence.R:318:3
2. ├─TrialEmulation::set_switch_weight_model(...)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
5. │ └─TrialEmulation (local) .local(object, data, ...)
6. │ ├─methods::callNextMethod(...)
7. │ │ └─base::eval(call, callEnv)
8. │ │ └─base::eval(call, callEnv)
9. │ └─TrialEmulation (local) .nextMethod(...)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
12. │ ├─...[]
13. │ └─data.table:::`[.data.table`(...)
14. ├─base::.handleSimpleError(...)
15. │ └─base (local) h(simpleError(msg, call))
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:370:3'): calculate_weights works for PP with switch_weights ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'expand_trials': error in evaluating the argument 'object' in selecting a method for function 'set_expansion_options': error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_switch_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::expand_trials(...) at test-trial_sequence.R:370:3
2. ├─TrialEmulation::set_expansion_options(...)
3. ├─TrialEmulation::set_outcome_model(...)
4. ├─TrialEmulation::calculate_weights(...)
5. ├─TrialEmulation::set_switch_weight_model(...)
6. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
7. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
8. │ └─TrialEmulation (local) .local(object, data, ...)
9. │ ├─methods::callNextMethod(...)
10. │ │ └─base::eval(call, callEnv)
11. │ │ └─base::eval(call, callEnv)
12. │ └─TrialEmulation (local) .nextMethod(...)
13. │ └─TrialEmulation (local) .local(object, data, ...)
14. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
15. │ ├─...[]
16. │ └─data.table:::`[.data.table`(...)
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. ├─base::.handleSimpleError(...)
20. │ └─base (local) h(simpleError(msg, call))
21. ├─base::.handleSimpleError(...)
22. │ └─base (local) h(simpleError(msg, call))
23. ├─base::.handleSimpleError(...)
24. │ └─base (local) h(simpleError(msg, call))
25. └─base::.handleSimpleError(...)
26. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:397:3'): set_outcome_model works for PP with defaults ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:397:3
2. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:412:3'): set_outcome_model works for ITT ──────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:412:3
2. ├─TrialEmulation::set_data(trial_sequence("ITT"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("ITT"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:427:3'): set_outcome_model works for ATT ──────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:427:3
2. ├─TrialEmulation::set_data(trial_sequence("AT"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("AT"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:446:3'): set_outcome_model doesn't work if with unknown variables ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-trial_sequence.R:446:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─TrialEmulation::set_outcome_model(...)
8. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
9. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ ├─methods::callNextMethod(...)
12. │ │ └─base::eval(call, callEnv)
13. │ │ └─base::eval(call, callEnv)
14. │ └─TrialEmulation (local) .nextMethod(...)
15. │ └─TrialEmulation (local) .local(object, data, ...)
16. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
17. │ ├─...[]
18. │ └─data.table:::`[.data.table`(...)
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:455:3'): set_outcome_model works with strings ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:455:3
2. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:466:3'): stabilised weight terms are included in outcome model ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:466:3
2. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:505:3'): interaction terms work as expected ───
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:505:3
2. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:529:3'): weights are 1 when not calculated by calculate_weights ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'load_expanded_data': error in evaluating the argument 'object' in selecting a method for function 'expand_trials': error in evaluating the argument 'object' in selecting a method for function 'set_expansion_options': error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::load_expanded_data(...) at test-trial_sequence.R:529:3
2. ├─TrialEmulation::expand_trials(...)
3. ├─TrialEmulation::set_expansion_options(...)
4. ├─TrialEmulation::set_outcome_model(...)
5. ├─TrialEmulation::set_data(trial_sequence("ITT"), trial_ex)
6. ├─TrialEmulation::set_data(trial_sequence("ITT"), trial_ex)
7. │ └─TrialEmulation (local) .local(object, data, ...)
8. │ ├─methods::callNextMethod(...)
9. │ │ └─base::eval(call, callEnv)
10. │ │ └─base::eval(call, callEnv)
11. │ └─TrialEmulation (local) .nextMethod(...)
12. │ └─TrialEmulation (local) .local(object, data, ...)
13. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
14. │ ├─...[]
15. │ └─data.table:::`[.data.table`(...)
16. ├─base::.handleSimpleError(...)
17. │ └─base (local) h(simpleError(msg, call))
18. ├─base::.handleSimpleError(...)
19. │ └─base (local) h(simpleError(msg, call))
20. ├─base::.handleSimpleError(...)
21. │ └─base (local) h(simpleError(msg, call))
22. └─base::.handleSimpleError(...)
23. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:563:3'): load_expanded_data works with trial_sequence objects containing te_datastore_datatable objects ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:563:3
2. ├─TrialEmulation::calculate_weights(...)
