Skip to contents

AET04 Table 1 (Default) Adverse Events by Highest NCI CTACAE AE Grade Table 1.

Source: R/aet04.R
aet04.Rd

The AET04 table provides an overview of adverse event with the highest NCI CTCAE grade per individual.

Usage 

aet04_main(
  adam_db,
  arm_var = "ACTARM",
  lbl_overall = NULL,
  grade_groups = NULL,
  ...
)

aet04_pre(adam_db, ...)

aet04_post(tlg, prune_0 = TRUE, ...)

aet04

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

grade_groups

(list) putting in correspondence toxicity grades and labels.

...

not used.

tlg

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

prune_0

(flag) remove 0 count rows

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).

Details

  • Numbers represent absolute numbers of patients and fraction of N, or absolute number of event when specified.

  • Remove zero-count rows unless overridden with prune_0 = FALSE.

  • Events with missing grading values are excluded.

  • Split columns by arm, typically ACTARM.

  • Does not include a total column by default.

  • Sort Body System or Organ Class and Dictionary-Derived Term by highest overall frequencies. Analysis Toxicity Grade is sorted by severity.

Functions

  • aet04_main(): Main TLG function

  • aet04_pre(): Preprocessing

  • aet04_post(): Postprocessing

Note

  • adam_db object must contain an adae table with the columns "AEBODSYS", "AEDECOD" and "ATOXGR".

Examples 

grade_groups <- list(
  "Grade 1-2" = c("1", "2"),
  "Grade 3-4" = c("3", "4"),
  "Grade 5" = c("5")
)
proc_data <- dunlin::log_filter(syn_data, AEBODSYS == "cl A.1", "adae")
run(aet04, proc_data, grade_groups = grade_groups)
#>   MedDRA System Organ Class                                                          
#>     MedDRA Preferred Term                     A: Drug X   B: Placebo   C: Combination
#>                               Grade            (N=15)       (N=15)         (N=15)    
#>   ———————————————————————————————————————————————————————————————————————————————————
#>   - Any adverse events -                                                             
#>                               - Any Grade -   7 (46.7%)   6 (40.0%)      10 (66.7%)  
#>                               Grade 1-2       7 (46.7%)   6 (40.0%)      10 (66.7%)  
#>                               1               2 (13.3%)       0          4 (26.7%)   
#>                               2               5 (33.3%)   6 (40.0%)      6 (40.0%)   
#>   cl A.1                                                                             
#>     - Overall -                                                                      
#>                               - Any Grade -   7 (46.7%)   6 (40.0%)      10 (66.7%)  
#>                               Grade 1-2       7 (46.7%)   6 (40.0%)      10 (66.7%)  
#>                               1               2 (13.3%)       0          4 (26.7%)   
#>                               2               5 (33.3%)   6 (40.0%)      6 (40.0%)   
#>     dcd A.1.1.1.2                                                                    
#>                               - Any Grade -   5 (33.3%)   6 (40.0%)      6 (40.0%)   
#>                               Grade 1-2       5 (33.3%)   6 (40.0%)      6 (40.0%)   
#>                               2               5 (33.3%)   6 (40.0%)      6 (40.0%)   
#>     dcd A.1.1.1.1                                                                    
#>                               - Any Grade -   3 (20.0%)    1 (6.7%)      6 (40.0%)   
#>                               Grade 1-2       3 (20.0%)    1 (6.7%)      6 (40.0%)   
#>                               1               3 (20.0%)    1 (6.7%)      6 (40.0%)