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EXT01 Exposure Summary Table.

Source: R/ext01.R
ext01.Rd

The EXT01 table provides an overview of the of the exposure of the patients in terms of Total dose administered or missed, and treatment duration.

Usage 

ext01_main(
  adam_db,
  arm_var = "ACTARM",
  lbl_overall = NULL,
  summaryvars = "AVAL",
  row_split_var = "PARCAT2",
  page_var = NULL,
  map = NULL,
  stats = list(default = c("n", "mean_sd", "median", "range", "count_fraction")),
  precision = list(default = 0),
  ...
)

ext01_pre(adam_db, ...)

ext01_post(tlg, prune_0 = TRUE, ...)

ext01

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

summaryvars

(character) variables to be analyzed. The label attribute of the corresponding column in adex table of adam_db is used as label.

row_split_var

(character) additional row split variables.

page_var

(string) variable name prior to which the row split is by page.

map

(data.frame) of mapping for split rows.

stats

(named list of character) where names are values found in the PARAMCD column and the values indicate the statistical analysis to perform. If default is set, and parameter precision not specified, the value for default will be used.

precision

(named list of integer) where names are values found in the PARAMCD column and the values

...

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

  • Default Exposure table

  • The n row provides the number of non-missing values. The percentages for categorical variables is based on n. The percentages for Total number of patients with at least one dose modification are based on the number of patients in the corresponding analysis population given by N.

  • Split columns by arm, typically ACTARM.

  • Does not include a total column by default.

  • Sorted by alphabetic order of the PARAM value. Transform to factor and re-level for custom order.

  • ANL01FL is not relevant subset.

Functions

  • ext01_main(): Main TLG function

  • ext01_pre(): Preprocessing

  • ext01_post(): Postprocessing

Note

  • adam_db object must contain an adex table with columns specified in summaryvars.

Examples 

run(ext01, syn_data)
#>                                  A: Drug X        B: Placebo      C: Combination 
#>   PARCAT2                         (N=15)            (N=15)            (N=15)     
#>   ———————————————————————————————————————————————————————————————————————————————
#>   Drug A                                                                         
#>     Overall duration (days)                                                      
#>       n                             11                 7                 7       
#>       Mean (SD)                157.5 (67.4)      115.4 (62.8)       98.6 (68.8)  
#>       Median                       174.0             119.0             89.0      
#>       Min - Max                  53 - 239          22 - 219           1 - 182    
#>     Total dose administered                                                      
#>       n                             11                 7                 7       
#>       Mean (SD)               6567.3 (1127.1)   7028.6 (1626.1)   6377.1 (863.7) 
#>       Median                      6720.0            7200.0            6480.0     
#>       Min - Max                 4800 - 8400       5280 - 9360       5280 - 7440  
#>   Drug B                                                                         
#>     Overall duration (days)                                                      
#>       n                              4                 8                 8       
#>       Mean (SD)                142.2 (100.3)     105.9 (60.0)      158.2 (96.2)  
#>       Median                       160.0             95.0              203.0     
#>       Min - Max                  17 - 232          37 - 211          27 - 249    
#>     Total dose administered                                                      
#>       n                              4                 8                 8       
#>       Mean (SD)               7020.0 (1148.9)   5250.0 (864.7)    5940.0 (1187.9)
#>       Median                      6960.0            5160.0            5880.0     
#>       Min - Max                 5760 - 8400       4080 - 6480       4320 - 7680  

