CPMT3

Cox Proportional Hazards Model Tables with Separate Models for Each Covariate

CPM

We prepare the data in the same way as in CPMT1.

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 separate Cox Proportional Hazards models for each covariate can be fitted and summarized in a table using the summarize_coxreg() function in tern. This function 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.

We input these three arguments into the summarize_coxreg() function to summarize the model fit in a table layout, and then build the table with our pre-processed adtte data set.

Code

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

build_table(lyt = lyt, df = 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 
  Age                                                              
    All                           1.01       (0.98, 1.03)   0.5600

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_0.9.5.9022       rtables_0.6.9.9014   
[4] magrittr_2.0.3        formatters_0.5.9.9001

loaded via a namespace (and not attached):
 [1] Matrix_1.7-0                  gtable_0.3.5                 
 [3] jsonlite_1.8.8                compiler_4.4.1               
 [5] tidyselect_1.2.1              stringr_1.5.1                
 [7] tidyr_1.3.1                   splines_4.4.1                
 [9] scales_1.3.0                  yaml_2.3.10                  
[11] fastmap_1.2.0                 lattice_0.22-6               
[13] ggplot2_3.5.1                 R6_2.5.1                     
[15] generics_0.1.3                knitr_1.48                   
[17] forcats_1.0.0                 rbibutils_2.2.16             
[19] htmlwidgets_1.6.4             backports_1.5.0              
[21] checkmate_2.3.2               tibble_3.2.1                 
[23] car_3.1-2                     munsell_0.5.1                
[25] pillar_1.9.0                  rlang_1.1.4                  
[27] utf8_1.2.4                    broom_1.0.6                  
[29] stringi_1.8.4                 xfun_0.47                    
[31] cli_3.6.3                     Rdpack_2.6.1                 
[33] digest_0.6.37                 grid_4.4.1                   
[35] lifecycle_1.0.4               vctrs_0.6.5                  
[37] evaluate_0.24.0               glue_1.7.0                   
[39] codetools_0.2-20              abind_1.4-8                  
[41] survival_3.7-0                carData_3.0-5                
[43] random.cdisc.data_0.3.15.9009 fansi_1.0.6                  
[45] colorspace_2.1-1              purrr_1.0.2                  
[47] rmarkdown_2.28                tools_4.4.1                  
[49] pkgconfig_2.0.3               htmltools_0.5.8.1

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