Last updated on 2026-04-07 18:00:12 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-fedora-clang | 0.3.3 | 25.00 | 290.92 | 315.92 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.3.3 | 25.00 | 377.80 | 402.80 | ERROR |
Version: 0.3.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [2m/90m]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(ukbflow)
>
> test_check("ukbflow")
v Logged in to DNAnexus as: "TestUser"
v Logged out from DNAnexus.
v Project selected: "project-XXXXXXXXXXXX"
v Renamed 1 column.
* date_of_attending_assessment_centre_i0
v derive_hes (t2d): 26 cases, 26 with date.
v derive_icd10 (t2d): 26 cases across 1 source, 26 with date.
v derive_age: 1 event processed.
Read '/tmp/RtmpGDZMfx/working_dir/RtmpkEDi7D/file37d82c2a661ef8.csv': 3 rows, 2 columns.
Read '/tmp/RtmpGDZMfx/working_dir/RtmpkEDi7D/file37d82c7a9b7888.csv': 5 rows, 3 columns.
Read '/tmp/RtmpGDZMfx/working_dir/RtmpkEDi7D/file37d82c125a8618.csv': 5 rows, 3 columns.
v No NA values.
Read '/tmp/RtmpGDZMfx/working_dir/RtmpkEDi7D/file37d82c30c45d2c.csv': 3 rows, 3 columns.
v No NA values.
v No duplicate SNPs.
v All SNP IDs match rs[0-9]+ format.
v All effect alleles are A/T/C/G.
Read '/tmp/RtmpGDZMfx/working_dir/RtmpkEDi7D/file37d82c6047b891.csv': 5 rows, 3 columns.
v No NA values.
v No duplicate SNPs.
v All effect alleles are A/T/C/G.
Beta summary:
Range : -0.2 to 0.3
Mean |beta|: 0.16
Positive : 3 (60%)
Negative : 2 (40%)
Zero : 0
v Weights file passed checks: 5 SNPs ready for UKB RAP.
v Saved: '/tmp/RtmpGDZMfx/working_dir/RtmpkEDi7D/file37d82cd8fe08c.txt'
Read '/tmp/RtmpGDZMfx/working_dir/RtmpkEDi7D/file37d82c4fe8c8f6.csv': 5 rows, 3 columns.
v No NA values.
v No duplicate SNPs.
v All SNP IDs match rs[0-9]+ format.
Beta summary:
Range : -0.2 to 0.3
Mean |beta|: 0.16
Positive : 3 (60%)
Negative : 2 (40%)
Zero : 0
v Weights file passed checks: 5 SNPs ready for UKB RAP.
v Saved: '/tmp/RtmpGDZMfx/working_dir/RtmpkEDi7D/file37d82c7bff6220.txt'
Read '/tmp/RtmpGDZMfx/working_dir/RtmpkEDi7D/file37d82cb9cf34b.csv': 5 rows, 3 columns.
v No NA values.
v No duplicate SNPs.
v All SNP IDs match rs[0-9]+ format.
v All effect alleles are A/T/C/G.
Beta summary:
Range : -0.2 to 0.3
Mean |beta|: 0.16
Positive : 3 (60%)
Negative : 2 (40%)
Zero : 0
v Weights file passed checks: 5 SNPs ready for UKB RAP.
v Saved: '/tmp/RtmpGDZMfx/working_dir/RtmpkEDi7D/file37d82cac5d83c.txt'
Auto-detected 1 GRS column(s): "GRS_flat"
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
v GRS_b_z -> GRS_b_z_z [mean=-0.0275, sd=0.9886]
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
Auto-detected 2 GRS column(s): "GRS_a_z" and "GRS_b_z"
-- Creating GRS groups ---------------------------------------------------------
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_quad ----------------------------------------------------
GRS_a_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_tri -----------------------------------------------------
GRS_a_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Source: GRS_b_z -------------------------------------------------------------
GRS_b_z: mean=-0.03, median=-0.06, sd=0.99, Q1=-0.64, Q3=0.67, NA=0% (n=0)
-- New column: GRS_b_z_quad ----------------------------------------------------
GRS_b_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_b_z -------------------------------------------------------------
GRS_b_z: mean=-0.03, median=-0.06, sd=0.99, Q1=-0.64, Q3=0.67, NA=0% (n=0)
-- New column: GRS_b_z_tri -----------------------------------------------------
GRS_b_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Effect per SD (OR) ----------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 2 exposures x 1 model = 2 logistic regressions
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z --
v Unadjusted | GRS_a_z: OR 1.10 (0.81-1.49), p = 0.556
-- GRS_b_z --
v Unadjusted | GRS_b_z: OR 0.86 (0.63-1.17), p = 0.328
v Done: 2 result rows across 2 exposures and 1 model.
