Summarise Table as gtsummary

Source: R/data.frame.R

Summarise a data.frame as gtsummary with Dutch defaults. These objects are based on the gt package by RStudio. To provide Certe style and compatibility with MS Word, use tbl_flextable() to transform the gtsummary object.

tbl_gtsummary(
  x,
  by = NULL,
  label = NULL,
  digits = 1,
  ...,
  language = "nl",
  column1_name = "Eigenschap",
  add_n = FALSE,
  add_p = FALSE,
  add_ci = FALSE,
  add_overall = FALSE,
  decimal.mark = dec_mark(),
  big.mark = big_mark()
)

Arguments

x

a data.frame

by

A column name (quoted or unquoted) in data. Summary statistics will be calculated separately for each level of the by variable (e.g. by = trt). If NULL, summary statistics are calculated using all observations. To stratify a table by two or more variables, use tbl_strata()

label

List of formulas specifying variables labels, e.g. list(age ~ "Age", stage ~ "Path T Stage"). If a variable's label is not specified here, the label attribute (attr(data$age, "label")) is used. If attribute label is NULL, the variable name will be used.

digits

List of formulas specifying the number of decimal places to round summary statistics. If not specified, tbl_summary guesses an appropriate number of decimals to round statistics. When multiple statistics are displayed for a single variable, supply a vector rather than an integer. For example, if the statistic being calculated is "{mean} ({sd})" and you want the mean rounded to 1 decimal place, and the SD to 2 use digits = list(age ~ c(1, 2)). User may also pass a styling function: digits = age ~ style_sigfig

...

Arguments passed on to gtsummary::tbl_summary()

language

the language to use, defaults to Dutch

column1_name

name to use for the first column

add_n

add the overall N using gtsummary::add_n()

add_p

add the p values gtsummary::add_p() (tests will be determined automatcally)

add_ci

add the confidence interval using gtsummary::add_ci()

add_overall

add the overall statistics using gtsummary::add_overall()

decimal.mark

decimal separator, defaults to dec_mark()

big.mark

thousands separator, defaults to big_mark()

Details

tbl_gtsummary() creates a summary table with gtsummary::tbl_summary(), to which different extra columns can be added e.g. with add_p = TRUE and add_overall = TRUE.

Examples

# These examples default to the Dutch language

iris |>
  tbl_gtsummary()
#> Setting theme "language: nl"
#> Warning: The `quiet` argument of `set_gtsummary_theme()` is deprecated as of gtsummary
#> 2.0.0.
#> ℹ Argument has been ignored.
#> ℹ The deprecated feature was likely used in the certetoolbox package.
#>   Please report the issue to the authors.



  
Karakteristiek
      N = 1501
    
Sepal.Length
5.8 (5.1 – 6.4)
Sepal.Width
3.0 (2.8 – 3.3)
Petal.Length
4.4 (1.6 – 5.1)
Petal.Width
1.3 (0.3 – 1.8)
Species

    setosa
50.0 (33.3%)
    versicolor
50.0 (33.3%)
    virginica
50.0 (33.3%)
1 Mediaan (Q1 – Q3); n (%)
    

iris |> 
  tbl_gtsummary(Species, add_p = TRUE)
#> Setting theme "language: nl"
#> Setting theme "language: nl"



  
Karakteristiek
      setosa

N = 501		
      versicolor

N = 501		
      virginica

N = 501		
      p-waarde2
    
Sepal.Length
5.0 (4.8 – 5.2)
5.9 (5.6 – 6.3)
6.5 (6.2 – 6.9)

Sepal.Width
3.4 (3.2 – 3.7)
2.8 (2.5 – 3.0)
3.0 (2.8 – 3.2)

Petal.Length
1.5 (1.4 – 1.6)
4.4 (4.0 – 4.6)
5.6 (5.1 – 5.9)

Petal.Width
0.2 (0.2 – 0.3)
1.3 (1.2 – 1.5)
2.0 (1.8 – 2.3)

1 Mediaan (Q1 – Q3)
    
2 Kruskal-Wallistoets
    
  
iris |> 
  tbl_gtsummary(Species, add_n = TRUE)
#> Setting theme "language: nl"
#> Setting theme "language: nl"



  
Karakteristiek
      setosa

N = 501		
      versicolor

N = 501		
      virginica

N = 501		
      N
    
Sepal.Length
5.0 (4.8 – 5.2)
5.9 (5.6 – 6.3)
6.5 (6.2 – 6.9)
150
Sepal.Width
3.4 (3.2 – 3.7)
2.8 (2.5 – 3.0)
3.0 (2.8 – 3.2)
150
Petal.Length
1.5 (1.4 – 1.6)
4.4 (4.0 – 4.6)
5.6 (5.1 – 5.9)
150
Petal.Width
0.2 (0.2 – 0.3)
1.3 (1.2 – 1.5)
2.0 (1.8 – 2.3)
150
1 Mediaan (Q1 – Q3)
    
