R Under development (unstable) (2026-09-30 r90605 ucrt) -- "Unsuffered Consequences"
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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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(BaHZING)
Loading required package: rjags
Loading required package: coda
Linked to JAGS 4.3.1
Loaded modules: basemod,bugs
> 
> test_check("BaHZING")
#### Checking input data ####
Exposure and Covariate Data:
- Total sample size: 105
- Number of exposures: 2
Microbiome Data:
- Number of unique genus in data: 83
- Number of unique family in data: 13
- Number of unique order in data: 6
- Number of unique class in data: 5
- Number of unique phylum in data: 5
#### Running BaHZING with the following parameters #### 
Exposure standardization: None
Library size offset: Included
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 23310
   Unobserved stochastic nodes: 26424
   Total graph size: 337232

Initializing model

Note: q is not required when exposure_standardization is standard_normal. q will be ignored.
#### Checking input data ####
Exposure and Covariate Data:
- Total sample size: 105
- Number of exposures: 2
Microbiome Data:
- Number of unique genus in data: 83
- Number of unique family in data: 13
- Number of unique order in data: 6
- Number of unique class in data: 5
- Number of unique phylum in data: 5
#### Running BaHZING with the following parameters #### 
Exposure standardization: Standard Normal
Library size offset: Included
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 23310
   Unobserved stochastic nodes: 25980
   Total graph size: 315814

Initializing model

Note: q is not required when exposure_standardization is standard_normal. q will be ignored.
#### Checking input data ####
Exposure and Covariate Data:
- Total sample size: 105
- Number of exposures: 2
Microbiome Data:
- Number of unique genus in data: 83
- Number of unique family in data: 13
- Number of unique order in data: 6
- Number of unique class in data: 5
- Number of unique phylum in data: 5
#### Running BaHZING with the following parameters #### 
Exposure standardization: Standard Normal
Library size offset: Not included
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 23310
   Unobserved stochastic nodes: 25980
   Total graph size: 239236

Initializing model

#### Checking input data ####
Exposure and Covariate Data:
- Total sample size: 105
- Number of exposures: 2
Microbiome Data:
- Number of unique genus in data: 83
- Number of unique family in data: 13
- Number of unique order in data: 6
- Number of unique class in data: 5
- Number of unique phylum in data: 5
#### Running BaHZING with the following parameters #### 
Exposure standardization: Quantiles, with q = 2
Library size offset: Included
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 23310
   Unobserved stochastic nodes: 25980
   Total graph size: 310042

Initializing model

Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 23310
   Unobserved stochastic nodes: 25914
   Total graph size: 315483

Initializing model

Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 23310
   Unobserved stochastic nodes: 25980
   Total graph size: 315814

