Last updated on 2026-10-24 03:56:24 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.4 | 14.62 | 216.55 | 231.17 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.3.4 | 11.56 | 143.39 | 154.95 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.3.4 | 11.00 | 159.64 | 170.64 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.3.4 | 170.70 | OK | |||
| r-devel-windows-x86_64 | 0.3.4 | 18.00 | 231.00 | 249.00 | OK | |
| r-patched-linux-x86_64 | 0.3.4 | 14.39 | 202.55 | 216.94 | OK | |
| r-release-linux-x86_64 | 0.3.4 | 12.79 | 203.97 | 216.76 | OK | |
| r-release-macos-arm64 | 0.3.4 | 4.00 | 51.00 | 55.00 | OK | |
| r-release-macos-x86_64 | 0.3.4 | 10.00 | 221.00 | 231.00 | OK | |
| r-release-windows-x86_64 | 0.3.4 | 18.00 | 311.00 | 329.00 | OK | |
| r-oldrel-macos-arm64 | 0.3.4 | 3.00 | 52.00 | 55.00 | OK | |
| r-oldrel-macos-x86_64 | 0.3.4 | 10.00 | 221.00 | 231.00 | OK | |
| r-oldrel-windows-x86_64 | 0.3.4 | 24.00 | 279.00 | 303.00 | OK |
Version: 0.3.4
Check: examples
Result: ERROR
Running examples in ‘ukbflow-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assoc_coxph_zph
> ### Title: Proportional hazards assumption test for Cox regression
> ### Aliases: assoc_coxph_zph assoc_zph
>
> ### ** Examples
>
> dt <- ops_toy(scenario = "association", n = 500)
✔ ops_toy: 500 participants | 33 columns | scenario = "association" | seed = 42
> dt <- dt[dm_timing != 1L]
>
> zph <- assoc_coxph_zph(
+ data = dt,
+ outcome_col = "dm_status",
+ time_col = "dm_followup_years",
+ exposure_col = "p20116_i0",
+ covariates = c("bmi_cat", "tdi_cat"),
+ base = FALSE
+ )
ℹ outcome_col dm_status: logical detected, converting TRUE/FALSE -> 1/0
── assoc_coxph_zph ─────────────────────────────────────────────────────────────
ℹ 1 exposure x 1 model = 1 PH assumption test
── p20116_i0 ──
! [Fully adjusted | p20116_i0] cox.zph failed: subscript out of bounds
! No results returned - check model warnings above.
> zph[ph_satisfied == FALSE]
Error in .checkTypos(e, names_x) :
Object 'ph_satisfied' not found amongst []
Calls: [ ... <Anonymous> -> .checkTypos -> stopf -> raise_condition -> signal
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [36s/45s]
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")
Saving _problems/test-assoc-301.R
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 '/home/hornik/tmp/scratch/RtmpnxgUJO/file2f4b85e04b685.csv': 3 rows, 2 columns.
Read '/home/hornik/tmp/scratch/RtmpnxgUJO/file2f4b87be01d96.csv': 5 rows, 3 columns.
Read '/home/hornik/tmp/scratch/RtmpnxgUJO/file2f4b85b6201fc.csv': 5 rows, 3 columns.
v No NA values.
Read '/home/hornik/tmp/scratch/RtmpnxgUJO/file2f4b86cf66c52.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 '/home/hornik/tmp/scratch/RtmpnxgUJO/file2f4b833c3d492.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: '/home/hornik/tmp/scratch/RtmpnxgUJO/file2f4b868fe9c35.txt'
Read '/home/hornik/tmp/scratch/RtmpnxgUJO/file2f4b84854e66b.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: '/home/hornik/tmp/scratch/RtmpnxgUJO/file2f4b8184a2fc1.txt'
Read '/home/hornik/tmp/scratch/RtmpnxgUJO/file2f4b822f33038.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: '/home/hornik/tmp/scratch/RtmpnxgUJO/file2f4b84f5be315.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.
xlim, ticks_at will be deprecated, use set_xaxis() instead.
arrow_lab will be deprecated, use set_labs() instead.
theme will be deprecated, use style of forest() instead.
[ FAIL 1 | WARN 0 | SKIP 11 | PASS 1022 ]
══ Skipped tests (11) ══════════════════════════════════════════════════════════
• On CRAN (11): 'test-integration-assoc.R:11:1', 'test-integration-auth.R:7:1',
'test-integration-decode.R:8:1', 'test-integration-derive.R:13:1',
'test-integration-extract.R:7:1', 'test-integration-fetch.R:7:1',
'test-integration-grs.R:12:1', 'test-integration-job.R:7:1',
'test-integration-plot.R:12:1', 'test-plot.R:337:3', 'test-plot.R:347:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-assoc.R:300:3'): assoc_coxph_zph() returns data.table with zph columns ──
Expected `all(...)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 0 | SKIP 11 | PASS 1022 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc