CPMT1

Cox Proportional Hazards Model Tables with a Single Covariate

CPM

We will use the cadtte data set from the random.cdisc.data package to illustrate the tables. We start by selecting the biomarker evaluable population (BEP) and the time-to-event endpoint of interest, here overall survival. We then convert time of overall survival to months and create a new variable for the event information.

Code

library(tern)
library(dplyr)

adtte <- random.cdisc.data::cadtte %>%
  df_explicit_na() %>%
  filter(PARAMCD == "OS", BEP01FL == "Y") %>%
  mutate(
    AVAL = day2month(AVAL),
    AVALU = "Months",
    event = 1 - CNSR
  )

The summarize_coxreg() function in tern takes the same variables, at, and control arguments that are used to fit a model using the fit_coxreg_univar() function - specifying the time, event and covariate in a variables list, and control and at with any further customizations to the model. Note that the default confidence level is 95% but this can be customized via the conf_level element in control.

Rather than fitting the model and then tidying the output via the broom::tidy() function, we can directly input these three arguments into the summarize_coxreg() function to summarize the model fit in a table layout, building the table with our pre-processed adtte data set.

Code

lyt <- basic_table() %>%
  summarize_coxreg(variables = list(
    time = "AVAL",
    event = "event",
    covariates = "COUNTRY"
  ))

build_table(lyt, adtte)

                              Hazard Ratio      95% CI      p-value
———————————————————————————————————————————————————————————————————
Covariate:                                                         
  Country (reference = CHN)                                 0.1604 
    USA                           1.67       (0.87, 3.19)   0.1230 
    BRA                           0.43       (0.17, 1.07)   0.0698 
    PAK                           0.38       (0.12, 1.22)   0.1043 
    NGA                           1.67       (0.76, 3.66)   0.2048 
    RUS                           0.91       (0.33, 2.50)   0.8488 
    JPN                           1.40       (0.51, 3.85)   0.5206 
    GBR                           0.78       (0.24, 2.49)   0.6738 
    CAN                           1.31       (0.41, 4.21)   0.6460

Code

sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] dplyr_1.1.4      tern_0.9.5       rtables_0.6.9    magrittr_2.0.3  
[5] formatters_0.5.9

loaded via a namespace (and not attached):
 [1] Matrix_1.7-0             gtable_0.3.5             jsonlite_1.8.8          
 [4] compiler_4.4.1           tidyselect_1.2.1         stringr_1.5.1           
 [7] tidyr_1.3.1              splines_4.4.1            scales_1.3.0            
[10] yaml_2.3.10              fastmap_1.2.0            lattice_0.22-6          
[13] ggplot2_3.5.1            R6_2.5.1                 generics_0.1.3          
[16] knitr_1.48               forcats_1.0.0            rbibutils_2.2.16        
[19] htmlwidgets_1.6.4        backports_1.5.0          checkmate_2.3.2         
[22] tibble_3.2.1             car_3.1-2                munsell_0.5.1           
[25] pillar_1.9.0             rlang_1.1.4              utf8_1.2.4              
[28] broom_1.0.6              stringi_1.8.4            xfun_0.47               
[31] cli_3.6.3                Rdpack_2.6.1             digest_0.6.37           
[34] grid_4.4.1               lifecycle_1.0.4          vctrs_0.6.5             
[37] evaluate_0.24.0          glue_1.7.0               codetools_0.2-20        
[40] abind_1.4-8              survival_3.7-0           carData_3.0-5           
[43] random.cdisc.data_0.3.15 fansi_1.0.6              colorspace_2.1-1        
[46] purrr_1.0.2              rmarkdown_2.28           tools_4.4.1             
[49] pkgconfig_2.0.3          htmltools_0.5.8.1

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