-- High vs Low -----------------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 2 exposures x 1 model = 2 logistic regressions
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z_tri --
v Unadjusted | GRS_a_z_triMid: OR 1.00 (0.46-2.19), p = 1
v Unadjusted | GRS_a_z_triHigh: OR 1.25 (0.49-3.16), p = 0.637
-- GRS_b_z_tri --
v Unadjusted | GRS_b_z_triMid: OR 0.51 (0.25-1.04), p = 0.063
v Unadjusted | GRS_b_z_triHigh: OR 0.67 (0.28-1.62), p = 0.377
v Done: 4 result rows across 2 exposures and 1 model.
-- Trend test ------------------------------------------------------------------
! Exposures GRS_a_z_quad and GRS_b_z_quad are not an ordered factor -- levels will be scored 0, 1, 2, ... (equal spacing assumed).
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_trend -----------------------------------------------------------------
i 2 exposures x 1 model (categorical + trend model per combination)
-- GRS_a_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_a_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_a_z_quadQ2: OR 0.90 (0.37-2.20), p = 0.821
v Unadjusted | GRS_a_z_quadQ3: OR 1.54 (0.68-3.50), p = 0.303
v Unadjusted | GRS_a_z_quadQ4: OR 1.00 (0.42-2.39), p = 1
i Unadjusted | trend: OR_per_score = 1.06 (0.81-1.38), p_trend = 0.682
-- GRS_b_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_b_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_b_z_quadQ2: OR 0.49 (0.21-1.14), p = 0.0976
v Unadjusted | GRS_b_z_quadQ3: OR 0.66 (0.30-1.48), p = 0.315
v Unadjusted | GRS_b_z_quadQ4: OR 0.54 (0.24-1.25), p = 0.151
i Unadjusted | trend: OR_per_score = 0.84 (0.65-1.11), p_trend = 0.221
v Done: 8 result rows across 2 exposures and 1 model.
-- AUC -------------------------------------------------------------------------
v Validation complete.
-- Creating GRS groups ---------------------------------------------------------
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_quad ----------------------------------------------------
GRS_a_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_tri -----------------------------------------------------
GRS_a_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Source: GRS_b_z -------------------------------------------------------------
GRS_b_z: mean=-0.03, median=-0.06, sd=0.99, Q1=-0.64, Q3=0.67, NA=0% (n=0)
-- New column: GRS_b_z_quad ----------------------------------------------------
GRS_b_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_b_z -------------------------------------------------------------
GRS_b_z: mean=-0.03, median=-0.06, sd=0.99, Q1=-0.64, Q3=0.67, NA=0% (n=0)
-- New column: GRS_b_z_tri -----------------------------------------------------
GRS_b_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Effect per SD (OR) ----------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 2 exposures x 1 model = 2 logistic regressions
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z --
v Unadjusted | GRS_a_z: OR 1.10 (0.81-1.49), p = 0.556
-- GRS_b_z --
v Unadjusted | GRS_b_z: OR 0.86 (0.63-1.17), p = 0.328
v Done: 2 result rows across 2 exposures and 1 model.
-- High vs Low -----------------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 2 exposures x 1 model = 2 logistic regressions
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z_tri --
v Unadjusted | GRS_a_z_triMid: OR 1.00 (0.46-2.19), p = 1
v Unadjusted | GRS_a_z_triHigh: OR 1.25 (0.49-3.16), p = 0.637
-- GRS_b_z_tri --
v Unadjusted | GRS_b_z_triMid: OR 0.51 (0.25-1.04), p = 0.063
v Unadjusted | GRS_b_z_triHigh: OR 0.67 (0.28-1.62), p = 0.377
v Done: 4 result rows across 2 exposures and 1 model.
-- Trend test ------------------------------------------------------------------
! Exposures GRS_a_z_quad and GRS_b_z_quad are not an ordered factor -- levels will be scored 0, 1, 2, ... (equal spacing assumed).