3. ├─TrialEmulation::set_censor_weight_model(...)
4. ├─TrialEmulation::set_data(...)
5. ├─TrialEmulation::set_data(...)
6. │ └─TrialEmulation (local) .local(object, data, ...)
7. │ ├─methods::callNextMethod(...)
8. │ │ └─base::eval(call, callEnv)
9. │ │ └─base::eval(call, callEnv)
10. │ └─TrialEmulation (local) .nextMethod(...)
11. │ └─TrialEmulation (local) .local(object, data, ...)
12. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
13. │ ├─...[]
14. │ └─data.table:::`[.data.table`(...)
15. ├─base::.handleSimpleError(...)
16. │ └─base (local) h(simpleError(msg, call))
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
[ FAIL 55 | WARN 4 | SKIP 22 | PASS 181 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.0.4.8
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Extending-TrialEmulation.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Extending-TrialEmulation.Rmd’
--- re-building ‘Getting-Started.Rmd’ using rmarkdown
Quitting from Getting-Started.Rmd:65-78 [initiators]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 10/10 in VECTOR_ELT
---
Backtrace:
▆
1. └─TrialEmulation::initiators(...)
2. └─TrialEmulation::data_preparation(...)
3. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Getting-Started.Rmd' failed with diagnostics:
attempt access index 10/10 in VECTOR_ELT
--- failed re-building ‘Getting-Started.Rmd’
--- re-building ‘new-interface.Rmd’ using rmarkdown
Quitting from new-interface.Rmd:57-79 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 12/12 in VECTOR_ELT
---
Backtrace:
▆
1. ├─TrialEmulation::set_data(...)
2. └─TrialEmulation::set_data(...)
3. └─TrialEmulation (local) .local(object, data, ...)
4. ├─methods::callNextMethod(...)
5. │ └─base::eval(call, callEnv)
6. │ └─base::eval(call, callEnv)
7. └─TrialEmulation (local) .nextMethod(...)
8. └─TrialEmulation (local) .local(object, data, ...)
9. └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'new-interface.Rmd' failed with diagnostics:
attempt access index 12/12 in VECTOR_ELT
--- failed re-building ‘new-interface.Rmd’
SUMMARY: processing the following files failed:
‘Getting-Started.Rmd’ ‘new-interface.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.0.4.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [167s/186s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(TrialEmulation)
>
> data.table::setDTthreads(2)
> test_check("TrialEmulation")
Saving _problems/test-data_extension-89.R
Saving _problems/test-data_extension-136.R
Saving _problems/test-data_extension-189.R
Saving _problems/test-data_manipulation-3.R
Saving _problems/test-data_manipulation-25.R
Saving _problems/test-data_manipulation-52.R
Saving _problems/test-data_manipulation-69.R
Starting data manipulation
Saving _problems/test-data_preparation-13.R
Saving _problems/test-data_preparation-94.R
Starting data manipulation
Saving _problems/test-data_preparation-121.R
Starting data manipulation
Saving _problems/test-data_preparation-144.R
Saving _problems/test-data_preparation-170.R
Saving _problems/test-generics-24.R
Saving _problems/test-generics-64.R
Saving _problems/test-generics-94.R
Saving _problems/test-modelling-404.R
Saving _problems/test-modelling-464.R
Saving _problems/test-predict-21.R
Saving _problems/test-predict-156.R
Saving _problems/test-sampling-83.R
Saving _problems/test-sampling-100.R
Saving _problems/test-sampling-119.R
Saving _problems/test-sampling-238.R
Saving _problems/test-te_datastore-5.R
Saving _problems/test-te_datastore_csv-73.R
Saving _problems/test-te_datastore_csv-179.R
Saving _problems/test-te_datastore_duckdb-22.R
Saving _problems/test-te_datastore_duckdb-63.R
Saving _problems/test-te_datastore_duckdb-147.R
Saving _problems/test-te_weights-16.R
Saving _problems/test-te_weights-52.R
Saving _problems/test-te_weights-85.R
Saving _problems/test-trial_sequence-55.R
Saving _problems/test-trial_sequence-70.R
Saving _problems/test-trial_sequence-85.R
Saving _problems/test-trial_sequence-101.R
Saving _problems/test-trial_sequence-164.R
Saving _problems/test-trial_sequence-191.R
Saving _problems/test-trial_sequence-210.R
Saving _problems/test-trial_sequence-224.R
Saving _problems/test-trial_sequence-243.R
Saving _problems/test-trial_sequence-264.R
Saving _problems/test-trial_sequence-280.R
Saving _problems/test-trial_sequence-325.R
Saving _problems/test-trial_sequence-380.R
Saving _problems/test-trial_sequence-399.R
Saving _problems/test-trial_sequence-414.R
Saving _problems/test-trial_sequence-429.R
Saving _problems/test-trial_sequence-451.R
Saving _problems/test-trial_sequence-457.R
Saving _problems/test-trial_sequence-468.R
Saving _problems/test-trial_sequence-507.R
Saving _problems/test-trial_sequence-538.R
Saving _problems/test-trial_sequence-580.R
[ FAIL 55 | WARN 4 | SKIP 22 | PASS 181 ]
══ Skipped tests (22) ══════════════════════════════════════════════════════════
• On CRAN (22): 'test-data_utils.R:1:1', 'test-data_utils.R:100:1',
'test-data_utils.R:115:1', 'test-modelling.R:99:3', 'test-modelling.R:154:3',
