Helpers for grouped tables generated with gtsummary — grouped_tbl_pivot

A series of helpers for grouped tables generated by 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 regression table generated with 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

mod <- nnet::multinom(
  grade ~ stage + marker + age,
  data = gtsummary::trial,
  trace = FALSE
)
tbl <- mod |> gtsummary::tbl_regression(exponentiate = TRUE)
#> ℹ Multinomial 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.
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
    

# \donttest{
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
    
# }

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

Characteristic	II			III
Characteristic	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