  
# support strata by providing 
iris2 <- iris
iris2$Category <- sample(LETTERS[1:2], size = 150, replace = TRUE)
head(iris2)
#>   Sepal.Length Sepal.Width Petal.Length Petal.Width Species Category
#> 1          5.1         3.5          1.4         0.2  setosa        B
#> 2          4.9         3.0          1.4         0.2  setosa        B
#> 3          4.7         3.2          1.3         0.2  setosa        A
#> 4          4.6         3.1          1.5         0.2  setosa        A
#> 5          5.0         3.6          1.4         0.2  setosa        A
#> 6          5.4         3.9          1.7         0.4  setosa        A

iris2 |> 
  tbl_gtsummary(c(Category, Species))
#> Setting theme "language: nl"
#> Setting theme "language: nl"



  
Karakteristiek
      
        
A

      		
      
        
B

      		
    
setosa

N = 271		
      versicolor

N = 251		
      virginica

N = 251		
      setosa

N = 231		
      versicolor

N = 251		
      virginica

N = 251		
    
Sepal.Length
5.0 (4.8 – 5.3)
5.8 (5.6 – 6.3)
6.3 (6.1 – 6.9)
5.0 (4.6 – 5.1)
6.0 (5.6 – 6.2)
6.5 (6.4 – 7.2)
Sepal.Width
3.4 (3.1 – 3.6)
2.8 (2.6 – 3.0)
2.8 (2.7 – 3.0)
3.4 (3.2 – 3.8)
2.9 (2.5 – 3.0)
3.0 (2.9 – 3.2)
Petal.Length
1.5 (1.4 – 1.6)
4.2 (4.0 – 4.5)
5.4 (5.1 – 5.6)
1.4 (1.4 – 1.6)
4.5 (4.0 – 4.7)
5.7 (5.3 – 6.0)
Petal.Width
0.2 (0.2 – 0.2)
1.3 (1.2 – 1.4)
2.0 (1.8 – 2.1)
0.2 (0.2 – 0.4)
1.4 (1.3 – 1.5)
2.1 (1.8 – 2.3)
1 Mediaan (Q1 – Q3)
    

