Last updated on 2026-04-08 20:52:14 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-gcc | 0.3.3 | 9.91 | 190.20 | 200.11 | OK | |
| 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 | |
| r-devel-windows-x86_64 | 0.3.3 | 23.00 | 299.00 | 322.00 | OK | |
| r-release-macos-x86_64 | 0.3.3 | 10.00 | 313.00 | 323.00 | OK | |
| r-oldrel-macos-x86_64 | 0.3.3 | 10.00 | 298.00 | 308.00 | OK |
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.
Health stats visible at Monitor.