R Under development (unstable) (2025-07-14 r88410 ucrt) -- "Unsuffered Consequences" Copyright (C) 2025 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(comorbidPGS) Attaching package: 'comorbidPGS' The following object is masked from 'package:graphics': assocplot > > test_check("comorbidPGS") --- Association testing: PGS: ldl_PGS Phenotype: WRONG_PHENO Covariate: NA --- Association testing: PGS: ldl_PGS Phenotype: test Covariate: NA Phenotype type: Continuous `test` ~ `ldl_PGS` Using a Linear regression Sample Size: 10000 Beta ( SE ): 0.2770361 ( 0.01000134 ) P-value: 8.815594e-163 --- Association testing: PGS: ldl_PGS Phenotype: test2 Covariate: NA Phenotype type: Continuous `test2` ~ `ldl_PGS` Using a Linear regression Sample Size: 4000 Beta ( SE ): 0.2817405 ( 0.01581361 ) P-value: 2.180928e-68 --- Association testing: PGS: ldl_PGS Phenotype: WRONG_PHENO Covariate: NA# weights: 12 (6 variable) initial value 13862.943611 iter 10 value 9697.260945 final value 9696.463691 converged # weights: 12 (6 variable) initial value 13862.943611 iter 10 value 9697.368074 final value 9696.630119 converged # weights: 12 (6 variable) initial value 13862.943611 iter 10 value 9699.063415 final value 9697.386957 converged ------ Multiple associations ( 4 ) testing: No parallelisation, this operation may be slower | | | 0% --- Association testing: PGS: brc_PGS Phenotype: ethnicity Covariate: NA Phenotype type: Categorical `ethnicity` ~ `brc_PGS`# weights: 12 (6 variable) initial value 13862.943611 iter 10 value 9697.260945 final value 9696.463691 converged Using a Multinomial logistic regression Sample Size: 8523 7586 6653 OR [ 95% CI ]: 1.007334 1.028451 0.9348368 [ 0.9592139 0.9670665 0.8277834 - 1.057869 1.093732 1.055735 ] P-value: 0.7698207 0.3716085 0.27751 | |================== | 25% --- Association testing: PGS: t2d_PGS Phenotype: t2d Covariate: NA Phenotype type: Cases/Controls `t2d` ~ `t2d_PGS` Using a Binary logistic regression Cases: 730 Controls: 9270 Sample Size: 10000 OR [ 95% CI ]: 1.688258 [ 1.561821 - 1.824931 ] P-value: 1.059304e-39 | |=================================== | 50% --- Association testing: PGS: ldl_PGS Phenotype: log_ldl Covariate: NA Phenotype type: Continuous `log_ldl` ~ `ldl_PGS` Using a Linear regression Sample Size: 10000 Beta ( SE ): 0.08287867 ( 0.002176973 ) P-value: 2.794232e-296 | |==================================================== | 75% --- Association testing: PGS: brc_PGS Phenotype: sbp_cat Covariate: NA Phenotype type: Ordered Categorical `sbp_cat` ~ `brc_PGS` Using a Ordinal logistic regression Sample Size: 10000 OR [ 95% CI ]: 0.9885508 [ 0.9526072 - 1.025851 ] P-value: 0.5422738 | |======================================================================| 100% --- Mendelian Randomization Two-Stage Least Square (2SLS): PGS --> Exposure -> Outcome: ldl_PGS --> WRONG_PHENO -> bmi --- Mendelian Randomization Two-Stage Least Square (2SLS): PGS --> Exposure -> Outcome: ldl_PGS --> sbp_cat -> bmi --- Mendelian Randomization Two-Stage Least Square (2SLS): PGS --> Exposure -> Outcome: ldl_PGS --> bmi -> sbp_cat --- Mendelian Randomization Two-Stage Least Square (2SLS): PGS --> Exposure -> Outcome: t2d_PGS --> t2d -> bmi Exposure phenotype type: Cases/Controls Outcome phenotype type: Continuous --- Mendelian Randomization Ratio: PGS --> Exposure -> Outcome: ldl_PGS --> WRONG_PHENO -> bmi --- Mendelian Randomization Ratio: PGS --> Exposure -> Outcome: ldl_PGS --> sbp_cat -> bmi --- Mendelian Randomization Ratio: PGS --> Exposure -> Outcome: ldl_PGS --> bmi -> sbp_cat --- Mendelian Randomization Ratio: PGS --> Exposure -> Outcome: t2d_PGS --> t2d -> bmi Exposure phenotype type: Cases/Controls Outcome phenotype type: Continuous ------ Multiple associations ( 1 ) testing: No parallelisation, this operation may be slower | | | 0% --- Association testing: PGS: ldl_PGS Phenotype: t2d Covariate: NA Phenotype type: Cases/Controls `t2d` ~ `ldl_PGS` Using a Binary logistic regression Cases: 730 Controls: 9270 Sample Size: 10000 OR [ 95% CI ]: 0.9843712 [ 0.913016 - 1.061303 ] P-value: 0.6815914 | |======================================================================| 100% ------ Multiple phenotypes associations ( 1 ) testing: | | | 0% --- Association testing: PGS: ldl_PGS Phenotype: brc Covariate: NA Phenotype type: Cases/Controls `brc` ~ `ldl_PGS` Using a Binary logistic regression Cases: 402 Controls: 5041 Sample Size: 5443 OR [ 95% CI ]: 1.102213 [ 0.9947429 - 1.221295 ] P-value: 0.06298496 | |======================================================================| 100% | | | 0%# weights: 24 (15 variable) initial value 13862.943611 iter 10 value 9889.147974 iter 20 value 9695.268994 final value 9695.223614 converged | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100%[ FAIL 0 | WARN 59 | SKIP 2 | PASS 170 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On CRAN (2): 'test-multiassoc.R:46:3', 'test-multiassoc.R:56:3' [ FAIL 0 | WARN 59 | SKIP 2 | PASS 170 ] > > proc.time() user system elapsed 28.95 2.50 31.50