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COXT02 Multi-Variable Cox Regression Model Table.

Source: R/coxt02.R
coxt02.Rd

The COXT02 table follows the same principles as the general Cox model analysis and produces the estimates for each of the covariates included in the model (usually the main effects without interaction terms).

Usage 

coxt02_main(
  adam_db,
  arm_var = "ARM",
  time_var = "AVAL",
  event_var = "EVENT",
  covariates = c("SEX", "RACE", "AAGE"),
  strata = NULL,
  lbl_vars = "Effect/Covariate Included in the Model",
  multivar = TRUE,
  ...
)

coxt02

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) the arm variable used for arm splitting.

time_var

(string) the time variable in a Cox proportional hazards regression model.

event_var

(string) the event variable in a Cox proportional hazards regression model.

covariates

(character) will be fitted and the corresponding effect will be estimated.

strata

(character) will be fitted for the stratified analysis.

lbl_vars

(string) text label for the a Cox regression model variables.

multivar

(flag) indicator of whether multivariate cox regression is conducted.

...

Further arguments passed to tern::control_coxreg().

Value

the main function returns an rtables object.

Details

  • The reference arm will always the first level of arm_var. Please change the level if you want to change the reference arms.

  • The table allows confidence level to be adjusted, default is two-sided 95%.

  • The stratified analysis is with DISCRETE tie handling (equivalent to tern::control_coxreg(ties = "exact") in R).

  • Model includes treatment plus specified covariate(s) as factor(s) or numeric(s), with "SEX", "RACE" and "AAGE" as default candidates.

  • The selection of the covariates and whether or not there is a selection process (vs. a fixed, pre-specified list) needs to be pre-specified.

  • For pairwise comparisons using the hazard ratio, the value for the control group is the denominator.

  • Keep zero-count rows unless overridden with prune_0 = TRUE.

Functions

  • coxt02_main(): Main TLG function

Note

  • adam_db object must contain an adtte table with "PARAMCD", "ARM", "AVAL", "CNSR, and the columns specified by "covariates" which is denoted as c("SEX", "RACE", "AAGE") by default.

Examples 

library(dunlin)

proc_data <- log_filter(syn_data, PARAMCD == "CRSD", "adtte")

run(coxt02, proc_data)
#>   Effect/Covariate Included in the Model                  Hazard Ratio      95% CI      p-value
#>   —————————————————————————————————————————————————————————————————————————————————————————————
#>   Treatment:                                                                                   
#>     Description of Planned Arm (reference = A: Drug X)                                  0.1107 
#>       B: Placebo                                              3.16       (1.05, 9.53)   0.0414 
#>       C: Combination                                          2.23       (0.81, 6.17)   0.1215 
#>   Covariate:                                                                                   
#>     Sex (reference = F)                                                                        
#>       M                                                       0.63       (0.23, 1.73)   0.3665 
#>     RACE (reference = AMERICAN INDIAN OR ALASKA NATIVE)                                 0.9055 
#>       ASIAN                                                   0.86       (0.18, 4.10)   0.8534 
#>       BLACK OR AFRICAN AMERICAN                               1.35       (0.21, 8.44)   0.7511 
#>       WHITE                                                   1.06       (0.18, 6.36)   0.9463 
#>     Age (yr)                                                                                   
#>       All                                                     1.03       (0.95, 1.13)   0.4598 

run(coxt02, proc_data, covariates = c("SEX", "AAGE"), strata = c("RACE"), conf_level = 0.90)
#>   Effect/Covariate Included in the Model                 Hazard Ratio      90% CI      p-value
#>   ————————————————————————————————————————————————————————————————————————————————————————————
#>   Treatment:                                                                                  
#>     Description of Planned Arm (reference = A: Drug X)                                 0.2028 
#>       B: Placebo                                             2.77       (1.06, 7.19)   0.0801 
#>       C: Combination                                         2.00       (0.82, 4.88)   0.1995 
#>   Covariate:                                                                                  
#>     Sex (reference = F)                                                                       
#>       M                                                      0.77       (0.34, 1.77)   0.6058 
#>     Age (yr)                                                                                  
#>       All                                                    1.02       (0.95, 1.10)   0.6610