Format a <summarised_result> object into a gt, flextable, or tibble object

This function combines the functionalities of formatEstimateValue(), estimateName(), formatHeader(), and formatTable() into a single function specifically for <summarised_result> objects.

Usage

visOmopTable(
  result,
  estimateName = character(),
  header = character(),
  settingsColumns = character(),
  groupColumn = character(),
  rename = character(),
  type = "gt",
  hide = character(),
  showMinCellCount = TRUE,
  .options = list(),
  split = lifecycle::deprecated(),
  excludeColumns = lifecycle::deprecated(),
  formatEstimateName = lifecycle::deprecated(),
  renameColumns = lifecycle::deprecated()
)

Arguments

result

A <summarised_result> object.

estimateName

A named list of estimate names to join, sorted by computation order. Use <...> to indicate estimate names.

header

A vector specifying the elements to include in the header. The order of elements matters, with the first being the topmost header. The input vector elements can be:

1. Column names from the split summarised result generated by splitAll()

2. Settings specified in the settings argument

3. group, strata, additional, variable, estimate, and/or settings to refer to all columns within these groups

4. