R version 4.6.0 alpha (2026-03-30 r89742 ucrt) Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(SEQTaRget) > > test_check("SEQTaRget") Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed SEQuential process completed in 4.31 seconds : Initialized with: Outcome covariates: outcome~tx_init_bas+followup+followup_sq+trial+trial_sq+sex+N_bas+L_bas+P_bas Numerator covariates: NA Denominator covariates: NA Full Model Information ========================================== Outcome Model ==================================================== Coefficients and Weighting: Estimate Std. Error (Intercept) -6.828506036 5.668367e-01 tx_init_bas1 0.189350031 3.005120e-02 followup 0.033715157 3.276751e-03 followup_sq -0.000146912 6.466141e-05 trial 0.044566166 1.124702e-02 trial_sq 0.000578777 1.001866e-04 sex1 0.127172410 2.595630e-02 N_bas 0.003290667 2.589182e-03 L_bas -0.013392420 1.428081e-02 P_bas 0.200724099 5.956440e-02 Diagnostic Tables ================================================== Unique Outcome Table: |tx_init_bas | outcome| n| |:-----------|-------:|---:| |0 | 1| 203| |1 | 1| 185| Non-Unique Outcome Table: |tx_init_bas | outcome| n| |:-----------|-------:|----:| |0 | 1| 1928| |1 | 1| 4432| Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with dose-response analysis dose-response model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with dose-response analysis dose-response model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Completed SEQuential process completed in 3.78 seconds : Initialized with: Outcome covariates: outcome~tx_init_bas+followup+followup_sq+trial+trial_sq+sex+N_bas+L_bas+P_bas Numerator covariates: tx_init~sex+N_bas+L_bas+P_bas+followup+followup_sq+trial+trial_sq Denominator covariates: tx_init~sex+N+L+P+N_bas+L_bas+P_bas+followup+followup_sq+trial+trial_sq Full Model Information ========================================== Outcome Model ==================================================== Coefficients and Weighting: Estimate Std. Error (Intercept) -9.172267e+00 1.0184896378 tx_init_bas1 4.707555e-01 0.0754700155 followup 2.902109e-02 0.0059331026 followup_sq 7.893723e-05 0.0001503305 trial 6.700192e-02 0.0199677453 trial_sq 5.834324e-04 0.0001645977 sex1 8.162617e-02 0.0426609502 N_bas 4.870213e-03 0.0043044760 L_bas 1.350320e-02 0.0201298657 P_bas 4.466574e-01 0.1067432887 Weight Information ============================================= Treatment Lag = 0 Treatment = 0 Model ==================================== Numerator ========================== Estimate Std. Error (Intercept) -2.193331e+00 0.8210905172 sex1 9.923401e-02 0.0444029222 N_bas 5.358074e-03 0.0042477833 L_bas 5.037576e-02 0.0271687461 P_bas 6.073560e-02 0.0862417921 followup -1.940028e-02 0.0102456861 followup_sq 6.990437e-04 0.0004402889 trial 3.102854e-03 0.0164633560 trial_sq 8.187077e-05 0.0001596555 Denominator ========================== Estimate Std. Error (Intercept) -2.1964004237 0.8389945343 sex1 0.1115038988 0.0448358549 N 0.0138112100 0.0042418351 L 0.2018464069 0.0939947430 P 0.2493386716 0.1746750692 N_bas 0.0054225321 0.0042524259 L_bas -0.1994854025 0.1209594413 P_bas -0.1918628340 0.1796764856 followup 0.0031086820 0.0291995931 followup_sq 0.0006774622 0.0004754205 trial -0.0036625482 0.0165738866 trial_sq 0.0001651636 0.0001616484 Treatment Lag = 1 Treatment = 1 Model ==================================== Numerator ========================== Estimate Std. Error (Intercept) 1.649611e+00 0.7631653967 sex1 -2.305417e-02 0.0336411919 N_bas 3.372025e-03 0.0033742654 L_bas 2.152857e-01 0.0222488621 P_bas 1.447137e-01 0.0803485430 followup -3.908546e-04 0.0050640759 followup_sq -8.277615e-05 0.0001334700 trial 1.342118e-02 0.0154036387 trial_sq -2.556265e-04 0.0001441489 Denominator ========================== Estimate Std. Error (Intercept) 2.623571e+00 0.7924936074 sex1 -1.423666e-02 0.0337589761 N 3.487202e-03 0.0033845960 L 1.718756e-01 0.0387393419 P -4.534041e-01 0.1121357803 N_bas 3.435633e-03 0.0033781822 L_bas -2.988004e-02 0.0599689746 P_bas 4.726444e-01 0.1182438150 followup -6.244483e-02 0.0149117833 followup_sq 1.511044e-05 0.0001395120 trial 7.135764e-03 0.0155653350 trial_sq -2.722492e-04 0.0001488754 Weights: Min: 0.5060308 Max: 3.101522 StDev: 0.04174202 P01: 0.8809239 P25: 0.9894742 P50: 1 P75: 1.009571 P99: 1.094614 Diagnostic Tables ================================================== Unique Outcome Table: |tx_init_bas | outcome| n| |:-----------|-------:|---:| |1 | 1| 153| |0 | 1| 50| Non-Unique Outcome Table: |tx_init_bas | outcome| n| |:-----------|-------:|----:| |1 | 1| 2157| |0 | 1| 222| Unique Switch Table: |switch | n| |:------|----:| |FALSE | 8399| |TRUE | 804| Non-Unique Switch Table: |switch | n| |:------|-----:| |FALSE | 96251| |TRUE | 6498| Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Completed Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Creating Survival curves Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Creating Survival curves Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Creating Survival curves Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Creating Survival curves Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Creating Survival curves Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Non-required columns provided, pruning for efficiency Pruned Non-required columns provided, pruning for efficiency Pruned Non-required columns provided, pruning for efficiency Pruned Non-required columns provided, pruning for efficiency Pruned Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis Bootstrapping with 80 % of data 2 times Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Creating Survival curves Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis Bootstrapping with 80 % of data 3 times Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis Bootstrapping with 80 % of data 3 times Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis Bootstrapping with 80 % of data 3 times Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis Bootstrapping with 80 % of data 3 times Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with censoring analysis Bootstrapping with 80 % of data 2 times censoring model created successfully Creating Survival curves Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed SEQuential process completed in 2.59 seconds : Initialized with: Outcome covariates: outcome~tx_init_bas+followup+followup_sq+trial+trial_sq+sex+N_bas+L_bas+P_bas Numerator covariates: NA Denominator covariates: NA Full Model Information ========================================== Outcome Model ==================================================== Coefficients and Weighting: Estimate Std. Error (Intercept) -38.978779416 3.409464e+02 tx_init_bas1 -2.503954665 4.007514e-01 tx_init_bas2 -0.743287992 2.649302e-01 followup 0.079771224 3.667124e-02 followup_sq -0.002419149 8.922022e-04 trial 0.394571195 1.108810e-01 trial_sq -0.006193912 1.297688e-03 sex1 16.957722545 3.409015e+02 N_bas 0.052387854 2.433698e-02 L_bas 0.821748856 1.789139e-01 P_bas 1.369965886 5.745552e-01 Diagnostic Tables ================================================== Unique Outcome Table: |tx_init_bas | outcome| n| |:-----------|-------:|--:| |0 | 1| 1| |2 | 1| 1| |1 | 1| 1| Non-Unique Outcome Table: |tx_init_bas | outcome| n| |:-----------|-------:|--:| |0 | 1| 16| |2 | 1| 16| |1 | 1| 4| Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Completed SEQuential process completed in 1.65 seconds : Initialized with: Outcome covariates: outcome~tx_init_bas+followup+followup_sq+trial+trial_sq+sex Numerator covariates: tx_init~sex+time+time_sq Denominator covariates: tx_init~sex+N+L+P+time+time_sq Full Model Information ========================================== Outcome Model ==================================================== Coefficients and Weighting: Estimate Std. Error (Intercept) -449.4546587 583.13313021 tx_init_bas1 18.0766427 511.49215430 tx_init_bas2 -0.8437755 602.47106682 followup 0.7748579 0.09922328 followup_sq -0.2841586 0.02612846 trial 24.3387137 1.54157176 trial_sq -0.3620991 0.02295692 sex1 18.6694631 278.84600145 Weight Information ============================================= Treatment Lag = 0 Treatment = 0 Model ==================================== Numerator ========================== Nested Model: Treatment = 1 ========= Estimate Std. Error (Intercept) -2.8103864967 0.2212072625 sex1 0.1873115163 0.2004785952 time 0.0512985381 0.0200733213 time_sq -0.0007563168 0.0003755601 Nested Model: Treatment = 2 ========= Estimate Std. Error (Intercept) -2.8937823168 0.2305297041 sex1 0.3513709713 0.2093988237 time 0.0271767008 0.0205735302 time_sq -0.0002310837 0.0003751378 Denominator ========================== Nested Model: Treatment = 1 ========= Estimate Std. Error (Intercept) -6.1573660554 4.5273799854 sex1 0.2235735812 0.2032073663 N -0.0133612096 0.0210609505 