'test-modelling.R:175:3', 'test-modelling.R:205:3', 'test-modelling.R:229:3',
'test-modelling.R:266:3', 'test-modelling.R:290:3', 'test-modelling.R:314:3',
'test-modelling.R:357:3', 'test-predict.R:34:1', 'test-predict.R:86:1',
'test-sampling.R:1:1', 'test-sampling.R:11:1', 'test-sampling.R:18:1',
'test-sampling.R:40:1', 'test-sampling.R:180:3',
'test-trial_sequence.R:40:1', 'test-trial_sequence.R:44:1',
'test-trial_sequence.R:48:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-data_extension.R:78:3'): expand works as expected ──────────────
Error in ``[.data.table`(temp_data, , `:=`(wtprod, 1), by = id)`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation:::expand(...) at test-data_extension.R:78:3
2. ├─temp_data[, `:=`(wtprod, 1), by = id]
3. └─data.table:::`[.data.table`(temp_data, , `:=`(wtprod, 1), by = id)
── Error ('test-data_extension.R:124:3'): data extensions works as expected with first and last periods ──
Error in ``[.data.table`(temp_data, , `:=`(wtprod, 1), by = id)`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation:::data_extension(...) at test-data_extension.R:124:3
2. └─TrialEmulation:::expand(...)
3. ├─temp_data[, `:=`(wtprod, 1), by = id]
4. └─data.table:::`[.data.table`(temp_data, , `:=`(wtprod, 1), by = id)
── Error ('test-data_extension.R:176:3'): data extensions works as expected with separate_files=TRUE ──
Error in ``[.data.table`(temp_data, , `:=`(wtprod, 1), by = id)`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation:::data_extension(...) at test-data_extension.R:176:3
2. └─TrialEmulation:::expand(...)
3. ├─temp_data[, `:=`(wtprod, 1), by = id]
4. └─data.table:::`[.data.table`(temp_data, , `:=`(wtprod, 1), by = id)
── Error ('test-data_manipulation.R:3:3'): data_manipulation works as expected with no censoring ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation:::data_manipulation(object, use_censor = FALSE) at test-data_manipulation.R:3:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-data_manipulation.R:25:3'): data_manipulation works as expected with censoring ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation:::data_manipulation(object, use_censor = TRUE) at test-data_manipulation.R:25:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-data_manipulation.R:49:3'): data_manipulation works as expected with observations before eligibilitiy ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-data_manipulation.R:49:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─TrialEmulation:::data_manipulation(object, use_censor = TRUE)
8. ├─...[]
9. └─data.table:::`[.data.table`(...)
── Error ('test-data_manipulation.R:66:3'): data_manipulation works as expected with observations after outcome ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-data_manipulation.R:66:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─TrialEmulation:::data_manipulation(object, use_censor = TRUE)
8. ├─...[]
9. └─data.table:::`[.data.table`(...)
── Error ('test-data_preparation.R:4:3'): data_preparation works as expected ───
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-data_preparation.R:4:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-data_preparation.R:26:3'): data_preparation can be quiet ───────
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-data_preparation.R:26:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─TrialEmulation::data_preparation(...)
10. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
11. ├─...[]
12. └─data.table:::`[.data.table`(...)
── Error ('test-data_preparation.R:83:3'): data_preparation has correct values for 'treatment' ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-data_preparation.R:83:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-data_preparation.R:111:3'): data_preparation works with PP estimand type ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-data_preparation.R:111:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-data_preparation.R:133:3'): data_preparation works with As-Treated estimand type ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-data_preparation.R:133:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-data_preparation.R:156:3'): data_preparation works with ITT and censor weights ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-data_preparation.R:156:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-generics.R:5:3'): summary for data_preparation separate=TRUE ───
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-generics.R:5:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-generics.R:45:3'): summary for data_preparation separate=FALSE ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-generics.R:45:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-generics.R:75:3'): summary for initiators ──────────────────────
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-generics.R:75:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─TrialEmulation::initiators(...)