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_trend -----------------------------------------------------------------
i 2 exposures x 1 model (categorical + trend model per combination)
-- GRS_a_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_a_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_a_z_quadQ2: OR 0.90 (0.37-2.20), p = 0.821
v Unadjusted | GRS_a_z_quadQ3: OR 1.54 (0.68-3.50), p = 0.303
v Unadjusted | GRS_a_z_quadQ4: OR 1.00 (0.42-2.39), p = 1
i Unadjusted | trend: OR_per_score = 1.06 (0.81-1.38), p_trend = 0.682
-- GRS_b_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_b_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_b_z_quadQ2: OR 0.49 (0.21-1.14), p = 0.0976
v Unadjusted | GRS_b_z_quadQ3: OR 0.66 (0.30-1.48), p = 0.315
v Unadjusted | GRS_b_z_quadQ4: OR 0.54 (0.24-1.25), p = 0.151
i Unadjusted | trend: OR_per_score = 0.84 (0.65-1.11), p_trend = 0.221
v Done: 8 result rows across 2 exposures and 1 model.
-- AUC -------------------------------------------------------------------------
v Validation complete.
-- Creating GRS groups ---------------------------------------------------------
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_quad ----------------------------------------------------
GRS_a_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_tri -----------------------------------------------------
GRS_a_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Effect per SD (OR) ----------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 1 exposure x 1 model = 1 logistic regression
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z --
v Unadjusted | GRS_a_z: OR 1.10 (0.81-1.49), p = 0.556
v Done: 1 result row across 1 exposure and 1 model.
-- High vs Low -----------------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 1 exposure x 1 model = 1 logistic regression
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z_tri --
v Unadjusted | GRS_a_z_triMid: OR 1.00 (0.46-2.19), p = 1
v Unadjusted | GRS_a_z_triHigh: OR 1.25 (0.49-3.16), p = 0.637
v Done: 2 result rows across 1 exposure and 1 model.
-- Trend test ------------------------------------------------------------------
! Exposure GRS_a_z_quad is not an ordered factor -- levels will be scored 0, 1, 2, ... (equal spacing assumed).
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_trend -----------------------------------------------------------------
i 1 exposure x 1 model (categorical + trend model per combination)
-- GRS_a_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_a_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_a_z_quadQ2: OR 0.90 (0.37-2.20), p = 0.821
v Unadjusted | GRS_a_z_quadQ3: OR 1.54 (0.68-3.50), p = 0.303
v Unadjusted | GRS_a_z_quadQ4: OR 1.00 (0.42-2.39), p = 1
i Unadjusted | trend: OR_per_score = 1.06 (0.81-1.38), p_trend = 0.682
v Done: 4 result rows across 1 exposure and 1 model.
-- AUC -------------------------------------------------------------------------
v Validation complete.
-- Creating GRS groups ---------------------------------------------------------
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_quad ----------------------------------------------------
GRS_a_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_tri -----------------------------------------------------
GRS_a_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Effect per SD (HR) ----------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_coxph -----------------------------------------------------------------
i 1 exposure x 1 model = 1 Cox regression
i Input cohort: 300 participants (n/n_events/person_years reflect each model's actual analysis set)
-- GRS_a_z --
v Unadjusted | GRS_a_z: HR 1.12 (0.83-1.51), p = 0.465
v Done: 1 result row across 1 exposure and 1 model.
-- High vs Low -----------------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_coxph -----------------------------------------------------------------
i 1 exposure x 1 model = 1 Cox regression
i Input cohort: 300 participants (n/n_events/person_years reflect each model's actual analysis set)
-- GRS_a_z_tri --
v Unadjusted | GRS_a_z_triMid: HR 0.82 (0.40-1.68), p = 0.585
v Unadjusted | GRS_a_z_triHigh: HR 1.19 (0.51-2.76), p = 0.685
v Done: 2 result rows across 1 exposure and 1 model.
-- Trend test ------------------------------------------------------------------
! Exposure GRS_a_z_quad is not an ordered factor -- levels will be scored 0, 1, 2, ... (equal spacing assumed).
