cls5

Library

library(gtsummary)
library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

Data

#View(trial)
head(trial)

str(trial)

## tibble [200 × 8] (S3: tbl_df/tbl/data.frame)
##  $ trt     : chr [1:200] "Drug A" "Drug B" "Drug A" "Drug A" ...
##   ..- attr(*, "label")= chr "Chemotherapy Treatment"
##  $ age     : num [1:200] 23 9 31 NA 51 39 37 32 31 34 ...
##   ..- attr(*, "label")= chr "Age"
##  $ marker  : num [1:200] 0.16 1.107 0.277 2.067 2.767 ...
##   ..- attr(*, "label")= chr "Marker Level (ng/mL)"
##  $ stage   : Factor w/ 4 levels "T1","T2","T3",..: 1 2 1 3 4 4 1 1 1 3 ...
##   ..- attr(*, "label")= chr "T Stage"
##  $ grade   : Factor w/ 3 levels "I","II","III": 2 1 2 3 3 1 2 1 2 1 ...
##   ..- attr(*, "label")= chr "Grade"
##  $ response: int [1:200] 0 1 0 1 1 0 0 0 0 0 ...
##   ..- attr(*, "label")= chr "Tumor Response"
##  $ death   : int [1:200] 0 0 0 1 1 1 0 1 0 1 ...
##   ..- attr(*, "label")= chr "Patient Died"
##  $ ttdeath : num [1:200] 24 24 24 17.6 16.4 ...
##   ..- attr(*, "label")= chr "Months to Death/Censor"

Cross Table

trial %>% 
  tbl_summary(
    by=trt
  )

Characteristic	Drug A N = 981	Drug B N = 1021
Age	46 (37, 60)	48 (39, 56)
Unknown	7	4
Marker Level (ng/mL)	0.84 (0.23, 1.60)	0.52 (0.18, 1.21)
Unknown	6	4
T Stage
T1	28 (29%)	25 (25%)
T2	25 (26%)	29 (28%)
T3	22 (22%)	21 (21%)
T4	23 (23%)	27 (26%)
Grade
I	35 (36%)	33 (32%)
II	32 (33%)	36 (35%)
III	31 (32%)	33 (32%)
Tumor Response	28 (29%)	33 (34%)
Unknown	3	4
Patient Died	52 (53%)	60 (59%)
Months to Death/Censor	23.5 (17.4, 24.0)	21.2 (14.5, 24.0)
1 Median (Q1, Q3); n (%)

Add Statistic

trial %>% 
  tbl_summary(
    by=trt,
    statistic = list(
      all_categorical()~"{n}/{N} ({p}%)",
      all_continuous()~"{mean} ({sd})"
  )) %>% 
  add_p() %>% 
  add_overall() %>% 
  add_n()

Characteristic	N	Overall N = 2001	Drug A N = 981	Drug B N = 1021	p-value2
Age	189	47 (14)	47 (15)	47 (14)	0.7
Unknown		11	7	4
Marker Level (ng/mL)	190	0.92 (0.86)	1.02 (0.89)	0.82 (0.83)	0.085
Unknown		10	6	4
T Stage	200				0.9
T1		53/200 (27%)	28/98 (29%)	25/102 (25%)
T2		54/200 (27%)	25/98 (26%)	29/102 (28%)
T3		43/200 (22%)	22/98 (22%)	21/102 (21%)
T4		50/200 (25%)	23/98 (23%)	27/102 (26%)
Grade	200				0.9
I		68/200 (34%)	35/98 (36%)	33/102 (32%)
II		68/200 (34%)	32/98 (33%)	36/102 (35%)
III		64/200 (32%)	31/98 (32%)	33/102 (32%)
Tumor Response	193	61/193 (32%)	28/95 (29%)	33/98 (34%)	0.5
Unknown		7	3	4
Patient Died	200	112/200 (56%)	52/98 (53%)	60/102 (59%)	0.4
Months to Death/Censor	200	19.6 (5.3)	20.2 (5.0)	19.0 (5.5)	0.14
1 Mean (SD); n/N (%)
2 Wilcoxon rank sum test; Pearson’s Chi-squared test