TTET01 Binary Outcomes Summary — ttet01

TTET01 template may be used to summarize any binary outcome or response variable at a single time point. Typical application for oncology

Usage

ttet01_main(
  adam_db,
  dataset = "adtte",
  arm_var = "ARM",
  ref_group = NULL,
  summarize_event = TRUE,
  perform_analysis = "unstrat",
  strata = NULL,
  pval_method = "log-rank",
  conf_level = 0.95,
  conf_type = "log-log",
  quantiles = c(0.25, 0.75),
  ties = "efron",
  timepoint = c(6, 12),
  method = "both",
  ...
)

ttet01_pre(adam_db, dataset = "adtte", ...)

ttet01_post(tlg, prune_0 = TRUE, ...)

ttet01

Format

An object of class chevron_t of length 1.

Arguments

adam_db: (list of data.frames) object containing the ADaM datasets
dataset: (string) the name of a table in the adam_db object.
arm_var: (string) variable used for column splitting
ref_group: (string) The name of the reference group, the value should be identical to the values in arm_var, if not specified, it will by default use the first level or value of arm_var.
summarize_event: (flag) should the event description be displayed, default is TRUE
perform_analysis: (string) option to display statistical comparisons using stratified analyses, or unstratified analyses, or both, e.g. c("unstrat", "strat"). Only unstratified will be displayed by default
strata: (string) stratification factors, e.g. strata = c("STRATA1", "STRATA2"), by default as NULL
pval_method: (string) p-value method for testing hazard ratio = 1. Default method is "log-rank", can also be set to "wald" or "likelihood".
conf_level: (numeric) the level of confidence interval, default is 0.95.
conf_type: (string) confidence interval type. Options are "plain" (default), "log", "log-log", see more in survival::survfit(). Note option "none" is no longer supported.
quantiles: (numeric) of length two to specify the quantiles of survival time.
ties: (string) specifying the method for tie handling. Default is "efron", can also be set to "breslow" or "exact". see more in survival::coxph()
timepoint: (numeric) survival time point of interest.
method: (string) either "surv" (survival estimations), "surv_diff" (difference in survival with the control) or "both".
...: not used.
tlg: (TableTree, Listing or ggplot) object typically produced by a main function.
prune_0: (flag) remove 0 count rows

Details

No overall value.

Functions

ttet01_main(): Main TLG function
ttet01_pre(): Preprocessing
ttet01_post(): Postprocessing

Examples

library(dplyr)
library(dunlin)

syn_data2 <- log_filter(syn_data, PARAMCD == "PFS", "adtte")
run(ttet01, syn_data2)
#>                                       A: Drug X        B: Placebo      C: Combination
#>                                        (N=134)           (N=134)          (N=132)    
#>   ———————————————————————————————————————————————————————————————————————————————————
#>   Patients with event (%)             86 (64.2%)       90 (67.2%)        92 (69.7%)  
#>     Earliest contributing event                                                      
#>       Death                           38 (44.2%)       48 (53.3%)        41 (44.6%)  
#>       Disease Progression             48 (55.8%)       42 (46.7%)        51 (55.4%)  
#>   Patients without event (%)          48 (35.8%)       44 (32.8%)        40 (30.3%)  
#>   Time to Event (MONTHS)                                                             
#>     Median                               16.9             19.7              12.3     
#>       95% CI                         (12.8, 19.0)     (13.2, 25.2)      (8.4, 14.9)  
#>     25% and 75%-ile                   7.7, 30.0         7.2, 34.1        4.5, 25.3   
#>     Range (censored)                 0.3 to 65.9       0.4 to 83.0      1.0 to 81.8  
#>     Range (event)                    0.5 to 85.8       0.1 to 58.7      0.2 to 77.8  
#>   Unstratified Analysis                                                              
#>     p-value (log-rank)                                   0.4808            0.0429    
#>     Hazard Ratio                                          0.90              1.36     
#>     95% CI                                            (0.67, 1.21)      (1.01, 1.82) 
#>   6 MONTHS                                                                           
#>     Patients remaining at risk            87               92                77      
#>     Event Free Rate (%)                 77.27             77.85            67.70     
#>     95% CI                          (68.76, 83.74)   (69.53, 84.15)    (58.64, 75.20)
#>     Difference in Event Free Rate                         0.57             -9.57     
#>       95% CI                                         (-9.82, 10.97)    (-20.70, 1.57)
#>       p-value (Z-test)                                   0.9137            0.0921    
#>   12 MONTHS                                                                          
#>     Patients remaining at risk            65               68                51      
#>     Event Free Rate (%)                 62.83             62.69            50.16     
#>     95% CI                          (53.36, 70.91)   (53.31, 70.71)    (40.69, 58.89)
#>     Difference in Event Free Rate                         -0.14            -12.68    
#>       95% CI                                         (-12.53, 12.25)   (-25.38, 0.03)
#>       p-value (Z-test)                                   0.9822            0.0505    
run(ttet01, syn_data2,
  summarize_event = FALSE, perform_analysis = c("unstrat", "strat"),
  strata = c("STRATA1", "STRATA2")
)
#>                                       A: Drug X        B: Placebo      C: Combination
#>                                        (N=134)           (N=134)          (N=132)    
#>   ———————————————————————————————————————————————————————————————————————————————————
#>   Patients with event (%)             86 (64.2%)       90 (67.2%)        92 (69.7%)  
#>   Patients without event (%)          48 (35.8%)       44 (32.8%)        40 (30.3%)  
#>   Time to Event (MONTHS)                                                             
#>     Median                               16.9             19.7              12.3     
#>       95% CI                         (12.8, 19.0)     (13.2, 25.2)      (8.4, 14.9)  
#>     25% and 75%-ile                   7.7, 30.0         7.2, 34.1        4.5, 25.3   
#>     Range (censored)                 0.3 to 65.9       0.4 to 83.0      1.0 to 81.8  
#>     Range (event)                    0.5 to 85.8       0.1 to 58.7      0.2 to 77.8  
#>   Unstratified Analysis                                                              
#>     p-value (log-rank)                                   0.4808            0.0429    
#>     Hazard Ratio                                          0.90              1.36     
#>     95% CI                                            (0.67, 1.21)      (1.01, 1.82) 
#>   Stratified Analysis                                                                
#>     p-value (log-rank)                                   0.8068            0.0252    
#>     Hazard Ratio                                          0.96              1.42     
#>     95% CI                                            (0.71, 1.31)      (1.04, 1.92) 
#>   6 MONTHS                                                                           
#>     Patients remaining at risk            87               92                77      
#>     Event Free Rate (%)                 77.27             77.85            67.70     
#>     95% CI                          (68.76, 83.74)   (69.53, 84.15)    (58.64, 75.20)
#>     Difference in Event Free Rate                         0.57             -9.57     
#>       95% CI                                         (-9.82, 10.97)    (-20.70, 1.57)
#>       p-value (Z-test)                                   0.9137            0.0921    
#>   12 MONTHS                                                                          
#>     Patients remaining at risk            65               68                51      
#>     Event Free Rate (%)                 62.83             62.69            50.16     
#>     95% CI                          (53.36, 70.91)   (53.31, 70.71)    (40.69, 58.89)
#>     Difference in Event Free Rate                         -0.14            -12.68    
#>       95% CI                                         (-12.53, 12.25)   (-25.38, 0.03)
#>       p-value (Z-test)                                   0.9822            0.0505