8. └─TrialEmulation::data_preparation(...)
9. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-modelling.R:383:3'): fit_msm works ─────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-modelling.R:383:3
2. ├─TrialEmulation::calculate_weights(...)
3. ├─TrialEmulation::set_censor_weight_model(...)
4. ├─TrialEmulation::set_data(...)
5. ├─TrialEmulation::set_data(...)
6. │ └─TrialEmulation (local) .local(object, data, ...)
7. │ ├─methods::callNextMethod(...)
8. │ │ └─base::eval(call, callEnv)
9. │ │ └─base::eval(call, callEnv)
10. │ └─TrialEmulation (local) .nextMethod(...)
11. │ └─TrialEmulation (local) .local(object, data, ...)
12. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
13. │ ├─...[]
14. │ └─data.table:::`[.data.table`(...)
15. ├─base::.handleSimpleError(...)
16. │ └─base (local) h(simpleError(msg, call))
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-modelling.R:443:3'): fit_msm works with weight functions ───────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-modelling.R:443:3
2. ├─TrialEmulation::calculate_weights(...)
3. ├─TrialEmulation::set_censor_weight_model(...)
4. ├─TrialEmulation::set_data(...)
5. ├─TrialEmulation::set_data(...)
6. │ └─TrialEmulation (local) .local(object, data, ...)
7. │ ├─methods::callNextMethod(...)
8. │ │ └─base::eval(call, callEnv)
9. │ │ └─base::eval(call, callEnv)
10. │ └─TrialEmulation (local) .nextMethod(...)
11. │ └─TrialEmulation (local) .local(object, data, ...)
12. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
13. │ ├─...[]
14. │ └─data.table:::`[.data.table`(...)
15. ├─base::.handleSimpleError(...)
16. │ └─base (local) h(simpleError(msg, call))
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-predict.R:7:3'): predict.TE_msm works as expected ──────────────
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::initiators(...) at test-predict.R:7:3
2. └─TrialEmulation::data_preparation(...)
3. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test-predict.R:146:3'): predict.TE_msm gives the same results as new predict ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'fit_msm': error in evaluating the argument 'object' in selecting a method for function 'load_expanded_data': error in evaluating the argument 'object' in selecting a method for function 'expand_trials': error in evaluating the argument 'object' in selecting a method for function 'set_expansion_options': error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::fit_msm(...) at test-predict.R:146:3
2. ├─TrialEmulation::load_expanded_data(...)
3. ├─TrialEmulation::expand_trials(...)
4. ├─TrialEmulation::set_expansion_options(...)
5. ├─TrialEmulation::set_outcome_model(...)
6. ├─TrialEmulation::set_data(trial_sequence("ITT"), trial_ex)
7. ├─TrialEmulation::set_data(trial_sequence("ITT"), trial_ex)
8. │ └─TrialEmulation (local) .local(object, data, ...)
9. │ ├─methods::callNextMethod(...)
10. │ │ └─base::eval(call, callEnv)
11. │ │ └─base::eval(call, callEnv)
12. │ └─TrialEmulation (local) .nextMethod(...)
13. │ └─TrialEmulation (local) .local(object, data, ...)
14. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
15. │ ├─...[]
16. │ └─data.table:::`[.data.table`(...)
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. ├─base::.handleSimpleError(...)
20. │ └─base (local) h(simpleError(msg, call))
21. ├─base::.handleSimpleError(...)
22. │ └─base (local) h(simpleError(msg, call))
23. ├─base::.handleSimpleError(...)
24. │ └─base (local) h(simpleError(msg, call))
25. └─base::.handleSimpleError(...)
26. └─base (local) h(simpleError(msg, call))
── Error ('test-sampling.R:74:3'): case_control_sampling_trials works with separate_files = TRUE ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-sampling.R:74:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-sampling.R:92:3'): case_control_sampling_trials works with separate_files = FALSE ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-sampling.R:92:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-sampling.R:110:3'): case_control_sampling_trials works with separate_files = TRUE is reproducible ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─TrialEmulation::data_preparation(...) at test-sampling.R:110:3
2. └─TrialEmulation:::data_manipulation(data, use_censor = args$censor_at_switch)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-sampling.R:221:3'): sample_controls works with trial_sequence objects containing te_datastore_datatable objects ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-sampling.R:221:3
2. ├─TrialEmulation::calculate_weights(...)
3. ├─TrialEmulation::set_censor_weight_model(...)
4. ├─TrialEmulation::set_data(...)
5. ├─TrialEmulation::set_data(...)
6. │ └─TrialEmulation (local) .local(object, data, ...)
