pdt01_1 Table 1 (Default) Major Protocol Deviations.

A major protocol deviations table with the number of subjects and the total number of treatments by medication class sorted alphabetically and medication name sorted by frequencies.

Usage

pdt01_1_main(
  adam_db,
  arm_var = "ARM",
  dvcode_var = "DVDECOD",
  lbl_dvcode_var = "Protocol Deviation Coded Term",
  dvterm_var = "DVTERM",
  lbl_dvterm_var = "Category",
  lbl_overall = NULL,
  deco = std_deco("pdt01_1"),
  ...
)

pdt01_1_lyt(
  arm_var,
  lbl_overall,
  dvcode_var,
  lbl_dvcode_var,
  dvterm_var,
  lbl_dvterm_var,
  deco
)

pdt01_1_pre(adam_db, dvcode_var = "DVDECOD", dvterm_var = "DVTERM", ...)

pdt01_1_post(
  tlg,
  prune_0 = TRUE,
  dvcode_var = "DVDECOD",
  dvterm_var = "DVTERM",
  ...
)

pdt01_1

Format

An object of class chevron_t of length 1.

Arguments

adam_db: (dm) object containing the ADaM datasets
arm_var: (string) variable used for column splitting
dvcode_var: (string) the variable defining the protocol deviation coded term. By default DVDECOD.
lbl_dvcode_var: (string) label for the variable defining the protocol deviation coded term.
dvterm_var: (string) the variable defining the protocol deviation term. By default DVTERM.
lbl_dvterm_var: (string) label for the variable defining the protocol deviation term.
lbl_overall: (string) label used for overall column, if set to NULL the overall column is omitted
deco: (character) decoration with title, subtitles and main_footer content
...: not used.
tlg: (TableTree, Listing or ggplot) object typically produced by a main function.
prune_0: (flag) remove 0 count rows

Details

Data should be filtered for major protocol deviations. (DVCAT == "MAJOR").
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.

Functions

pdt01_1_main(): Main TLG function
pdt01_1_lyt(): Layout
pdt01_1_pre(): Preprocessing
pdt01_1_post(): Postprocessing

Note

adam_db object must contain an addv table with the columns specified in dvcode_var and dvterm_var as well as "DVSEQ".

Examples

library(magrittr)
library(dm)

db <- syn_data %>%
  dm_zoom_to("addv") %>%
  filter(.data$DVCAT == "MAJOR") %>%
  dm_update_zoomed()

run(pdt01_1, db)
#>   Category                                                              A: Drug X    B: Placebo   C: Combination
#>     Description                                                          (N=134)      (N=134)        (N=132)    
#>   ——————————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Total number of patients with at least one major protocol deviation   22 (16.4%)   23 (17.2%)     13 (9.8%)   
#>   Total number of major protocol deviations                                 40           42             21      
#>   EXCLUSION CRITERIA                                                                                            
#>     Active or untreated or other excluded cns metastases                 5 (3.7%)     3 (2.2%)          0       
#>     Pregnancy criteria                                                   2 (1.5%)     4 (3.0%)          0       
#>     History of other malignancies within the last 5 years                3 (2.2%)     2 (1.5%)          0       
#>     Uncontrolled concurrent condition                                    3 (2.2%)     1 (0.7%)          0       
#>     Other exclusion criteria                                                0            0           3 (2.3%)   
#>     Received prior prohibited therapy or medication                         0         2 (1.5%)       1 (0.8%)   
#>   INCLUSION CRITERIA                                                                                            
#>     No signed ICF at study entry                                         6 (4.5%)     4 (3.0%)          0       
#>     Ineligible cancer type or current cancer stage                       6 (4.5%)     1 (0.7%)       1 (0.8%)   
#>     Inclusion lab values outside allowed limits                             0         3 (2.2%)          0       
#>     Does not meet prior therapy requirements                             1 (0.7%)        0              0       
#>     Inclusion-related test not done/out of window                           0            0           1 (0.8%)   
#>   MEDICATION                                                                                                    
#>     Significant deviation from planned dose                              3 (2.2%)     1 (0.7%)       2 (1.5%)   
#>     Received incorrect study medication                                  1 (0.7%)     2 (1.5%)       1 (0.8%)   
#>     Discontinued study drug for unspecified reason                       1 (0.7%)     1 (0.7%)       1 (0.8%)   
#>     Dose missed or significantly out of window                           2 (1.5%)        0           1 (0.8%)   
#>     Received prohibited concomitant medication                              0         2 (1.5%)          0       
#>   PROCEDURAL                                                                                                    
#>     Eligibility-related test not done/out of window                      1 (0.7%)     6 (4.5%)       1 (0.8%)   
#>     Omission of screening tumor assessment                                  0         4 (3.0%)       3 (2.3%)   
#>     Missed assessment affecting safety/study outcomes                    1 (0.7%)     2 (1.5%)       2 (1.5%)   
#>     Failure to sign updated ICF within two visits                        2 (1.5%)     1 (0.7%)       1 (0.8%)   
#>     Missed 2 or more efficacy assessments                                2 (1.5%)        0           1 (0.8%)   
#>     Omission of complete lab panel required by protocol                     0         1 (0.7%)       1 (0.8%)