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> # 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 ):  0.2811321  ( 0.0100008 )
   P-value:  2.077018e-167 


---
Association testing:
  PGS:  ldl_PGS
  Phenotype:  test2
  Covariate:  NA
  Phenotype type:  Continuous
    `test2` ~ `ldl_PGS`
   Using a  Linear regression
  Sample Size:  4000
   Beta ( SE ):  0.2828325  ( 0.01581671 )
   P-value:  7.353642e-69 


---
Association testing:
  PGS:  ldl_PGS
  Phenotype:  WRONG_PHENO
  Covariate:  NA

---
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 


---
Association testing:
  PGS:  brc_PGS
  Phenotype:  brc
  Covariate:  NA
  Phenotype type:  Cases/Controls
    `brc` ~ `brc_PGS`
   Using a  Binary logistic regression
  Cases:  402
  Controls:  5041
  Sample Size:  5443
   OR [ 95% CI ]:  1.540077  [ 1.390127 - 1.706201 ]
   P-value:  1.425869e-16 


---
Association testing:
  PGS:  brc_PGS
  Phenotype:  t2d
  Covariate:  NA
  Phenotype type:  Cases/Controls
    `t2d` ~ `brc_PGS`
   Using a  Binary logistic regression
  Cases:  730
  Controls:  9270
  Sample Size:  10000
   OR [ 95% CI ]:  1.065721  [ 0.988462 - 1.149018 ]
   P-value:  0.09736706 


---
Association testing:
  PGS:  brc_PGS
  Phenotype:  log_ldl
  Covariate:  NA
  Phenotype type:  Continuous
    `log_ldl` ~ `brc_PGS`
   Using a  Linear regression
  Sample Size:  10000
   Beta ( SE ):  0.001319107  ( 0.002329391 )
   P-value:  0.5712104 


---
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 


---
Association testing:
  PGS:  t2d_PGS
  Phenotype:  ethnicity
  Covariate:  NA
  Phenotype type:  Categorical
    `ethnicity` ~ `t2d_PGS`# weights:  12 (6 variable)
initial  value 13862.943611 
iter  10 value 9697.368074
final  value 9696.630119 
converged

   Using a  Multinomial logistic regression
  Sample Size:  8523 7586 6653
   OR [ 95% CI ]:  0.9816761 1.017569 0.944661  [ 0.9347786 0.9567993 0.8367048 - 1.030926 1.082199 1.066546 ]
   P-value:  0.4590068 0.5793326 0.3578543 


---
Association testing:
  PGS:  t2d_PGS
  Phenotype:  brc
  Covariate:  NA
  Phenotype type:  Cases/Controls
    `brc` ~ `t2d_PGS`
   Using a  Binary logistic regression
  Cases:  402
  Controls:  5041
  Sample Size:  5443
   OR [ 95% CI ]:  0.9968246  [ 0.9005324 - 1.103413 ]
   P-value:  0.9510713 


---
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 


---
Association testing:
  PGS:  t2d_PGS
  Phenotype:  log_ldl
  Covariate:  NA
  Phenotype type:  Continuous
    `log_ldl` ~ `t2d_PGS`
   Using a  Linear regression
  Sample Size:  10000
   Beta ( SE ):  0.004699851  ( 0.002328954 )
   P-value:  0.04361698 


---
Association testing:
  PGS:  t2d_PGS
  Phenotype:  sbp_cat
  Covariate:  NA
  Phenotype type:  Ordered Categorical
    `sbp_cat` ~ `t2d_PGS`
   Using a  Ordinal logistic regression
  Sample Size:  10000
   OR [ 95% CI ]:  1.043724  [ 1.005803 - 1.083074 ]
   P-value:  0.02342431 


---
Association testing:
  PGS:  ldl_PGS
  Phenotype:  ethnicity
  Covariate:  NA
  Phenotype type:  Categorical
    `ethnicity` ~ `ldl_PGS`# weights:  12 (6 variable)
initial  value 13862.943611 
iter  10 value 9699.063415
final  value 9697.386957 
converged