Initializing model

#### Checking input data ####
Exposure and Covariate Data:
- Total sample size: 105
- Number of exposures: 2
Microbiome Data:
- Number of unique species in data: 222
- Number of unique genus in data: 83
- Number of unique family in data: 13
- Number of unique order in data: 6
- Number of unique class in data: 5
- Number of unique phylum in data: 5
#### Running BaHZING with the following parameters #### 
Exposure standardization: None
Library size offset: Included
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x             222
           > rows only in p_value_df (    0)
           > matched rows             1,110
           >                         =======
           > rows total               1,332
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            83
           > rows only in p_value_df (  0)
           > matched rows             415
           >                         =====
           > rows total               498
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x           13
           > rows only in p_value_df ( 0)
           > matched rows             65
           >                         ====
           > rows total               78
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            6
           > rows only in p_value_df ( 0)
           > matched rows             30
           >                         ====
           > rows total               36
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            5
           > rows only in p_value_df ( 0)
           > matched rows             25
           >                         ====
           > rows total               30
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            5
           > rows only in p_value_df ( 0)
           > matched rows             25
           >                         ====
           > rows total               30
Note: q is not required when exposure_standardization is standard_normal. q will be ignored.
#### Checking input data ####
Exposure and Covariate Data:
- Total sample size: 105
- Number of exposures: 2
Microbiome Data:
- Number of unique species in data: 222
- Number of unique genus in data: 83
- Number of unique family in data: 13
- Number of unique order in data: 6
- Number of unique class in data: 5
- Number of unique phylum in data: 5
#### Running BaHZING with the following parameters #### 
Exposure standardization: Standard Normal
Library size offset: Included
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x             222
           > rows only in p_value_df (    0)
           > matched rows             1,110
           >                         =======
           > rows total               1,332
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            83
           > rows only in p_value_df (  0)
           > matched rows             415
           >                         =====
           > rows total               498
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x           13
           > rows only in p_value_df ( 0)
           > matched rows             65
           >                         ====
           > rows total               78
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            6
           > rows only in p_value_df ( 0)
           > matched rows             30
           >                         ====
           > rows total               36
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            5
           > rows only in p_value_df ( 0)
           > matched rows             25
           >                         ====
           > rows total               30
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            5
           > rows only in p_value_df ( 0)
           > matched rows             25
           >                         ====
           > rows total               30
Note: q is not required when exposure_standardization is standard_normal. q will be ignored.
#### Checking input data ####
Exposure and Covariate Data:
- Total sample size: 105
- Number of exposures: 2
Microbiome Data:
- Number of unique species in data: 222
- Number of unique genus in data: 83
- Number of unique family in data: 13
- Number of unique order in data: 6
- Number of unique class in data: 5
- Number of unique phylum in data: 5
#### Running BaHZING with the following parameters #### 
Exposure standardization: Standard Normal
Library size offset: Not included
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x             222
           > rows only in p_value_df (    0)
           > matched rows             1,110
           >                         =======
           > rows total               1,332
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            83
           > rows only in p_value_df (  0)
           > matched rows             415
           >                         =====
           > rows total               498
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x           13
           > rows only in p_value_df ( 0)
           > matched rows             65
           >                         ====
           > rows total               78
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            6
           > rows only in p_value_df ( 0)
           > matched rows             30
           >                         ====
           > rows total               36
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            5
           > rows only in p_value_df ( 0)
           > matched rows             25
           >                         ====
           > rows total               30
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            5
           > rows only in p_value_df ( 0)
           > matched rows             25
           >                         ====
           > rows total               30
#### Checking input data ####
Exposure and Covariate Data:
- Total sample size: 105
- Number of exposures: 2
Microbiome Data:
- Number of unique species in data: 222
- Number of unique genus in data: 83
- Number of unique family in data: 13
- Number of unique order in data: 6
- Number of unique class in data: 5
- Number of unique phylum in data: 5
#### Running BaHZING with the following parameters #### 
Exposure standardization: Quantiles, with q = 2
Library size offset: Included
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x             222
           > rows only in p_value_df (    0)
           > matched rows             1,110
           >                         =======
           > rows total               1,332
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            83
           > rows only in p_value_df (  0)
           > matched rows             415
           >                         =====
           > rows total               498
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x           13
           > rows only in p_value_df ( 0)
           > matched rows             65
           >                         ====
           > rows total               78
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            6
           > rows only in p_value_df ( 0)
           > matched rows             30
           >                         ====
           > rows total               36
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            5
           > rows only in p_value_df ( 0)
           > matched rows             25
           >                         ====
           > rows total               30
left_join: added 3 columns (pdir, prope, pmap)
           > rows only in x            5
           > rows only in p_value_df ( 0)
           > matched rows             25
           >                         ====
           > rows total               30
#### Checking input data ####
Exposure and Covariate Data:
- Total sample size: 105
- Number of exposures: 2
- Number of covariates 1
Microbiome Data:
- Number of unique species in data: 222
- Number of unique genus in data: 83
- Number of unique family in data: 13
- Number of unique order in data: 6
- Number of unique class in data: 5
- Number of unique phylum in data: 5
#### Running qgcomp with the following parameters #### 
Quantiles, with q = 4
#### Checking input data ####
Exposure and Covariate Data:
- Total sample size: 105
- Number of exposures: 2
- Number of covariates 0
Microbiome Data:
- Number of unique species in data: 222
- Number of unique genus in data: 83
- Number of unique family in data: 13
- Number of unique order in data: 6
- Number of unique class in data: 5
- Number of unique phylum in data: 5
#### Running qgcomp with the following parameters #### 
Quantiles, with q = 4
#### Checking input data ####
Exposure and Covariate Data:
- Total sample size: 105
- Number of exposures: 2
- Number of covariates 1
Microbiome Data:
- Number of unique species in data: 222
- Number of unique genus in data: 83
- Number of unique family in data: 13
- Number of unique order in data: 6
- Number of unique class in data: 5
- Number of unique phylum in data: 5
#### Running qgcomp with the following parameters #### 
No quantile transformation applied.
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-BaHZING_Model_parallel.R:2:3'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]
> 
> proc.time()
   user  system elapsed 
 865.60   12.67  879.26