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LBT05 Table 1 (Default) Laboratory Abnormalities with Single and Replicated Marked.

Source: R/lbt05.R
lbt05.Rd

LBT05 Table 1 (Default) Laboratory Abnormalities with Single and Replicated Marked.

Usage 

lbt05_main(
  adam_db,
  arm_var = "ACTARM",
  lbl_overall = NULL,
  map = lab_paramcd_abn_dir(),
  ...
)

lbt05_pre(adam_db, ...)

lbt05_post(tlg, prune_0 = FALSE, keep = "Any Abnormality", ...)

lbt05

lab_paramcd_abn_dir()

Format

An object of class chevron_t of length 1.

Arguments

adam_db

(list of data.frames) object containing the ADaM datasets

arm_var

(string) variable used for column splitting

lbl_overall

(string) label used for overall column, if set to NULL the overall column is omitted

map

(data.frame) with two columns mapping of parameters code (PARAMCD) to directions of abnormality (ABN_DIR). If a parameter is not in the map or if map is NULL, both directions are analyzed.

...

not used.

tlg

(TableTree, Listing or ggplot) object typically produced by a main function.

prune_0

(flag) remove 0 count rows

keep

(character) the levels to keep in the table even if they are empty. If NULL, all levels are pruned.

Value

the main function returns an rtables object.

the preprocessing function returns a list of data.frame.

the postprocessing function returns an rtables object or an ElementaryTable (null report).

a data.frame with the direction of abnormality of each lab parameter code.

Details

  • Does not remove rows with zero counts by default.

  • Lab test results with missing AVAL values are excluded.

  • Split columns by arm, typically ACTARM.

Functions

  • lbt05_main(): Main TLG function

  • lbt05_pre(): Preprocessing

  • lbt05_post(): Postprocessing

  • lab_paramcd_abn_dir():

Note

  • adam_db object must contain an adlb table with columns "ONTRTFL", "PARCAT2", "PARAM", "ANRIND", "AVALCAT1", and column specified by arm_var.

Examples 

run(lbt05, syn_data)
#>   Laboratory Test                            A: Drug X   B: Placebo   C: Combination
#>       Direction of Abnormality                (N=15)       (N=15)         (N=15)    
#>   ——————————————————————————————————————————————————————————————————————————————————
#>   Alanine Aminotransferase Measurement (n)      15           14             14      
#>     Low                                                                             
#>       Single, not last                       1 (6.7%)        0          4 (28.6%)   
#>       Last or replicated                     5 (33.3%)   4 (28.6%)      4 (28.6%)   
#>       Any Abnormality                        6 (40.0%)   4 (28.6%)      8 (57.1%)   
#>     High                                                                            
#>       Single, not last                           0           0              0       
#>       Last or replicated                         0           0              0       
#>       Any Abnormality                            0           0              0       
#>   C-Reactive Protein Measurement (n)            15           15             15      
#>     Low                                                                             
#>       Single, not last                       4 (26.7%)       0          3 (20.0%)   
#>       Last or replicated                     3 (20.0%)   5 (33.3%)      6 (40.0%)   
#>       Any Abnormality                        7 (46.7%)   5 (33.3%)      9 (60.0%)   
#>     High                                                                            
#>       Single, not last                       1 (6.7%)    3 (20.0%)          0       
#>       Last or replicated                     4 (26.7%)   3 (20.0%)      6 (40.0%)   
#>       Any Abnormality                        5 (33.3%)   6 (40.0%)      6 (40.0%)   
#>   Immunoglobulin A Measurement (n)              13           14             14      
#>     Low                                                                             
#>       Single, not last                           0           0              0       
#>       Last or replicated                         0           0              0       
#>       Any Abnormality                            0           0              0       
#>     High                                                                            
#>       Single, not last                       6 (46.2%)    1 (7.1%)      2 (14.3%)   
#>       Last or replicated                     3 (23.1%)   4 (28.6%)      3 (21.4%)   
#>       Any Abnormality                        9 (69.2%)   5 (35.7%)      5 (35.7%)   

map <- data.frame(PARAMCD = c("ALT", "ALT", "CRP", "CRP", "IGA", "XXX"), ABN_DIR = c("Low", "High"))
run(lbt05, syn_data, map = map)
#>   Laboratory Test                            A: Drug X   B: Placebo   C: Combination
#>       Direction of Abnormality                (N=15)       (N=15)         (N=15)    
#>   ——————————————————————————————————————————————————————————————————————————————————
#>   Alanine Aminotransferase Measurement (n)      15           14             14      
#>     Low                                                                             
#>       Single, not last                       1 (6.7%)        0          4 (28.6%)   
#>       Last or replicated                     5 (33.3%)   4 (28.6%)      4 (28.6%)   
#>       Any Abnormality                        6 (40.0%)   4 (28.6%)      8 (57.1%)   
#>     High                                                                            
#>       Single, not last                           0           0              0       
#>       Last or replicated                         0           0              0       
#>       Any Abnormality                            0           0              0       
#>   C-Reactive Protein Measurement (n)            15           15             15      
#>     Low                                                                             
#>       Single, not last                       4 (26.7%)       0          3 (20.0%)   
#>       Last or replicated                     3 (20.0%)   5 (33.3%)      6 (40.0%)   
#>       Any Abnormality                        7 (46.7%)   5 (33.3%)      9 (60.0%)   
#>     High                                                                            
#>       Single, not last                       1 (6.7%)    3 (20.0%)          0       
#>       Last or replicated                     4 (26.7%)   3 (20.0%)      6 (40.0%)   
#>       Any Abnormality                        5 (33.3%)   6 (40.0%)      6 (40.0%)   
#>   Immunoglobulin A Measurement (n)              13           14             14      
#>     Low                                                                             
#>       Single, not last                           0           0              0       
#>       Last or replicated                         0           0              0       
#>       Any Abnormality                            0           0              0       
# example code
head(lab_paramcd_abn_dir())
#>    PARAMCD ABN_DIR
#> 1 HCRIT1SI     Low
#> 2 HCRIT2SI    High
#> 3   HGB1SI     Low
#> 4   HGB2SI    High
#> 5   WBC1SI     Low
#> 6   WBC2SI    High