7. │ ├─methods::callNextMethod(...)
8. │ │ └─base::eval(call, callEnv)
9. │ │ └─base::eval(call, callEnv)
10. │ └─TrialEmulation (local) .nextMethod(...)
11. │ └─TrialEmulation (local) .local(object, data, ...)
12. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
13. │ ├─...[]
14. │ └─data.table:::`[.data.table`(...)
15. ├─base::.handleSimpleError(...)
16. │ └─base (local) h(simpleError(msg, call))
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-te_datastore.R:2:3'): read_expanded_data can read te_datastore_datatable data ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_expansion_options': error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_expansion_options(...) at test-te_datastore.R:2:3
2. ├─TrialEmulation::set_outcome_model(...)
3. ├─TrialEmulation::set_data(trial_sequence("ITT"), data = data_censored)
4. ├─TrialEmulation::set_data(trial_sequence("ITT"), data = data_censored)
5. │ └─TrialEmulation (local) .local(object, data, ...)
6. │ ├─methods::callNextMethod(...)
7. │ │ └─base::eval(call, callEnv)
8. │ │ └─base::eval(call, callEnv)
9. │ └─TrialEmulation (local) .nextMethod(...)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
12. │ ├─...[]
13. │ └─data.table:::`[.data.table`(...)
14. ├─base::.handleSimpleError(...)
15. │ └─base (local) h(simpleError(msg, call))
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-te_datastore_csv.R:56:3'): sample_controls works with trial_sequence objects containing te_datastore_csv objects ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-te_datastore_csv.R:56:3
2. ├─TrialEmulation::calculate_weights(...)
3. ├─TrialEmulation::set_censor_weight_model(...)
4. ├─TrialEmulation::set_data(...)
5. ├─TrialEmulation::set_data(...)
6. │ └─TrialEmulation (local) .local(object, data, ...)
7. │ ├─methods::callNextMethod(...)
8. │ │ └─base::eval(call, callEnv)
9. │ │ └─base::eval(call, callEnv)
10. │ └─TrialEmulation (local) .nextMethod(...)
11. │ └─TrialEmulation (local) .local(object, data, ...)
12. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
13. │ ├─...[]
14. │ └─data.table:::`[.data.table`(...)
15. ├─base::.handleSimpleError(...)
16. │ └─base (local) h(simpleError(msg, call))
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-te_datastore_csv.R:162:3'): load_expanded_data works with trial_sequence objects containing te_datastore_csv objects ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-te_datastore_csv.R:162:3
2. ├─TrialEmulation::calculate_weights(...)
3. ├─TrialEmulation::set_censor_weight_model(...)
4. ├─TrialEmulation::set_data(...)
5. ├─TrialEmulation::set_data(...)
6. │ └─TrialEmulation (local) .local(object, data, ...)
7. │ ├─methods::callNextMethod(...)
8. │ │ └─base::eval(call, callEnv)
9. │ │ └─base::eval(call, callEnv)
10. │ └─TrialEmulation (local) .nextMethod(...)
11. │ └─TrialEmulation (local) .local(object, data, ...)
12. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
13. │ ├─...[]
14. │ └─data.table:::`[.data.table`(...)
15. ├─base::.handleSimpleError(...)
16. │ └─base (local) h(simpleError(msg, call))
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-te_datastore_duckdb.R:19:3'): read_expanded_data can read te_datastore_duckdb data ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_expansion_options': error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_expansion_options(...) at test-te_datastore_duckdb.R:19:3
2. ├─TrialEmulation::set_outcome_model(...)
3. ├─TrialEmulation::set_data(trial_sequence("ITT"), data = data)
4. ├─TrialEmulation::set_data(trial_sequence("ITT"), data = data)
5. │ └─TrialEmulation (local) .local(object, data, ...)
6. │ ├─methods::callNextMethod(...)
7. │ │ └─base::eval(call, callEnv)
8. │ │ └─base::eval(call, callEnv)
9. │ └─TrialEmulation (local) .nextMethod(...)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
12. │ ├─...[]
13. │ └─data.table:::`[.data.table`(...)
14. ├─base::.handleSimpleError(...)
15. │ └─base (local) h(simpleError(msg, call))
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-te_datastore_duckdb.R:61:3'): sample_controls works with trial_sequence objects containing te_datastore_duckdb objects ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-te_datastore_duckdb.R:61:3
2. ├─TrialEmulation::set_data(trial_sequence(estimand = "ITT"), data = data_censored)
3. ├─TrialEmulation::set_data(trial_sequence(estimand = "ITT"), data = data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-te_datastore_duckdb.R:145:3'): load_expanded_data works with trial_sequence objects containing te_datastore_duckdb objects ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-te_datastore_duckdb.R:145:3
2. ├─TrialEmulation::set_data(trial_sequence(estimand = "ITT"), data = data_censored)
3. ├─TrialEmulation::set_data(trial_sequence(estimand = "ITT"), data = data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-te_weights.R:3:3'): show works for te_weights_spec objects ─────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_switch_weight_model': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_switch_weight_model(...) at test-te_weights.R:3:3
2. ├─TrialEmulation::set_censor_weight_model(...)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
5. │ └─TrialEmulation (local) .local(object, data, ...)
