R Under development (unstable) (2026-01-16 r89305 ucrt) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(bregr) Welcome to 'bregr' package! ======================================================================= You are using bregr version 1.3.2 Project home : https://github.com/WangLabCSU/bregr Documentation: https://wanglabcsu.github.io/bregr/ Cite as : https://doi.org/10.1002/mdr2.70028 Wang, S., Peng, Y., Shu, C., Wang, C., Yang, Y., Zhao, Y., Cui, Y., Hu, D. and Zhou, J.-G. (2025), bregr: An R Package for Streamlined Batch Processing and Visualization of Biomedical Regression Models. Med Research. ======================================================================= > > test_check("bregr") filtered variables: "x2" and "x3" filtered variables: "x2" Pre-filtering removed 2 out of 2 focal variables (100%) filtered variables: "x1" and "x2" filtered variables: "x2" filtered variables: "x2" exponentiate estimates of model(s) constructed from coxph method at default `idx` not set, use the first model Cox model: intercept term present but no intercept coefficient (as expected for semi-parametric models) `idx` not set, use the first model Cox model: intercept term present but no intercept coefficient (as expected for semi-parametric models) Cox model: intercept term present but no intercept coefficient (as expected for semi-parametric models) `idx` not set, use the first model `idx` not set, use the first model `idx` not set, use the first model exponentiate estimates of model(s) constructed from coxph method at default exponentiate estimates of model(s) constructed from coxph method at default `idx` not set, use the first model Cox model: intercept term present but no intercept coefficient (as expected for semi-parametric models) Cox model: intercept term present but no intercept coefficient (as expected for semi-parametric models) `idx` not set, use the first model exponentiate estimates of model(s) constructed from coxph method at default `idx` not set, use the first model `type` is not specified, use lp for the model exponentiate estimates of model(s) constructed from coxph method at default `idx` not set, use the first model `idx` not set, use the first model `type` is not specified, use response for the model `idx` not set, use the first model subset model list with idx: 1 model call: stats::glm(formula = mpg ~ cyl + vs, family = stats::gaussian, data = data) model call: stats::glm(formula = mpg ~ cyl + vs, family = stats::gaussian, data = data) exponentiate estimates of model(s) constructed from coxph method at default exponentiate estimates of model(s) constructed from coxph method at default `idx` not set, use the first model Cox model: intercept term present but no intercept coefficient (as expected for semi-parametric models) `idx` not set, use the first model exponentiate estimates of model(s) constructed from coxph method at default Loading required namespace: ggnewscale please note only continuous focal terms analyzed and visualized exponentiate estimates of model(s) constructed from coxph method at default -- Model Diagnostics Summary --------------------------------------------------- -- Model: "ph.ecog" (coxph) -- Sample size: 227 Events: 164 Log-likelihood: -729.23 Concordance: 12544, 7117, 126, 28, 0, 0.637, and 0.025 Proportional Hazards Test (Schoenfeld Residuals): + ph.ecog: χ² = 2.054, df = 1, p = 0.152 + age: χ² = 0.188, df = 1, p = 0.665 + sex: χ² = 2.305, df = 1, p = 0.129 Global test: p = 0.216 - Assumption + SATISFIED -- Model: "ph.karno" (coxph) -- Sample size: 227 Events: 164 Log-likelihood: -735.078 Concordance: 12578, 7145, 65, 28, 0, 0.637, and 0.025 Proportional Hazards Test (Schoenfeld Residuals): x ph.karno: χ² = 8.017, df = 1, p = 0.00463 + age: χ² = 0.478, df = 1, p = 0.489 + sex: χ² = 3.085, df = 1, p = 0.079 Global test: p = 0.0157 - Assumption x VIOLATED -- Model: "pat.karno" (coxph) -- Sample size: 225 Events: 162 Log-likelihood: -721.587 Concordance: 12343, 6957, 57, 26, 0, 0.639, and 0.025 Proportional Hazards Test (Schoenfeld Residuals): x pat.karno: χ² = 4.226, df = 1, p = 0.0398 + age: χ² = 0.054, df = 1, p = 0.817 + sex: χ² = 2.752, df = 1, p = 0.0971 Global test: p = 0.0819 - Assumption + SATISFIED -- Model: "meal.cal" (coxph) -- Sample size: 181 Events: 134 Log-likelihood: -573.568 Concordance: 7761, 5080, 7, 17, 0, 0.604, and 0.029 Proportional Hazards Test (Schoenfeld Residuals): x meal.cal: χ² = 4.65, df = 1, p = 0.031 + age: χ² = 0.622, df = 1, p = 0.43 + sex: χ² = 1.481, df = 1, p = 0.224 Global test: p = 0.0942 - Assumption + SATISFIED -- Model: "wt.loss" (coxph) -- Sample size: 214 Events: 152 Log-likelihood: -673.056 Concordance: 10531, 6672, 10, 22, 0, 0.612, and 0.027 Proportional Hazards Test (Schoenfeld Residuals): + wt.loss: χ² = 0.014, df = 1, p = 0.904 + age: χ² = 0.508, df = 1, p = 0.476 + sex: χ² = 2.549, df = 1, p = 0.11 Global test: p = 0.391 - Assumption + SATISFIED exponentiate estimates of model(s) constructed from coxph method at default `idx` not set, use the first model `idx` not set, use the first model [ FAIL 0 | WARN 1 | SKIP 6 | PASS 113 ] ══ Skipped tests (6) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-nomogram-interactions.R:2:3' • empty test (5): 'test-roxytest-testexamples-02-pipeline.R:5:1', 'test-roxytest-testexamples-03-accessors.R:5:1', 'test-roxytest-testexamples-04-show.R:5:1', 'test-roxytest-testexamples-04-show.R:201:1', 'test-roxytest-testexamples-05-polar.R:5:1' [ FAIL 0 | WARN 1 | SKIP 6 | PASS 113 ] > > proc.time() user system elapsed 63.06 1.34 64.40