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CMT01A Concomitant Medication by Medication Class and Preferred Name.

Source: R/cmt01a.R
cmt01a.Rd

A concomitant medication table with the number of subjects and the total number of treatments by medication class.

Usage 

cmt01_label

cmt01a_main(
  adam_db,
  arm_var = "ARM",
  lbl_overall = NULL,
  row_split_var = "ATC2",
  medname_var = "CMDECOD",
  summary_labels = setNames(rep(list(cmt01_label), length(row_split_var) + 1L),
    c("TOTAL", row_split_var)),
  ...
)

cmt01a_pre(adam_db, ...)

cmt01a_post(
  tlg,
  prune_0 = TRUE,
  sort_by_freq = FALSE,
  row_split_var = "ATC2",
  medname_var = "CMDECOD",
  ...
)

cmt01a

Format

An object of class character of length 2.

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

row_split_var

(character) the variable defining the medication category. By default ATC2.

medname_var

(string) variable name of medical treatment name.

summary_labels

(list) of summarize labels. See details.

...

not used.

tlg

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

prune_0

(flag) remove 0 count rows

sort_by_freq

(flag) whether to sort medication class by frequency.

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

  • Data should be filtered for concomitant medication. (ATIREL == "CONCOMITANT").

  • Numbers represent absolute numbers of subjects and fraction of N, or absolute numbers when specified.

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

  • Split columns by arm.

  • Does not include a total column by default.

  • Sort by medication class alphabetically and within medication class by decreasing total number of patients with the specific medication. summary_labels is used to control the summary for each level. If "all" is used, then each split will have that summary statistic with the labels. One special case is "TOTAL", this is for the overall population.

Functions

  • cmt01_label: Default labels

  • cmt01a_main(): Main TLG function

  • cmt01a_pre(): Preprocessing

  • cmt01a_post(): Postprocessing

Note

  • adam_db object must contain an adcm table with the columns specified in row_split_var and medname_var as well as "CMSEQ".

Examples 

library(dplyr)

proc_data <- syn_data
proc_data$adcm <- proc_data$adcm %>%
  filter(ATIREL == "CONCOMITANT")

run(cmt01a, proc_data)
#>   ATC Level 2 Text                                         A: Drug X    B: Placebo   C: Combination
#>     Other Treatment                                          (N=15)       (N=15)         (N=15)    
#>   —————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one treatment     13 (86.7%)   14 (93.3%)     14 (93.3%)  
#>   Total number of treatments                                   40           40             61      
#>   ATCCLAS2 A                                                                                       
#>     Total number of patients with at least one treatment   7 (46.7%)    10 (66.7%)     10 (66.7%)  
#>     Total number of treatments                                 11           17             19      
#>     medname A_3/3                                          5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>     medname A_2/3                                          5 (33.3%)    6 (40.0%)      7 (46.7%)   
#>   ATCCLAS2 A p2                                                                                    
#>     Total number of patients with at least one treatment   5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>     Total number of treatments                                 6            8              8       
#>     medname A_3/3                                          5 (33.3%)    8 (53.3%)      6 (40.0%)   
#>   ATCCLAS2 B                                                                                       
#>     Total number of patients with at least one treatment   10 (66.7%)   8 (53.3%)      10 (66.7%)  
#>     Total number of treatments                                 16           15             23      
#>     medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>     medname B_4/4                                          4 (26.7%)    5 (33.3%)      8 (53.3%)   
#>   ATCCLAS2 B p2                                                                                    
#>     Total number of patients with at least one treatment   7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>     Total number of treatments                                 12           8              10      
#>     medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>   ATCCLAS2 B p3                                                                                    
#>     Total number of patients with at least one treatment   7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>     Total number of treatments                                 12           8              10      
#>     medname B_1/4                                          7 (46.7%)    6 (40.0%)      6 (40.0%)   
#>   ATCCLAS2 C                                                                                       
#>     Total number of patients with at least one treatment   9 (60.0%)    7 (46.7%)      12 (80.0%)  
#>     Total number of treatments                                 13           8              19      
#>     medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>     medname C_1/2                                          6 (40.0%)    2 (13.3%)      6 (40.0%)   
#>   ATCCLAS2 C p2                                                                                    
#>     Total number of patients with at least one treatment   9 (60.0%)    7 (46.7%)      12 (80.0%)  
#>     Total number of treatments                                 13           8              19      
#>     medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>     medname C_1/2                                          6 (40.0%)    2 (13.3%)      6 (40.0%)   
#>   ATCCLAS2 C p3                                                                                    
#>     Total number of patients with at least one treatment   4 (26.7%)    5 (33.3%)      7 (46.7%)   
#>     Total number of treatments                                 5            5              12      
#>     medname C_2/2                                          4 (26.7%)    5 (33.3%)      7 (46.7%)