6. │ ├─methods::callNextMethod(...)
7. │ │ └─base::eval(call, callEnv)
8. │ │ └─base::eval(call, callEnv)
9. │ └─TrialEmulation (local) .nextMethod(...)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
12. │ ├─...[]
13. │ └─data.table:::`[.data.table`(...)
14. ├─base::.handleSimpleError(...)
15. │ └─base (local) h(simpleError(msg, call))
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-te_weights.R:45:3'): weight_model_data_indices works ───────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_switch_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::calculate_weights(...) at test-te_weights.R:45:3
2. ├─TrialEmulation::set_switch_weight_model(...)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
5. │ └─TrialEmulation (local) .local(object, data, ...)
6. │ ├─methods::callNextMethod(...)
7. │ │ └─base::eval(call, callEnv)
8. │ │ └─base::eval(call, callEnv)
9. │ └─TrialEmulation (local) .nextMethod(...)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
12. │ ├─...[]
13. │ └─data.table:::`[.data.table`(...)
14. ├─base::.handleSimpleError(...)
15. │ └─base (local) h(simpleError(msg, call))
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-te_weights.R:78:3'): weight_model_data_indices catches bad input ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_switch_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::calculate_weights(...) at test-te_weights.R:78:3
2. ├─TrialEmulation::set_switch_weight_model(...)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
5. │ └─TrialEmulation (local) .local(object, data, ...)
6. │ ├─methods::callNextMethod(...)
7. │ │ └─base::eval(call, callEnv)
8. │ │ └─base::eval(call, callEnv)
9. │ └─TrialEmulation (local) .nextMethod(...)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
12. │ ├─...[]
13. │ └─data.table:::`[.data.table`(...)
14. ├─base::.handleSimpleError(...)
15. │ └─base (local) h(simpleError(msg, call))
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:53:3'): show works for trial_sequence_PP with data and outcome_model set ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:53:3
2. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:63:3'): set_data works for trial_sequence_ITT ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_data(...) at test-trial_sequence.R:63:3
2. └─TrialEmulation::set_data(...)
3. └─TrialEmulation (local) .local(object, data, ...)
4. ├─methods::callNextMethod(...)
5. │ └─base::eval(call, callEnv)
6. │ └─base::eval(call, callEnv)
7. └─TrialEmulation (local) .nextMethod(...)
8. └─TrialEmulation (local) .local(object, data, ...)
9. └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-trial_sequence.R:78:3'): set_data works for trial_sequence_PP ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_data(...) at test-trial_sequence.R:78:3
2. └─TrialEmulation::set_data(...)
3. └─TrialEmulation (local) .local(object, data, ...)
4. ├─methods::callNextMethod(...)
5. │ └─base::eval(call, callEnv)
6. │ └─base::eval(call, callEnv)
7. └─TrialEmulation (local) .nextMethod(...)
8. └─TrialEmulation (local) .local(object, data, ...)
9. └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-trial_sequence.R:94:3'): set_data works for trial_sequence_AT ──
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_data(...) at test-trial_sequence.R:94:3
2. └─TrialEmulation::set_data(...)
3. └─TrialEmulation (local) .local(object, data, ...)
4. ├─methods::callNextMethod(...)
5. │ └─base::eval(call, callEnv)
6. │ └─base::eval(call, callEnv)
7. └─TrialEmulation (local) .nextMethod(...)
8. └─TrialEmulation (local) .local(object, data, ...)
9. └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-trial_sequence.R:157:3'): ipw_data works as expected ───────────
Error in ``[.data.table`(data, , `:=`(after_eligibility, period >= .SD[eligible == 1, min(period, Inf)]), by = id)`: attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_data(...) at test-trial_sequence.R:157:3
2. └─TrialEmulation::set_data(...)
3. └─TrialEmulation (local) .local(object, data, ...)
4. ├─methods::callNextMethod(...)
5. │ └─base::eval(call, callEnv)
6. │ └─base::eval(call, callEnv)
7. └─TrialEmulation (local) .nextMethod(...)
8. └─TrialEmulation (local) .local(object, data, ...)
