Table 1

Last updated: 2024-12-03

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Some notes on generating Table 1 from the tbl_summary() tutorial using trial dataset as the example.

Setups depend on personal preferences and variable distributions. You can modify them based on your dataset. Things you might want to take into considerations are the following:
- Continuous variables: if a variable violates normality assumption, no need to specify Mean (SD) and t-test. Median (IQR) and Wilcoxon rank sum test are performed by default.
- Categorical variables: if any expected cell value of a variable is less than 5, Fisher’s exact test is performed by default.
tbl_summary()
- by= argument: summary statistics split by treatment group.
- label= argument: specify age label.
- statistic= argument: specify Mean (SD) to display for age.
- digits= argument: mean/median and SD/IQR round to 1 decimal place; n rounds to 0 decimal place and % rounds to 1 decimal place.
- missing_text= argument: change default text for missing observations.
add_p()
- test= argument: specify t-test to perform for age.
- pvalue_fun= argument: p-values round to 2 digits.

Warning: package 'gtsummary' was built under R version 4.4.1

trial %>%
  tbl_summary(by = trt,
              label = age ~ 'Age at Screening',
              statistic = age ~ '{mean} ({sd})',
              digits = list(all_continuous() ~ c(1, 1),
                            all_categorical() ~ c(0, 1)),
              missing_text = '(Missing)') %>%
  add_p(test = age ~ 't.test', 
        pvalue_fun = ~ style_pvalue(.x, digits = 2)) %>% # add p-values
  add_overall() %>% # add column with overall summary statistics
  modify_header(label ~ "") %>% # remove default header text
  modify_caption("**Table 1. Patient characteristics**") %>% # modify table title
  bold_labels() %>% # bold labels
  bold_p() # bold p-values if significant

**Table 1. Patient characteristics**
	Overall N = 200¹	Drug A N = 98¹	Drug B N = 102¹	p-value²
Age at Screening	47.2 (14.3)	47.0 (14.7)	47.4 (14.0)	0.83
(Missing)	11	7	4
Marker Level (ng/mL)	0.6 (0.2, 1.4)	0.8 (0.2, 1.6)	0.5 (0.2, 1.2)	0.085
(Missing)	10	6	4
T Stage				0.87
T1	53 (26.5%)	28 (28.6%)	25 (24.5%)
T2	54 (27.0%)	25 (25.5%)	29 (28.4%)
T3	43 (21.5%)	22 (22.4%)	21 (20.6%)
T4	50 (25.0%)	23 (23.5%)	27 (26.5%)
Grade				0.87
I	68 (34.0%)	35 (35.7%)	33 (32.4%)
II	68 (34.0%)	32 (32.7%)	36 (35.3%)
III	64 (32.0%)	31 (31.6%)	33 (32.4%)
Tumor Response	61 (31.6%)	28 (29.5%)	33 (33.7%)	0.53
(Missing)	7	3	4
Patient Died	112 (56.0%)	52 (53.1%)	60 (58.8%)	0.41
Months to Death/Censor	22.4 (15.9, 24.0)	23.5 (17.4, 24.0)	21.2 (14.5, 24.0)	0.14
¹ Mean (SD); Median (Q1, Q3); n (%)
² Welch Two Sample t-test; Wilcoxon rank sum test; Pearson’s Chi-squared test

sessionInfo()

R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS 15.1.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Detroit
tzcode source: internal

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

other attached packages:
[1] gtsummary_2.0.3 workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] gt_0.10.1         sass_0.4.9        utf8_1.2.4        generics_0.1.3   
 [5] tidyr_1.3.1       xml2_1.3.6        stringi_1.8.4     digest_0.6.37    
 [9] magrittr_2.0.3    evaluate_1.0.0    cards_0.3.0       fastmap_1.2.0    
[13] rprojroot_2.0.4   jsonlite_1.8.9    processx_3.8.4    whisker_0.4.1    
[17] cardx_0.2.1       backports_1.5.0   ps_1.7.6          promises_1.3.0   
[21] httr_1.4.7        purrr_1.0.2       fansi_1.0.6       jquerylib_0.1.4  
[25] cli_3.6.3         rlang_1.1.4       commonmark_1.9.1  withr_3.0.1      
[29] cachem_1.1.0      yaml_2.3.10       tools_4.4.0       dplyr_1.1.4      
[33] httpuv_1.6.15     broom_1.0.7       vctrs_0.6.5       R6_2.5.1         
[37] lifecycle_1.0.4   git2r_0.33.0      stringr_1.5.1     fs_1.6.4         
[41] pkgconfig_2.0.3   callr_3.7.6       pillar_1.9.0      bslib_0.8.0      
[45] later_1.3.2       glue_1.8.0        Rcpp_1.0.13       xfun_0.47        
[49] tibble_3.2.1      tidyselect_1.2.1  rstudioapi_0.16.0 knitr_1.48       
[53] htmltools_0.5.8.1 rmarkdown_2.28    compiler_4.4.0    getPass_0.2-4    
[57] markdown_1.12

Table 1

Chun-Hui Lin

2024-11-22