# transform to flextable 
# (formats to Certe style and allows rendering to Word)
iris |> 
  tbl_gtsummary(Species) |> 
  tbl_flextable()
#> Setting theme "language: nl"
#> Setting theme "language: nl"
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rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-c001bd48{margin:0;text-align:center;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-c001d8c8{width:1.742in;background-color:rgba(74, 100, 125, 1.00);vertical-align: middle;border-bottom: 2pt solid rgba(74, 100, 125, 1.00);border-top: 2pt solid rgba(74, 100, 125, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-c001d8d2{width:1.519in;background-color:rgba(74, 100, 125, 1.00);vertical-align: middle;border-bottom: 2pt solid rgba(74, 100, 125, 1.00);border-top: 2pt solid rgba(74, 100, 125, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-c001d8d3{width:1.742in;background-color:rgba(226, 231, 236, 1.00);vertical-align: top;border-bottom: 0.75pt solid rgba(255, 255, 255, 0.00);border-top: 0.75pt solid rgba(255, 255, 255, 0.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-c001d8d4{width:1.519in;background-color:rgba(226, 231, 236, 1.00);vertical-align: top;border-bottom: 0.75pt solid rgba(255, 255, 255, 0.00);border-top: 0.75pt solid rgba(255, 255, 255, 0.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-c001d8dc{width:1.742in;background-color:rgba(246, 247, 248, 1.00);vertical-align: top;border-bottom: 0.75pt solid rgba(255, 255, 255, 0.00);border-top: 0.75pt solid rgba(255, 255, 255, 0.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-c001d8e6{width:1.519in;background-color:rgba(246, 247, 248, 1.00);vertical-align: top;border-bottom: 0.75pt solid rgba(255, 255, 255, 0.00);border-top: 0.75pt solid rgba(255, 255, 255, 0.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-c001d8f0{width:1.742in;background-color:rgba(246, 247, 248, 1.00);vertical-align: top;border-bottom: 2pt solid rgba(74, 100, 125, 1.00);border-top: 0.75pt solid rgba(255, 255, 255, 0.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-c001d8f1{width:1.519in;background-color:rgba(246, 247, 248, 1.00);vertical-align: top;border-bottom: 2pt solid rgba(74, 100, 125, 1.00);border-top: 0.75pt solid rgba(255, 255, 255, 0.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-c001d8fa{width:1.742in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(255, 255, 255, 0.00);border-top: 0.75pt solid rgba(255, 255, 255, 0.00);border-left: 0 solid rgba(255, 255, 255, 0.00);border-right: 0 solid rgba(255, 255, 255, 0.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-c001d8fb{width:1.519in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(255, 255, 255, 0.00);border-top: 0.75pt solid rgba(255, 255, 255, 0.00);border-left: 0 solid rgba(255, 255, 255, 0.00);border-right: 0 solid rgba(255, 255, 255, 0.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.tabwid {\n  font-size: initial;\n  padding-bottom: 1em;\n}\n\n.tabwid table{\n  border-spacing:0px !important;\n  border-collapse:collapse;\n  line-height:1;\n  margin-left:auto;\n  margin-right:auto;\n  border-width: 0;\n  border-color: transparent;\n  caption-side: top;\n}\n.tabwid-caption-bottom table{\n  caption-side: bottom;\n}\n.tabwid_left table{\n  margin-left:0;\n}\n.tabwid_right table{\n  margin-right:0;\n}\n.tabwid td, .tabwid th {\n    padding: 0;\n}\n.tabwid a {\n  text-decoration: none;\n}\n.tabwid thead {\n    background-color: transparent;\n}\n.tabwid tfoot {\n    background-color: transparent;\n}\n.tabwid table tr {\nbackground-color: transparent;\n}\n.katex-display {\n    margin: 0 0 !important;\n}</style><table data-quarto-disable-processing='true' class='cl-c0052cbc'><thead><tr style=\"overflow-wrap:break-word;\"><th class=\"cl-c001d8c8\"><p class=\"cl-c001bd3e\"><span class=\"cl-bfff3816\">Karakteristiek</span></p></th><th class=\"cl-c001d8d2\"><p class=\"cl-c001bd3e\"><span class=\"cl-bfff3816\">setosa</span><span class=\"cl-bfff3816\">  </span><br><span class=\"cl-bfff3816\">N = 50</span><span class=\"cl-bfff3820\">1</span></p></th><th class=\"cl-c001d8d2\"><p class=\"cl-c001bd3e\"><span class=\"cl-bfff3816\">versicolor</span><span class=\"cl-bfff3816\">  </span><br><span class=\"cl-bfff3816\">N = 50</span><span class=\"cl-bfff3820\">1</span></p></th><th class=\"cl-c001d8d2\"><p class=\"cl-c001bd3e\"><span class=\"cl-bfff3816\">virginica</span><span class=\"cl-bfff3816\">  </span><br><span class=\"cl-bfff3816\">N = 50</span><span class=\"cl-bfff3820\">1</span></p></th></tr></thead><tbody><tr style=\"overflow-wrap:break-word;\"><td class=\"cl-c001d8d3\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">Sepal.Length</span></p></td><td class=\"cl-c001d8d4\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">5.0 (4.8 – 5.2)</span></p></td><td class=\"cl-c001d8d4\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">5.9 (5.6 – 6.3)</span></p></td><td class=\"cl-c001d8d4\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">6.5 (6.2 – 6.9)</span></p></td></tr><tr style=\"overflow-wrap:break-word;\"><td class=\"cl-c001d8dc\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">Sepal.Width</span></p></td><td class=\"cl-c001d8e6\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">3.4 (3.2 – 3.7)</span></p></td><td class=\"cl-c001d8e6\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">2.8 (2.5 – 3.0)</span></p></td><td class=\"cl-c001d8e6\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">3.0 (2.8 – 3.2)</span></p></td></tr><tr style=\"overflow-wrap:break-word;\"><td class=\"cl-c001d8d3\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">Petal.Length</span></p></td><td class=\"cl-c001d8d4\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">1.5 (1.4 – 1.6)</span></p></td><td class=\"cl-c001d8d4\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">4.4 (4.0 – 4.6)</span></p></td><td class=\"cl-c001d8d4\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">5.6 (5.1 – 5.9)</span></p></td></tr><tr style=\"overflow-wrap:break-word;\"><td class=\"cl-c001d8f0\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">Petal.Width</span></p></td><td class=\"cl-c001d8f1\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">0.2 (0.2 – 0.3)</span></p></td><td class=\"cl-c001d8f1\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">1.3 (1.2 – 1.5)</span></p></td><td class=\"cl-c001d8f1\"><p class=\"cl-c001bd48\"><span class=\"cl-bfff382a\">2.0 (1.8 – 2.3)</span></p></td></tr></tbody><tfoot><tr style=\"overflow-wrap:break-word;\"><td  colspan=\"4\"class=\"cl-c001d8fa\"><p class=\"cl-c001bd3e\"><span class=\"cl-bfff382b\">1</span><span class=\"cl-bfff382a\">Mediaan (Q1 – Q3)</span></p></td></tr></tfoot></table></div>"
#> attr(,"class")
#> [1] "knit_asis"
#> attr(,"knit_cacheable")
#> [1] NA