   Using a  Multinomial logistic regression
  Sample Size:  8523 7586 6653
   OR [ 95% CI ]:  0.9926441 1.008565 0.9760944  [ 0.9452463 0.9482935 0.8647736 - 1.042419 1.072667 1.101745 ]
   P-value:  0.7674098 0.7861848 0.6953251 


---
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 


---
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 


---
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 


---
Association testing:
  PGS:  ldl_PGS
  Phenotype:  sbp_cat
  Covariate:  NA
  Phenotype type:  Ordered Categorical
    `sbp_cat` ~ `ldl_PGS`
   Using a  Ordinal logistic regression
  Sample Size:  10000
   OR [ 95% CI ]:  1.009039  [ 0.9724275 - 1.047029 ]
   P-value:  0.6332175 


------
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%


------
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%


------
Multiple  phenotypes associations ( 5 ) testing:

  |                                                                            
  |                                                                      |   0%

---
Association testing:
  PGS:  brc_PGS
  Phenotype:  ethnicity
  Covariate:  age sex gen_array
  Phenotype type:  Categorical
    `ethnicity` ~ `brc_PGS` + `age` + `sex` + `gen_array`# weights:  24 (15 variable)
initial  value 13862.943611 
iter  10 value 9889.147974
iter  20 value 9695.268994
final  value 9695.223614 
converged

   Using a  Multinomial logistic regression
  Sample Size:  8523 7586 6653
   OR [ 95% CI ]:  1.007385 1.02833 0.9351081  [ 0.9592606 0.9669558 0.8280089 - 1.057924 1.0936 1.05606 ]
   P-value:  0.7682797 0.3735897 0.2796549 


  |                                                                            
  |==============                                                        |  20%


---
Association testing:
  PGS:  brc_PGS
  Phenotype:  brc
  Covariate:  age sex gen_array
  Phenotype type:  Cases/Controls
    `brc` ~ `brc_PGS` + `age` + `sex` + `gen_array`
   Using a  Binary logistic regression
  Cases:  402
  Controls:  5041
  Sample Size:  5443
   OR [ 95% CI ]:  1.547586  [ 1.395998 - 1.715634 ]
   P-value:  1.015466e-16 


  |                                                                            
  |============================                                          |  40%


---
Association testing:
  PGS:  brc_PGS
  Phenotype:  t2d
  Covariate:  age sex gen_array
  Phenotype type:  Cases/Controls
    `t2d` ~ `brc_PGS` + `age` + `sex` + `gen_array`
   Using a  Binary logistic regression
  Cases:  730
  Controls:  9270
  Sample Size:  10000
   OR [ 95% CI ]:  1.061921  [ 0.9840316 - 1.145976 ]
   P-value:  0.1221469 


  |                                                                            
  |==========================================                            |  60%


---
Association testing:
  PGS:  brc_PGS
  Phenotype:  log_ldl
  Covariate:  age sex gen_array
  Phenotype type:  Continuous
    `log_ldl` ~ `brc_PGS` + `age` + `sex` + `gen_array`
   Using a  Linear regression
  Sample Size:  10000
   Beta ( SE ):  0.0009742985  ( 0.002274659 )
   P-value:  0.6684221 


  |                                                                            
  |========================================================              |  80%


---
Association testing:
  PGS:  brc_PGS
  Phenotype:  sbp_cat
  Covariate:  age sex gen_array
  Phenotype type:  Ordered Categorical
    `sbp_cat` ~ `brc_PGS` + `age` + `sex` + `gen_array`
   Using a  Ordinal logistic regression
  Sample Size:  10000
   OR [ 95% CI ]:  0.9848488  [ 0.9485063 - 1.022584 ]
   P-value:  0.4261214 


  |                                                                            
  |======================================================================| 100%
[ FAIL 0 | WARN 17 | SKIP 3 | PASS 103 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-multiassoc.R:46:3', 'test-multiassoc.R:56:3',
  'test-multiassoc.R:64:3'

[ FAIL 0 | WARN 17 | SKIP 3 | PASS 103 ]
> 
> proc.time()
   user  system elapsed 
  12.34    0.82   13.17