Running ‘testthat.R’ [386s/439s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # 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/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(gfoRmulaICE)
  > 
  > test_check("gfoRmulaICE")
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                                         NP Risk Classical Pooled ICE Risk Ratio
  Natural Course (Direct Effect)         0.26851              0.26874    1.00000
  Dynamic Intervention 1 (Direct Effect)      NA              0.30568    1.13746
  Dynamic Intervention 2 (Direct Effect)      NA              0.25787    0.95957
  Dynamic Intervention 3 (Direct Effect)      NA              0.32326    1.20286
                                         Risk Difference
  Natural Course (Direct Effect)                 0.00000
  Dynamic Intervention 1 (Direct Effect)         0.03694
  Dynamic Intervention 2 (Direct Effect)        -0.01087
  Dynamic Intervention 3 (Direct Effect)         0.05452
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                                         NP Risk Classical Pooled ICE Risk Ratio
  Natural Course (Direct Effect)         0.26851              0.26874    1.00000
  Dynamic Intervention 1 (Direct Effect)      NA              0.30568    1.13746
  Dynamic Intervention 2 (Direct Effect)      NA              0.25787    0.95957
  Dynamic Intervention 3 (Direct Effect)      NA              0.32326    1.20286
                                         Risk Difference
  Natural Course (Direct Effect)                 0.00000
  Dynamic Intervention 1 (Direct Effect)         0.03694
  Dynamic Intervention 2 (Direct Effect)        -0.01087
  Dynamic Intervention 3 (Direct Effect)         0.05452
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                                                         NP Risk
  Natural Course (Direct Effect)                         0.26851
  Static Intervention (Direct Effect)                         NA
  Threshold Intervention (Direct Effect)                      NA
  Dynamic Intervention with Grace Period (Direct Effect)      NA
                                                         Classical Pooled ICE
  Natural Course (Direct Effect)                                      0.26874
  Static Intervention (Direct Effect)                                 0.24935
  Threshold Intervention (Direct Effect)                              0.26874
  Dynamic Intervention with Grace Period (Direct Effect)              0.28701
                                                         Risk Ratio
  Natural Course (Direct Effect)                            1.00000
  Static Intervention (Direct Effect)                       0.92784
  Threshold Intervention (Direct Effect)                    1.00000
  Dynamic Intervention with Grace Period (Direct Effect)    1.06799
                                                         Risk Difference
  Natural Course (Direct Effect)                                 0.00000
  Static Intervention (Direct Effect)                           -0.01939
  Threshold Intervention (Direct Effect)                         0.00000
  Dynamic Intervention with Grace Period (Direct Effect)         0.01827
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                                       NP Risk Classical Pooled ICE Risk Ratio
  Natural Course (Direct Effect)       0.26851              0.26874    1.00000
  Static Intervention (Direct Effect)       NA              0.24935    0.92784
  Dynamic Intervention (Direct Effect)      NA              0.34078    1.26807
                                       Risk Difference
  Natural Course (Direct Effect)               0.00000
  Static Intervention (Direct Effect)         -0.01939
  Dynamic Intervention (Direct Effect)         0.07204
  Running Natural Course... 
  
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                                      NP Risk Weighted ICE Risk Ratio
  Natural Course (Total Effect)       0.22982      0.22722    1.00000
  Static Intervention (Total Effect)       NA      0.19441    0.85562
  Dynamic Intervention (Total Effect)      NA      0.24194    1.06480
                                      Risk Difference
  Natural Course (Total Effect)               0.00000
  Static Intervention (Total Effect)         -0.03280
  Dynamic Intervention (Total Effect)         0.01472
  Running Natural Course... 
  
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        NP Risk ICE Risk Risk Ratio Risk Difference
   [1,] 0.26851  0.26874    1.00000         0.00000
   [2,]      NA  0.27218    1.01280         0.00344
   [3,]      NA  0.33107    1.23195         0.06234
   [4,] 0.26851  0.21482    1.00000         0.00000
   [5,]      NA  0.26318    1.22513         0.04836
   [6,]      NA  0.20892    0.97255        -0.00590
   [7,] 0.26851  0.21573    1.00000         0.00000
   [8,]      NA  0.23855    1.10579         0.02282
   [9,]      NA  0.21463    0.99492        -0.00110
  [10,] 0.26851  0.26811    1.00000         0.00000
  [11,]      NA  0.27992    1.04407         0.01181
  [12,]      NA  0.32020    1.19430         0.05209
  [13,] 0.26947  0.26967    1.00000         0.00000
  [14,]      NA  0.27646    1.02521         0.00680
  [15,]      NA  0.31554    1.17010         0.04587
  [16,] 0.26947  0.26941    1.00000         0.00000
  [17,]      NA  0.27523    1.02162         0.00582
  [18,]      NA  0.31377    1.16467         0.04436
  [19,] 0.26947  0.26118    1.00000         0.00000
  [20,]      NA  0.27455    1.05118         0.01337
  [21,]      NA  0.31287    1.19790         0.05169
  [22,] 0.22987  0.24359    1.00000         0.00000
  [23,]      NA  0.24675    1.01294         0.00315
  [24,]      NA  0.27024    1.10937         0.02664
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  Static Intervention Bootstrap Progress: 3/5
  
  Running Static Intervention... 
  
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  Static Intervention Bootstrap Progress: 4/5
  
  Running Static Intervention... 
  
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  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 5/5
  
  Running Dynamic Intervention... 
  
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  Running Dynamic Intervention... 
  
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  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 1/5
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 2/5
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 3/5
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 4/5
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 5/5
  
  Running Natural Course... 
  
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  Running Time 1...
  
  Running Static Intervention... 
  
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  Running Static Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 1/5
  
  Running Static Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 2/5
  
  Running Static Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 3/5
  
  Running Static Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Running Time 1...
  
  Static Intervention Bootstrap Progress: 4/5
  
  Running Static Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 5/5
  
  Running Dynamic Intervention... 
  
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  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 1/5
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 2/5
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Running Time 1...
  
  Dynamic Intervention Bootstrap Progress: 3/5
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 4/5
  
  Running Dynamic Intervention... 
  
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  Running Time 2...
  
  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 5/5
  
  Running Natural Course... 
  
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  Running Time 1...
  
  Running Static Intervention... 
  
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  Running Static Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 1/5
  
  Running Static Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 2/5
  
  Running Static Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Running Time 1...
  
  Static Intervention Bootstrap Progress: 3/5
  
  Running Static Intervention... 
  
  Running Time 4...
  
  Running Time 3...
  
  Running Time 2...
  
  Running Time 1...
  
  Running Natural Course... 
  
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  Running Time 1...
  
  Static Intervention Bootstrap Progress: 4/5
  
  Running Static Intervention... 
  
  Running Time 4...
  
  Running Time 3...
  
  Running Time 2...
  
  Running Time 1...
  
  Running Natural Course... 
  
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  Running Time 1...
  
  Static Intervention Bootstrap Progress: 5/5
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Running Time 1...
  
  Dynamic Intervention Bootstrap Progress: 1/5
  
  Running Dynamic Intervention... 
  
  Running Time 4...
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 2/5
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 3/5
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Running Time 1...
  
  Dynamic Intervention Bootstrap Progress: 4/5
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 5/5
  
  Running Natural Course... 
  
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  Running Static Intervention... 
  
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  Running Static Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 1/5
  
  Running Static Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 2/5
  
  Running Static Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 3/5
  
  Running Static Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 4/5
  
  Running Static Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 5/5
  
  Running Dynamic Intervention... 
  
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  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 1/5
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 2/5
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 3/5
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 4/5
  
  Running Dynamic Intervention... 
  