L -0.1302413795 0.0920059185 P 0.3745089433 0.4774276269 time 0.1139056376 0.0863576155 time_sq -0.0009749762 0.0006658756 Nested Model: Treatment = 2 ========= Estimate Std. Error (Intercept) -3.0960750569 4.7492673438 sex1 0.3534343281 0.2109184696 N -0.0102324367 0.0219051793 L 0.0103966369 0.0823995410 P 0.0314062718 0.5020658014 time 0.0330557847 0.0900848752 time_sq -0.0002854995 0.0006855675 Treatment Lag = 1 Treatment = 1 Model ==================================== Numerator ========================== Nested Model: Treatment = 1 ========= Estimate Std. Error (Intercept) 3.1764905836 0.3987875743 sex1 0.0844712237 0.1812162006 time -0.0231152755 0.0269086455 time_sq 0.0003245306 0.0004087089 Nested Model: Treatment = 2 ========= Estimate Std. Error (Intercept) -3.7589823652 0.549940204 sex1 -0.1304501693 0.263702284 time 0.0233261132 0.038572406 time_sq -0.0005009231 0.000605213 Denominator ========================== Nested Model: Treatment = 1 ========= Estimate Std. Error (Intercept) 1.067409e+00 5.2113129185 sex1 9.544187e-02 0.1834198450 N 3.205407e-03 0.0181951803 L -9.327781e-04 0.0560532799 P 2.208491e-01 0.5528419803 time 1.477305e-02 0.0982282345 time_sq 9.222484e-05 0.0007131821 Nested Model: Treatment = 2 ========= Estimate Std. Error (Intercept) 6.0684132486 7.499643748 sex1 -0.1873988269 0.268245435 N -0.0018730533 0.026577601 L -0.0260750112 0.090097226 P -1.0423958563 0.798942378 time -0.1557570583 0.141604685 time_sq 0.0006375347 0.001042245 Treatment Lag = 2 Treatment = 2 Model ==================================== Numerator ========================== Nested Model: Treatment = 1 ========= Estimate Std. Error (Intercept) -3.9248969631 0.5427431606 sex1 0.5488851180 0.2709203453 time 0.0195368316 0.0376244645 time_sq -0.0005399237 0.0005996696 Nested Model: Treatment = 2 ========= Estimate Std. Error (Intercept) 3.1183030947 0.3894238862 sex1 -0.5837652345 0.1925453945 time 0.0059811767 0.0262579725 time_sq -0.0000556412 0.0004033746 Denominator ========================== Nested Model: Treatment = 1 ========= Estimate Std. Error (Intercept) -12.436421376 7.385434743 sex1 0.563480111 0.268321769 N -0.030239977 0.026924199 L 0.241510655 0.105947644 P 0.919743753 0.778130858 time 0.182061121 0.141787363 time_sq -0.001910491 0.001086981 Nested Model: Treatment = 2 ========= Estimate Std. Error (Intercept) 5.9274607786 5.4667748606 sex1 -0.5842317988 0.1932440807 N -0.0036972302 0.0195214269 L -0.0252388768 0.0673760215 P -0.2937206401 0.5798380958 time -0.0450474286 0.1037496641 time_sq 0.0002941542 0.0007572408 Weights: Min: 0.2478252 Max: 6.309442 StDev: 0.1998333 P01: 0.757827 P25: 0.97187 P50: 0.9987108 P75: 1.020873 P99: 1.623825 Diagnostic Tables ================================================== Unique Outcome Table: |tx_init_bas | outcome| n| |:-----------|-------:|--:| |1 | 1| 1| Non-Unique Outcome Table: |tx_init_bas | outcome| n| |:-----------|-------:|--:| |1 | 1| 4| Unique Switch Table: |switch | n| |:------|----:| |FALSE | 2921| |TRUE | 251| Non-Unique Switch Table: |switch | n| |:------|-----:| |FALSE | 42297| |TRUE | 2713| Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Completed Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Completed Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with dose-response analysis Bootstrapping with 80 % of data 2 times dose-response model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with dose-response analysis Bootstrapping with 80 % of data 2 times dose-response model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Creating Survival curves Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis Bootstrapping with 80 % of data 2 times ITT model created successfully Creating Survival curves Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis Bootstrapping with 80 % of data 2 times ITT model created successfully Creating Survival curves Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis Bootstrapping with 80 % of data 2 times ITT model created successfully Creating Survival curves Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with ITT analysis ITT model created successfully Completed Non-required columns provided, pruning for efficiency Pruned Expanding Data... Expansion Successful Moving forward with censoring analysis censoring model created successfully Completed [ FAIL 0 | WARN 0 | SKIP 0 | PASS 192 ] > > proc.time() user system elapsed 306.67 87.25 376.76