9. └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-trial_sequence.R:185:3'): set_switch_weight_model works for PP ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_switch_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_switch_weight_model(...) at test-trial_sequence.R:185:3
2. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:201:3'): time_on_sequence doesn't get included in numerator ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_switch_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-trial_sequence.R:201:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─TrialEmulation::set_switch_weight_model(...)
8. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
9. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ ├─methods::callNextMethod(...)
12. │ │ └─base::eval(call, callEnv)
13. │ │ └─base::eval(call, callEnv)
14. │ └─TrialEmulation (local) .nextMethod(...)
15. │ └─TrialEmulation (local) .local(object, data, ...)
16. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
17. │ ├─...[]
18. │ └─data.table:::`[.data.table`(...)
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:216:3'): set_censor_weight_model works for ITT ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_censor_weight_model(...) at test-trial_sequence.R:216:3
2. ├─TrialEmulation::set_data(trial_sequence("ITT"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("ITT"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:235:3'): set_censor_weight_model works for PP ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_censor_weight_model(...) at test-trial_sequence.R:235:3
2. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:253:3'): time_on_sequence doesn't get included in numerator ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-trial_sequence.R:253:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─TrialEmulation::set_censor_weight_model(...)
8. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
9. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ ├─methods::callNextMethod(...)
12. │ │ └─base::eval(call, callEnv)
13. │ │ └─base::eval(call, callEnv)
14. │ └─TrialEmulation (local) .nextMethod(...)
15. │ └─TrialEmulation (local) .local(object, data, ...)
16. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
17. │ ├─...[]
18. │ └─data.table:::`[.data.table`(...)
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:271:3'): calculate_weights works for ITT with censor weights ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::calculate_weights(...) at test-trial_sequence.R:271:3
2. ├─TrialEmulation::set_censor_weight_model(...)
3. ├─TrialEmulation::set_data(trial_sequence("ITT"), data_censored)
4. ├─TrialEmulation::set_data(trial_sequence("ITT"), data_censored)
5. │ └─TrialEmulation (local) .local(object, data, ...)
6. │ ├─methods::callNextMethod(...)
7. │ │ └─base::eval(call, callEnv)
8. │ │ └─base::eval(call, callEnv)
9. │ └─TrialEmulation (local) .nextMethod(...)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
12. │ ├─...[]
13. │ └─data.table:::`[.data.table`(...)
14. ├─base::.handleSimpleError(...)
15. │ └─base (local) h(simpleError(msg, call))
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:318:3'): calculate_weights works for PP with switch_weights ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_switch_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::calculate_weights(...) at test-trial_sequence.R:318:3
2. ├─TrialEmulation::set_switch_weight_model(...)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
5. │ └─TrialEmulation (local) .local(object, data, ...)
6. │ ├─methods::callNextMethod(...)
7. │ │ └─base::eval(call, callEnv)
8. │ │ └─base::eval(call, callEnv)
9. │ └─TrialEmulation (local) .nextMethod(...)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
12. │ ├─...[]
13. │ └─data.table:::`[.data.table`(...)
14. ├─base::.handleSimpleError(...)
15. │ └─base (local) h(simpleError(msg, call))
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:370:3'): calculate_weights works for PP with switch_weights ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'expand_trials': error in evaluating the argument 'object' in selecting a method for function 'set_expansion_options': error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_switch_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::expand_trials(...) at test-trial_sequence.R:370:3
2. ├─TrialEmulation::set_expansion_options(...)
3. ├─TrialEmulation::set_outcome_model(...)
4. ├─TrialEmulation::calculate_weights(...)
5. ├─TrialEmulation::set_switch_weight_model(...)
6. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
7. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
8. │ └─TrialEmulation (local) .local(object, data, ...)
9. │ ├─methods::callNextMethod(...)
10. │ │ └─base::eval(call, callEnv)
11. │ │ └─base::eval(call, callEnv)
12. │ └─TrialEmulation (local) .nextMethod(...)
13. │ └─TrialEmulation (local) .local(object, data, ...)
14. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
15. │ ├─...[]
16. │ └─data.table:::`[.data.table`(...)
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. ├─base::.handleSimpleError(...)
20. │ └─base (local) h(simpleError(msg, call))
21. ├─base::.handleSimpleError(...)
22. │ └─base (local) h(simpleError(msg, call))
23. ├─base::.handleSimpleError(...)
24. │ └─base (local) h(simpleError(msg, call))
25. └─base::.handleSimpleError(...)
26. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:397:3'): set_outcome_model works for PP with defaults ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:397:3
2. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:412:3'): set_outcome_model works for ITT ──────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:412:3
2. ├─TrialEmulation::set_data(trial_sequence("ITT"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("ITT"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:427:3'): set_outcome_model works for ATT ──────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:427:3
2. ├─TrialEmulation::set_data(trial_sequence("AT"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("AT"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:446:3'): set_outcome_model doesn't work if with unknown variables ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-trial_sequence.R:446:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─TrialEmulation::set_outcome_model(...)
8. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
9. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
10. │ └─TrialEmulation (local) .local(object, data, ...)
11. │ ├─methods::callNextMethod(...)
12. │ │ └─base::eval(call, callEnv)
13. │ │ └─base::eval(call, callEnv)
14. │ └─TrialEmulation (local) .nextMethod(...)
15. │ └─TrialEmulation (local) .local(object, data, ...)
16. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
17. │ ├─...[]
18. │ └─data.table:::`[.data.table`(...)
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:455:3'): set_outcome_model works with strings ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:455:3
2. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:466:3'): stabilised weight terms are included in outcome model ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:466:3
2. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:505:3'): interaction terms work as expected ───
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:505:3
2. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
3. ├─TrialEmulation::set_data(trial_sequence("PP"), data_censored)
4. │ └─TrialEmulation (local) .local(object, data, ...)
5. │ ├─methods::callNextMethod(...)
6. │ │ └─base::eval(call, callEnv)
7. │ │ └─base::eval(call, callEnv)
8. │ └─TrialEmulation (local) .nextMethod(...)
9. │ └─TrialEmulation (local) .local(object, data, ...)
10. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
11. │ ├─...[]
12. │ └─data.table:::`[.data.table`(...)
13. └─base::.handleSimpleError(...)
14. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:529:3'): weights are 1 when not calculated by calculate_weights ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'load_expanded_data': error in evaluating the argument 'object' in selecting a method for function 'expand_trials': error in evaluating the argument 'object' in selecting a method for function 'set_expansion_options': error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': attempt access index 11/11 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::load_expanded_data(...) at test-trial_sequence.R:529:3
2. ├─TrialEmulation::expand_trials(...)
3. ├─TrialEmulation::set_expansion_options(...)
4. ├─TrialEmulation::set_outcome_model(...)
5. ├─TrialEmulation::set_data(trial_sequence("ITT"), trial_ex)
6. ├─TrialEmulation::set_data(trial_sequence("ITT"), trial_ex)
7. │ └─TrialEmulation (local) .local(object, data, ...)
8. │ ├─methods::callNextMethod(...)
9. │ │ └─base::eval(call, callEnv)
10. │ │ └─base::eval(call, callEnv)
11. │ └─TrialEmulation (local) .nextMethod(...)
12. │ └─TrialEmulation (local) .local(object, data, ...)
13. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
14. │ ├─...[]
15. │ └─data.table:::`[.data.table`(...)
16. ├─base::.handleSimpleError(...)
17. │ └─base (local) h(simpleError(msg, call))
18. ├─base::.handleSimpleError(...)
19. │ └─base (local) h(simpleError(msg, call))
20. ├─base::.handleSimpleError(...)
21. │ └─base (local) h(simpleError(msg, call))
22. └─base::.handleSimpleError(...)
23. └─base (local) h(simpleError(msg, call))
── Error ('test-trial_sequence.R:563:3'): load_expanded_data works with trial_sequence objects containing te_datastore_datatable objects ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'set_outcome_model': error in evaluating the argument 'object' in selecting a method for function 'calculate_weights': error in evaluating the argument 'object' in selecting a method for function 'set_censor_weight_model': attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─TrialEmulation::set_outcome_model(...) at test-trial_sequence.R:563:3
2. ├─TrialEmulation::calculate_weights(...)
3. ├─TrialEmulation::set_censor_weight_model(...)
4. ├─TrialEmulation::set_data(...)
5. ├─TrialEmulation::set_data(...)
6. │ └─TrialEmulation (local) .local(object, data, ...)
7. │ ├─methods::callNextMethod(...)
8. │ │ └─base::eval(call, callEnv)
9. │ │ └─base::eval(call, callEnv)
10. │ └─TrialEmulation (local) .nextMethod(...)
11. │ └─TrialEmulation (local) .local(object, data, ...)
12. │ └─TrialEmulation:::data_manipulation(trial_data, use_censor = censor_at_switch)
13. │ ├─...[]
14. │ └─data.table:::`[.data.table`(...)
15. ├─base::.handleSimpleError(...)
16. │ └─base (local) h(simpleError(msg, call))
17. ├─base::.handleSimpleError(...)
18. │ └─base (local) h(simpleError(msg, call))
19. └─base::.handleSimpleError(...)
20. └─base (local) h(simpleError(msg, call))
[ FAIL 55 | WARN 4 | SKIP 22 | PASS 181 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc