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Helpers for grouped tables generated with gtsummary

Source: R/grouped_tbl_pivot_wider.R
grouped_tbl_pivot_wider.Rd

A series of helpers for grouped tables generated by gtsummary::tbl_stack() or gtsummary::tbl_regression() in case of multinomial models, multi-components models or other grouped results. grouped_tbl_pivot_wider() allows to display results in a a wide format, with one set of columns per group. multinom_add_global_p_pivot_wider() is a specific case for multinomial models, when displaying global p-values in a wide format: it calls gtsummary::add_global_p(), followed by grouped_tbl_pivot_wider(), and then keep only the last column with p-values (see examples). Finally, as grouped regression tables doesn't have exactly the same structure as ungrouped tables, functions as gtsummary::bold_labels() do not always work properly. If the grouped table is kept in a long format, style_grouped_tbl() could be use to improve the output by styling variable labels, levels and/or group names. TO BE NOTED: to style group names, style_grouped_tbl() convert the table into a gt object with gtsummary::as_gt(). This function should therefore be used last. If the table is intended to be exported to another format, do not use style_grouped_tbl().

Usage

grouped_tbl_pivot_wider(x)

multinom_add_global_p_pivot_wider(
  x,
  ...,
  p_value_header = "**Likelihood-ratio test**"
)

style_grouped_tbl(
  x,
  bold_groups = TRUE,
  uppercase_groups = TRUE,
  bold_labels = FALSE,
  italicize_labels = TRUE,
  indent_labels = 4L,
  bold_levels = FALSE,
  italicize_levels = FALSE,
  indent_levels = 8L
)

Arguments

x

A grouped table generated with gtsummary::tbl_stack() or gtsummary::tbl_regression().

...

Additional arguments passed to gtsummary::add_global_p().

p_value_header

Header for the p-value column.

bold_groups

Bold group group names?

uppercase_groups

Convert group names to upper case?

bold_labels

Bold variable labels?

italicize_labels

Italicize variable labels?

indent_labels

Number of spaces to indent variable labels.

bold_levels

Bold levels?

italicize_levels

Italicize levels?

indent_levels

Number of spaces to indent levels.

Value

A gtsummary or a gt table.

Examples

# \donttest{
mod <- nnet::multinom(
  grade ~ stage + marker + age,
  data = gtsummary::trial,
  trace = FALSE
)
tbl <- mod |> gtsummary::tbl_regression(exponentiate = TRUE)
#> ℹ Multinomial models, multi-component models and other groups models have a
#>   different underlying structure than the models gtsummary was designed for.
#> • Functions designed to work with `tbl_regression()` objects may yield
#>   unexpected results.
#> ℹ Suppress this message with `?suppressMessages()`.
tbl



  
Characteristic
      OR
      95% CI
      p-value
    
II
    
T Stage





    T1
—
—

    T2
0.70
0.26, 1.86
0.5
    T3
0.35
0.12, 1.05
0.061
    T4
0.58
0.21, 1.64
0.3
Marker Level (ng/mL)
0.59
0.37, 0.94
0.027
Age
1.00
0.98, 1.03
0.7
III
    
T Stage





    T1
—
—

    T2
1.23
0.44, 3.44
0.7
    T3
0.82
0.28, 2.42
0.7
    T4
1.30
0.46, 3.73
0.6
Marker Level (ng/mL)
0.86
0.57, 1.28
0.5
Age
1.01
0.99, 1.04
0.3
Abbreviations: CI = Confidence Interval, OR = Odds Ratio
    
tbl |> grouped_tbl_pivot_wider()



  
Characteristic
      
        
II

      		
      
        
III

      		
    
OR
      95% CI
      p-value
      OR
      95% CI
      p-value
    
T Stage











    T1
—
—


—
—

    T2
0.70
0.26, 1.86
0.5
1.23
0.44, 3.44
0.7
    T3
0.35
0.12, 1.05
0.061
0.82
0.28, 2.42
0.7
    T4
0.58
0.21, 1.64
0.3
1.30
0.46, 3.73
0.6
Marker Level (ng/mL)
0.59
0.37, 0.94
0.027
0.86
0.57, 1.28
0.5
Age
1.00
0.98, 1.03
0.7
1.01
0.99, 1.04
0.3
Abbreviations: CI = Confidence Interval, OR = Odds Ratio
    

tbl |> multinom_add_global_p_pivot_wider() |> gtsummary::bold_labels()



  
Characteristic
      
        
II

      		
      
        
III

      		
      
        
Likelihood-ratio test

      		
    
OR
      95% CI
      OR
      95% CI
      p-value
    
T Stage








0.5
    T1
—
—
—
—

    T2
0.70
0.26, 1.86
1.23
0.44, 3.44

    T3
0.35
0.12, 1.05
0.82
0.28, 2.42

    T4
0.58
0.21, 1.64
1.30
0.46, 3.73

Marker Level (ng/mL)
0.59
0.37, 0.94
0.86
0.57, 1.28
0.068
Age
1.00
0.98, 1.03
1.01
0.99, 1.04
0.6
Abbreviations: CI = Confidence Interval, OR = Odds Ratio
    
tbl |> style_grouped_tbl()



  
Characteristic
      OR
      95% CI
      p-value
    
II
    
    T Stage





        T1
—
—

        T2
0.70
0.26, 1.86
0.5
        T3
0.35
0.12, 1.05
0.061
        T4
0.58
0.21, 1.64
0.3
    Marker Level (ng/mL)
0.59
0.37, 0.94
0.027
    Age
1.00
0.98, 1.03
0.7
III
    
    T Stage





        T1
—
—

        T2
1.23
0.44, 3.44
0.7
        T3
0.82
0.28, 2.42
0.7
        T4
1.30
0.46, 3.73
0.6
    Marker Level (ng/mL)
0.86
0.57, 1.28
0.5
    Age
1.01
0.99, 1.04
0.3
Abbreviations: CI = Confidence Interval, OR = Odds Ratio
    

t1 <- gtsummary::trial |>
  gtsummary::tbl_summary(include = grade, by = trt)
t2 <- gtsummary::trial |>
  gtsummary::tbl_summary(include = stage, by = trt)

gtsummary::tbl_stack(list(t1, t2), group_header = c("Table 1", "Table 2")) |>
  style_grouped_tbl()



  
Characteristic
      Drug A

N = 981		
      Drug B

N = 1021		
    
Table 1
    
    Grade



        I
35 (36%)
33 (32%)
        II
32 (33%)
36 (35%)
        III
31 (32%)
33 (32%)
Table 2
    
    T Stage



        T1
28 (29%)
25 (25%)
        T2
25 (26%)
29 (28%)
        T3
22 (22%)
21 (21%)
        T4
23 (23%)
27 (26%)
1 n (%)
    
# }