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  Running Time 1...
  
  Running Natural Course... 
  
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  Dynamic Intervention Bootstrap Progress: 5/5
  
  Running Natural Course... 
  
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  Running Static Intervention... 
  
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  Running Static Intervention... 
  
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  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 1/5
  
  Running Static Intervention... 
  
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  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 2/5
  
  Running Static Intervention... 
  
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  Static Intervention Bootstrap Progress: 3/5
  
  Running Static Intervention... 
  
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  Static Intervention Bootstrap Progress: 4/5
  
  Running Static Intervention... 
  
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  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 5/5
  
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  Dynamic Intervention Bootstrap Progress: 1/5
  
  Running Dynamic Intervention... 
  
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  Dynamic Intervention Bootstrap Progress: 2/5
  
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  Dynamic Intervention Bootstrap Progress: 3/5
  
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  Dynamic Intervention Bootstrap Progress: 4/5
  
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  Dynamic Intervention Bootstrap Progress: 5/5
  
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  Static Intervention Bootstrap Progress: 1/5
  
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  Static Intervention Bootstrap Progress: 2/5
  
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  Static Intervention Bootstrap Progress: 3/5
  
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  Static Intervention Bootstrap Progress: 4/5
  
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  Static Intervention Bootstrap Progress: 5/5
  
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  Dynamic Intervention Bootstrap Progress: 1/5
  
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  Dynamic Intervention Bootstrap Progress: 2/5
  
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  Dynamic Intervention Bootstrap Progress: 3/5
  
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  Dynamic Intervention Bootstrap Progress: 4/5
  
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  Dynamic Intervention Bootstrap Progress: 5/5
  
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  Static Intervention Bootstrap Progress: 1/5
  
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  Static Intervention Bootstrap Progress: 2/5
  
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  Static Intervention Bootstrap Progress: 3/5
  
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  Static Intervention Bootstrap Progress: 4/5
  
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  Static Intervention Bootstrap Progress: 5/5
  
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  Dynamic Intervention Bootstrap Progress: 1/5
  
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  Dynamic Intervention Bootstrap Progress: 2/5
  
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  Dynamic Intervention Bootstrap Progress: 3/5
  
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  Dynamic Intervention Bootstrap Progress: 4/5
  
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  Dynamic Intervention Bootstrap Progress: 5/5
  
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  Static Intervention Bootstrap Progress: 1/5
  
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  Static Intervention Bootstrap Progress: 2/5
  
  Running Static Intervention... 
  
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  Static Intervention Bootstrap Progress: 3/5
  
  Running Static Intervention... 
  
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  Static Intervention Bootstrap Progress: 4/5
  
  Running Static Intervention... 
  
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  Static Intervention Bootstrap Progress: 5/5
  
  Running Dynamic Intervention... 
  
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  Dynamic Intervention Bootstrap Progress: 1/5
  
  Running Dynamic Intervention... 
  
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  Dynamic Intervention Bootstrap Progress: 2/5
  
  Running Dynamic Intervention... 
  
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  Dynamic Intervention Bootstrap Progress: 3/5
  
  Running Dynamic Intervention... 
  
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  Dynamic Intervention Bootstrap Progress: 4/5
  
  Running Dynamic Intervention... 
  
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  Dynamic Intervention Bootstrap Progress: 5/5
  
  
  Attaching package: 'Hmisc'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  The following objects are masked from 'package:base':
  
      format.pval, units
  
  Running Natural Course... 
  
  Running Time 4...
  
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  Static Intervention Bootstrap Progress: 1/5
  
  Running Static Intervention... 
  
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  Static Intervention Bootstrap Progress: 2/5
  
  Running Static Intervention... 
  
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  Static Intervention Bootstrap Progress: 3/5
  
  Running Static Intervention... 
  
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  Static Intervention Bootstrap Progress: 4/5
  
  Running Static Intervention... 
  