run(ext01, syn_data, summaryvars = c("AVAL", "AVALCAT1"), prune_0 = FALSE)
#>                                  A: Drug X        B: Placebo      C: Combination 
#>   PARCAT2                         (N=15)            (N=15)            (N=15)     
#>   ———————————————————————————————————————————————————————————————————————————————
#>   Drug A                                                                         
#>     Overall duration (days)                                                      
#>       n                             11                 7                 7       
#>       Mean (SD)                157.5 (67.4)      115.4 (62.8)       98.6 (68.8)  
#>       Median                       174.0             119.0             89.0      
#>       Min - Max                  53 - 239          22 - 219           1 - 182    
#>       n                             11                 7                 7       
#>       < 1 month                      0             1 (14.3%)         1 (14.3%)   
#>       1 to <3 months             3 (27.3%)         1 (14.3%)         3 (42.9%)   
#>       3 to <6 months             3 (27.3%)         4 (57.1%)         2 (28.6%)   
#>       >=6 months                 5 (45.5%)         1 (14.3%)         1 (14.3%)   
#>       <700                           0                 0                 0       
#>       700-900                        0                 0                 0       
#>       900-1200                       0                 0                 0       
#>       >1200                          0                 0                 0       
#>       <5000                          0                 0                 0       
#>       5000-7000                      0                 0                 0       
#>       7000-9000                      0                 0                 0       
#>       >9000                          0                 0                 0       
#>       7                              0                 0                 0       
#>     Total dose administered                                                      
#>       n                             11                 7                 7       
#>       Mean (SD)               6567.3 (1127.1)   7028.6 (1626.1)   6377.1 (863.7) 
#>       Median                      6720.0            7200.0            6480.0     
#>       Min - Max                 4800 - 8400       5280 - 9360       5280 - 7440  
#>       n                             11                 7                 7       
#>       < 1 month                      0                 0                 0       
#>       1 to <3 months                 0                 0                 0       
#>       3 to <6 months                 0                 0                 0       
#>       >=6 months                     0                 0                 0       
#>       <700                           0                 0                 0       
#>       700-900                        0                 0                 0       
#>       900-1200                       0                 0                 0       
#>       >1200                          0                 0                 0       
#>       <5000                      1 (9.1%)              0                 0       
#>       5000-7000                  6 (54.5%)         3 (42.9%)         5 (71.4%)   
#>       7000-9000                  4 (36.4%)         3 (42.9%)         2 (28.6%)   
#>       >9000                          0             1 (14.3%)             0       
#>       7                              0                 0                 0       
#>   Drug B                                                                         
#>     Overall duration (days)                                                      
#>       n                              4                 8                 8       
#>       Mean (SD)                142.2 (100.3)     105.9 (60.0)      158.2 (96.2)  
#>       Median                       160.0             95.0              203.0     
#>       Min - Max                  17 - 232          37 - 211          27 - 249    
#>       n                              4                 8                 8       
#>       < 1 month                  1 (25.0%)             0             1 (12.5%)   
#>       1 to <3 months                 0             4 (50.0%)         2 (25.0%)   
#>       3 to <6 months             1 (25.0%)         3 (37.5%)             0       
#>       >=6 months                 2 (50.0%)         1 (12.5%)         5 (62.5%)   
#>       <700                           0                 0                 0       
#>       700-900                        0                 0                 0       
#>       900-1200                       0                 0                 0       
#>       >1200                          0                 0                 0       
#>       <5000                          0                 0                 0       
#>       5000-7000                      0                 0                 0       
#>       7000-9000                      0                 0                 0       
#>       >9000                          0                 0                 0       
#>       7                              0                 0                 0       
#>     Total dose administered                                                      
#>       n                              4                 8                 8       
#>       Mean (SD)               7020.0 (1148.9)   5250.0 (864.7)    5940.0 (1187.9)
#>       Median                      6960.0            5160.0            5880.0     
#>       Min - Max                 5760 - 8400       4080 - 6480       4320 - 7680  
#>       n                              4                 8                 8       
#>       < 1 month                      0                 0                 0       
#>       1 to <3 months                 0                 0                 0       
#>       3 to <6 months                 0                 0                 0       
#>       >=6 months                     0                 0                 0       
#>       <700                           0                 0                 0       
#>       700-900                        0                 0                 0       
#>       900-1200                       0                 0                 0       
#>       >1200                          0                 0                 0       
#>       <5000                          0             4 (50.0%)         2 (25.0%)   
#>       5000-7000                  2 (50.0%)         4 (50.0%)         4 (50.0%)   
#>       7000-9000                  2 (50.0%)             0             2 (25.0%)   
#>       >9000                          0                 0                 0       
#>       7                              0                 0                 0       

levels(syn_data$adex$AVALCAT1) <- c(levels(syn_data$adex$AVALCAT1), "12 months")
map <- data.frame(
  PARAMCD = "TDURD",
  AVALCAT1 = c("< 1 month", "1 to <3 months", ">=6 months", "3 to <6 months", "12 months")
)
run(
  ext01,
  syn_data,
  summaryvars = c("AVAL", "AVALCAT1"),
  prune_0 = FALSE,
  map = map,
  precision = list(TDOSE = 4, default = 4),
  stats = list(TDURD = "n", default = c("n", "count_fraction"))
)
#>                               A: Drug X   B: Placebo   C: Combination
#>   PARCAT2                      (N=15)       (N=15)         (N=15)    
#>   ———————————————————————————————————————————————————————————————————
#>   Drug A                                                             
#>     Overall duration (days)                                          
#>       n                          11           7              7       
#>       n                          11           7              7       
#>     Total dose administered                                          
#>       n                          11           7              7       
#>       n                          11           7              7       
#>       <5000                   1 (9.1%)        0              0       
#>       5000-7000               6 (54.5%)   3 (42.9%)      5 (71.4%)   
#>       7000-9000               4 (36.4%)   3 (42.9%)      2 (28.6%)   
#>       >9000                       0       1 (14.3%)          0       
#>   Drug B                                                             
#>     Overall duration (days)                                          
#>       n                           4           8              8       
#>       n                           4           8              8       
#>     Total dose administered                                          
#>       n                           4           8              8       
#>       n                           4           8              8       
#>       <5000                       0       4 (50.0%)      2 (25.0%)   
#>       5000-7000               2 (50.0%)   4 (50.0%)      4 (50.0%)   
#>       7000-9000               2 (50.0%)       0          2 (25.0%)   
#>       >9000                       0           0              0