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_trend -----------------------------------------------------------------
i 1 exposure x 1 model (categorical + trend model per combination)
-- GRS_a_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_a_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_a_z_quadQ2: HR 0.64 (0.28-1.47), p = 0.294
v Unadjusted | GRS_a_z_quadQ3: HR 1.10 (0.52-2.31), p = 0.805
v Unadjusted | GRS_a_z_quadQ4: HR 1.05 (0.47-2.34), p = 0.905
i Unadjusted | trend: HR_per_score = 1.08 (0.83-1.41), p_trend = 0.546
v Done: 4 result rows across 1 exposure and 1 model.
-- C-index ---------------------------------------------------------------------
v Validation complete.
-- Creating GRS groups ---------------------------------------------------------
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_quad ----------------------------------------------------
GRS_a_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_tri -----------------------------------------------------
GRS_a_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Effect per SD (OR) ----------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 1 exposure x 1 model = 1 logistic regression
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z --
v Unadjusted | GRS_a_z: OR 1.10 (0.81-1.49), p = 0.556
v Done: 1 result row across 1 exposure and 1 model.
-- High vs Low -----------------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 1 exposure x 1 model = 1 logistic regression
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z_tri --
v Unadjusted | GRS_a_z_triMid: OR 1.00 (0.46-2.19), p = 1
v Unadjusted | GRS_a_z_triHigh: OR 1.25 (0.49-3.16), p = 0.637
v Done: 2 result rows across 1 exposure and 1 model.
-- Trend test ------------------------------------------------------------------
! Exposure GRS_a_z_quad is not an ordered factor -- levels will be scored 0, 1, 2, ... (equal spacing assumed).
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_trend -----------------------------------------------------------------
i 1 exposure x 1 model (categorical + trend model per combination)
-- GRS_a_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_a_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_a_z_quadQ2: OR 0.90 (0.37-2.20), p = 0.821
v Unadjusted | GRS_a_z_quadQ3: OR 1.54 (0.68-3.50), p = 0.303
v Unadjusted | GRS_a_z_quadQ4: OR 1.00 (0.42-2.39), p = 1
i Unadjusted | trend: OR_per_score = 1.06 (0.81-1.38), p_trend = 0.682
v Done: 4 result rows across 1 exposure and 1 model.
-- AUC -------------------------------------------------------------------------
v Validation complete.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [2m/90m]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(ukbflow)
>
> test_check("ukbflow")
v Logged in to DNAnexus as: "TestUser"
v Logged out from DNAnexus.
v Project selected: "project-XXXXXXXXXXXX"
v Renamed 1 column.
* date_of_attending_assessment_centre_i0
v derive_hes (t2d): 26 cases, 26 with date.
v derive_icd10 (t2d): 26 cases across 1 source, 26 with date.
v derive_age: 1 event processed.
Read '/tmp/RtmpbYlGeJ/working_dir/RtmpKB6VlO/file27d6979e1d479.csv': 3 rows, 2 columns.
Read '/tmp/RtmpbYlGeJ/working_dir/RtmpKB6VlO/file27d697361bf8c.csv': 5 rows, 3 columns.
Read '/tmp/RtmpbYlGeJ/working_dir/RtmpKB6VlO/file27d691e5b8c3f.csv': 5 rows, 3 columns.
v No NA values.
Read '/tmp/RtmpbYlGeJ/working_dir/RtmpKB6VlO/file27d695a77c161.csv': 3 rows, 3 columns.
v No NA values.
v No duplicate SNPs.
v All SNP IDs match rs[0-9]+ format.
v All effect alleles are A/T/C/G.
Read '/tmp/RtmpbYlGeJ/working_dir/RtmpKB6VlO/file27d695fda206f.csv': 5 rows, 3 columns.
v No NA values.
v No duplicate SNPs.
v All effect alleles are A/T/C/G.
Beta summary:
Range : -0.2 to 0.3
Mean |beta|: 0.16
Positive : 3 (60%)
Negative : 2 (40%)
Zero : 0
v Weights file passed checks: 5 SNPs ready for UKB RAP.
v Saved: '/tmp/RtmpbYlGeJ/working_dir/RtmpKB6VlO/file27d6959ec7185.txt'
Read '/tmp/RtmpbYlGeJ/working_dir/RtmpKB6VlO/file27d692e6d73c3.csv': 5 rows, 3 columns.
v No NA values.
v No duplicate SNPs.
v All SNP IDs match rs[0-9]+ format.