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  Static Intervention Bootstrap Progress: 5/5
  
  Running Dynamic Intervention... 
  
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  Dynamic Intervention Bootstrap Progress: 1/5
  
  Running Dynamic Intervention... 
  
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  Dynamic Intervention Bootstrap Progress: 2/5
  
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  Dynamic Intervention Bootstrap Progress: 3/5
  
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  Dynamic Intervention Bootstrap Progress: 4/5
  
  Running Dynamic Intervention... 
  
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  Dynamic Intervention Bootstrap Progress: 5/5
  
  Running Static Intervention... 
  
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  Natural Course Bootstrap Progress: 1/5
  
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  Natural Course Bootstrap Progress: 2/5
  
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  Natural Course Bootstrap Progress: 3/5
  
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  Natural Course Bootstrap Progress: 4/5
  
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  Natural Course Bootstrap Progress: 5/5
  
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  Dynamic Intervention Bootstrap Progress: 1/5
  
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  Dynamic Intervention Bootstrap Progress: 2/5
  
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  Dynamic Intervention Bootstrap Progress: 3/5
  
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  Dynamic Intervention Bootstrap Progress: 4/5
  
  Running Dynamic Intervention... 
  
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  Dynamic Intervention Bootstrap Progress: 5/5
  
  Running Natural Course... 
  
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  Static Intervention Bootstrap Progress: 1/5
  
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  Static Intervention Bootstrap Progress: 2/5
  
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  Static Intervention Bootstrap Progress: 3/5
  
  Running Static Intervention... 
  
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  Static Intervention Bootstrap Progress: 4/5
  
  Running Static Intervention... 
  
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  Dynamic Intervention Bootstrap Progress: 5/5
  
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  [ FAIL 15 | WARN 176 | SKIP 0 | PASS 47 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_plot.R:27:5'): plot classical pooled ICE direct effect - dynamic interventions ──
  class(plot1) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  ── Failure ('test_plot.R:52:5'): check different interventions ─────────────────
  class(plot2) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  ── Failure ('test_plot.R:77:5'): check user-defined intervention ───────────────
  class(plot3) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  ── Failure ('test_plot.R:104:5'): plot hazard-based pooled ICE - time-specific hazard model same as the outcome model ──
  class(plot4a) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  ── Failure ('test_plot.R:132:5'): plot hazard-based pooled ICE - time-specific hazard model Y ~ L1 + L2 ──
  class(plot4b) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  ── Failure ('test_plot.R:161:5'): plot hazard-based pooled ICE - pooled-over-time hazard model ──
  class(plot4c) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  ── Failure ('test_plot.R:187:5'): plot classical stratified ICE ────────────────
  class(plot4d) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  ── Failure ('test_plot.R:215:5'): plot hazard-extended stratified ICE - time-specific hazard model Y ~ L1 ──
  class(plot4e) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  ── Failure ('test_plot.R:241:5'): plot doubly robust ICE ───────────────────────
  class(plot4f) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  ── Failure ('test_plot.R:270:5'): plot hazard-based stratified ICE with intervention-specific models ──
  class(plot4h) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  ── Failure ('test_plot.R:296:5'): plot flexible model specification - complicated terms ──
  class(plot5a) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  ── Failure ('test_plot.R:322:5'): plot flexible model specification - using static intervention as reference ──
  class(plot5b) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  ── Failure ('test_plot.R:351:5'): plot complicated scenario 1 ──────────────────
  class(plot6a) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  ── Failure ('test_plot.R:378:5'): plot complicated scenario 2 - doubly robust ICE with intervention-specific models ──
  class(plot6b) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  ── Failure ('test_plot.R:534:5'): plot complicated scenario 3 - intervention-specific time options ──
  class(plots) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  
  [ FAIL 15 | WARN 176 | SKIP 0 | PASS 47 ]
  Error: Test failures
  Execution halted