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pdt01 Major Protocol Deviations Table.

pdt01.Rd

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_main(
  adam_db,
  arm_var = "ARM",
  dvcode_var = "DVDECOD",
  dvterm_var = "DVTERM",
  lbl_overall = NULL,
  ...
)

pdt01_pre(adam_db, ...)

pdt01_post(
  tlg,
  prune_0 = TRUE,
  dvcode_var = "DVDECOD",
  dvterm_var = "DVTERM",
  ...
)

pdt01

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

dvcode_var

(string) the variable defining the protocol deviation coded term. By default DVDECOD.

dvterm_var

(string) the variable defining the protocol deviation term. By default DVTERM.

lbl_overall

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

...

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_main(): Main TLG function

  • pdt01_pre(): Preprocessing

  • pdt01_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(dplyr)

proc_data <- syn_data
proc_data$addv <- proc_data$addv %>%
  filter(DVCAT == "MAJOR")

run(pdt01, proc_data)
#>   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%)