Beta summary:
Range : -0.2 to 0.3
Mean |beta|: 0.16
Positive : 3 (60%)
Negative : 2 (40%)
Zero : 0
v Weights file passed checks: 5 SNPs ready for UKB RAP.
v Saved: '/tmp/RtmpbYlGeJ/working_dir/RtmpKB6VlO/file27d69704df9bc.txt'
Read '/tmp/RtmpbYlGeJ/working_dir/RtmpKB6VlO/file27d6912c6e969.csv': 5 rows, 3 columns.
v No NA values.
v No duplicate SNPs.
v All SNP IDs match rs[0-9]+ format.
v All effect alleles are A/T/C/G.
Beta summary:
Range : -0.2 to 0.3
Mean |beta|: 0.16
Positive : 3 (60%)
Negative : 2 (40%)
Zero : 0
v Weights file passed checks: 5 SNPs ready for UKB RAP.
v Saved: '/tmp/RtmpbYlGeJ/working_dir/RtmpKB6VlO/file27d697b2e6147.txt'
Auto-detected 1 GRS column(s): "GRS_flat"
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
v GRS_b_z -> GRS_b_z_z [mean=-0.0275, sd=0.9886]
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
Auto-detected 2 GRS column(s): "GRS_a_z" and "GRS_b_z"
-- Creating GRS groups ---------------------------------------------------------
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_quad ----------------------------------------------------
GRS_a_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_tri -----------------------------------------------------
GRS_a_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Source: GRS_b_z -------------------------------------------------------------
GRS_b_z: mean=-0.03, median=-0.06, sd=0.99, Q1=-0.64, Q3=0.67, NA=0% (n=0)
-- New column: GRS_b_z_quad ----------------------------------------------------
GRS_b_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_b_z -------------------------------------------------------------
GRS_b_z: mean=-0.03, median=-0.06, sd=0.99, Q1=-0.64, Q3=0.67, NA=0% (n=0)
-- New column: GRS_b_z_tri -----------------------------------------------------
GRS_b_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Effect per SD (OR) ----------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 2 exposures x 1 model = 2 logistic regressions
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z --
v Unadjusted | GRS_a_z: OR 1.10 (0.81-1.49), p = 0.556
-- GRS_b_z --
v Unadjusted | GRS_b_z: OR 0.86 (0.63-1.17), p = 0.328
v Done: 2 result rows across 2 exposures and 1 model.
-- High vs Low -----------------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 2 exposures x 1 model = 2 logistic regressions
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z_tri --
v Unadjusted | GRS_a_z_triMid: OR 1.00 (0.46-2.19), p = 1
v Unadjusted | GRS_a_z_triHigh: OR 1.25 (0.49-3.16), p = 0.637
-- GRS_b_z_tri --
v Unadjusted | GRS_b_z_triMid: OR 0.51 (0.25-1.04), p = 0.063
v Unadjusted | GRS_b_z_triHigh: OR 0.67 (0.28-1.62), p = 0.377
v Done: 4 result rows across 2 exposures and 1 model.
-- Trend test ------------------------------------------------------------------
! Exposures GRS_a_z_quad and GRS_b_z_quad are not an ordered factor -- levels will be scored 0, 1, 2, ... (equal spacing assumed).
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_trend -----------------------------------------------------------------
i 2 exposures x 1 model (categorical + trend model per combination)
-- GRS_a_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_a_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_a_z_quadQ2: OR 0.90 (0.37-2.20), p = 0.821
v Unadjusted | GRS_a_z_quadQ3: OR 1.54 (0.68-3.50), p = 0.303
v Unadjusted | GRS_a_z_quadQ4: OR 1.00 (0.42-2.39), p = 1
i Unadjusted | trend: OR_per_score = 1.06 (0.81-1.38), p_trend = 0.682
-- GRS_b_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_b_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_b_z_quadQ2: OR 0.49 (0.21-1.14), p = 0.0976
v Unadjusted | GRS_b_z_quadQ3: OR 0.66 (0.30-1.48), p = 0.315
v Unadjusted | GRS_b_z_quadQ4: OR 0.54 (0.24-1.25), p = 0.151
i Unadjusted | trend: OR_per_score = 0.84 (0.65-1.11), p_trend = 0.221
v Done: 8 result rows across 2 exposures and 1 model.
-- AUC -------------------------------------------------------------------------
v Validation complete.
-- Creating GRS groups ---------------------------------------------------------
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_quad ----------------------------------------------------
GRS_a_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_tri -----------------------------------------------------
GRS_a_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Source: GRS_b_z -------------------------------------------------------------
GRS_b_z: mean=-0.03, median=-0.06, sd=0.99, Q1=-0.64, Q3=0.67, NA=0% (n=0)
-- New column: GRS_b_z_quad ----------------------------------------------------
GRS_b_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_b_z -------------------------------------------------------------
GRS_b_z: mean=-0.03, median=-0.06, sd=0.99, Q1=-0.64, Q3=0.67, NA=0% (n=0)
-- New column: GRS_b_z_tri -----------------------------------------------------
GRS_b_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Effect per SD (OR) ----------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 2 exposures x 1 model = 2 logistic regressions
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z --
v Unadjusted | GRS_a_z: OR 1.10 (0.81-1.49), p = 0.556
-- GRS_b_z --
v Unadjusted | GRS_b_z: OR 0.86 (0.63-1.17), p = 0.328
v Done: 2 result rows across 2 exposures and 1 model.
-- High vs Low -----------------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 2 exposures x 1 model = 2 logistic regressions
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z_tri --
v Unadjusted | GRS_a_z_triMid: OR 1.00 (0.46-2.19), p = 1
v Unadjusted | GRS_a_z_triHigh: OR 1.25 (0.49-3.16), p = 0.637
-- GRS_b_z_tri --
v Unadjusted | GRS_b_z_triMid: OR 0.51 (0.25-1.04), p = 0.063
v Unadjusted | GRS_b_z_triHigh: OR 0.67 (0.28-1.62), p = 0.377
v Done: 4 result rows across 2 exposures and 1 model.
-- Trend test ------------------------------------------------------------------
! Exposures GRS_a_z_quad and GRS_b_z_quad are not an ordered factor -- levels will be scored 0, 1, 2, ... (equal spacing assumed).
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_trend -----------------------------------------------------------------
i 2 exposures x 1 model (categorical + trend model per combination)
-- GRS_a_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_a_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_a_z_quadQ2: OR 0.90 (0.37-2.20), p = 0.821
v Unadjusted | GRS_a_z_quadQ3: OR 1.54 (0.68-3.50), p = 0.303
v Unadjusted | GRS_a_z_quadQ4: OR 1.00 (0.42-2.39), p = 1
i Unadjusted | trend: OR_per_score = 1.06 (0.81-1.38), p_trend = 0.682
-- GRS_b_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_b_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_b_z_quadQ2: OR 0.49 (0.21-1.14), p = 0.0976
v Unadjusted | GRS_b_z_quadQ3: OR 0.66 (0.30-1.48), p = 0.315
v Unadjusted | GRS_b_z_quadQ4: OR 0.54 (0.24-1.25), p = 0.151
i Unadjusted | trend: OR_per_score = 0.84 (0.65-1.11), p_trend = 0.221
v Done: 8 result rows across 2 exposures and 1 model.
-- AUC -------------------------------------------------------------------------
v Validation complete.
-- Creating GRS groups ---------------------------------------------------------
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_quad ----------------------------------------------------
GRS_a_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_tri -----------------------------------------------------
GRS_a_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Effect per SD (OR) ----------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 1 exposure x 1 model = 1 logistic regression
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z --
v Unadjusted | GRS_a_z: OR 1.10 (0.81-1.49), p = 0.556
v Done: 1 result row across 1 exposure and 1 model.
-- High vs Low -----------------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 1 exposure x 1 model = 1 logistic regression
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z_tri --
v Unadjusted | GRS_a_z_triMid: OR 1.00 (0.46-2.19), p = 1
v Unadjusted | GRS_a_z_triHigh: OR 1.25 (0.49-3.16), p = 0.637
v Done: 2 result rows across 1 exposure and 1 model.
-- Trend test ------------------------------------------------------------------
! Exposure GRS_a_z_quad is not an ordered factor -- levels will be scored 0, 1, 2, ... (equal spacing assumed).
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_trend -----------------------------------------------------------------
i 1 exposure x 1 model (categorical + trend model per combination)
-- GRS_a_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_a_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_a_z_quadQ2: OR 0.90 (0.37-2.20), p = 0.821
v Unadjusted | GRS_a_z_quadQ3: OR 1.54 (0.68-3.50), p = 0.303
v Unadjusted | GRS_a_z_quadQ4: OR 1.00 (0.42-2.39), p = 1
i Unadjusted | trend: OR_per_score = 1.06 (0.81-1.38), p_trend = 0.682
v Done: 4 result rows across 1 exposure and 1 model.
-- AUC -------------------------------------------------------------------------
v Validation complete.
-- Creating GRS groups ---------------------------------------------------------
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_quad ----------------------------------------------------
GRS_a_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_tri -----------------------------------------------------
GRS_a_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Effect per SD (HR) ----------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_coxph -----------------------------------------------------------------
i 1 exposure x 1 model = 1 Cox regression
i Input cohort: 300 participants (n/n_events/person_years reflect each model's actual analysis set)
-- GRS_a_z --
v Unadjusted | GRS_a_z: HR 1.12 (0.83-1.51), p = 0.465
v Done: 1 result row across 1 exposure and 1 model.
-- High vs Low -----------------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_coxph -----------------------------------------------------------------
i 1 exposure x 1 model = 1 Cox regression
i Input cohort: 300 participants (n/n_events/person_years reflect each model's actual analysis set)
-- GRS_a_z_tri --
v Unadjusted | GRS_a_z_triMid: HR 0.82 (0.40-1.68), p = 0.585
v Unadjusted | GRS_a_z_triHigh: HR 1.19 (0.51-2.76), p = 0.685
v Done: 2 result rows across 1 exposure and 1 model.
-- Trend test ------------------------------------------------------------------
! Exposure GRS_a_z_quad is not an ordered factor -- levels will be scored 0, 1, 2, ... (equal spacing assumed).
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_trend -----------------------------------------------------------------
i 1 exposure x 1 model (categorical + trend model per combination)
-- GRS_a_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_a_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_a_z_quadQ2: HR 0.64 (0.28-1.47), p = 0.294
v Unadjusted | GRS_a_z_quadQ3: HR 1.10 (0.52-2.31), p = 0.805
v Unadjusted | GRS_a_z_quadQ4: HR 1.05 (0.47-2.34), p = 0.905
i Unadjusted | trend: HR_per_score = 1.08 (0.83-1.41), p_trend = 0.546
v Done: 4 result rows across 1 exposure and 1 model.
-- C-index ---------------------------------------------------------------------
v Validation complete.
-- Creating GRS groups ---------------------------------------------------------
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_quad ----------------------------------------------------
GRS_a_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_tri -----------------------------------------------------
GRS_a_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Effect per SD (OR) ----------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 1 exposure x 1 model = 1 logistic regression
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z --
v Unadjusted | GRS_a_z: OR 1.10 (0.81-1.49), p = 0.556
v Done: 1 result row across 1 exposure and 1 model.
-- High vs Low -----------------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 1 exposure x 1 model = 1 logistic regression
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z_tri --
v Unadjusted | GRS_a_z_triMid: OR 1.00 (0.46-2.19), p = 1
v Unadjusted | GRS_a_z_triHigh: OR 1.25 (0.49-3.16), p = 0.637
v Done: 2 result rows across 1 exposure and 1 model.
-- Trend test ------------------------------------------------------------------
! Exposure GRS_a_z_quad is not an ordered factor -- levels will be scored 0, 1, 2, ... (equal spacing assumed).
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_trend -----------------------------------------------------------------
i 1 exposure x 1 model (categorical + trend model per combination)
-- GRS_a_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_a_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_a_z_quadQ2: OR 0.90 (0.37-2.20), p = 0.821
v Unadjusted | GRS_a_z_quadQ3: OR 1.54 (0.68-3.50), p = 0.303
v Unadjusted | GRS_a_z_quadQ4: OR 1.00 (0.42-2.39), p = 1
i Unadjusted | trend: OR_per_score = 1.06 (0.81-1.38), p_trend = 0.682
v Done: 4 result rows across 1 exposure and 1 model.
-- AUC -------------------------------------------------------------------------
v Validation complete.
! Interrupting test: assoc_logistic() OR > 0, CI spans OR, p in [0,1]
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.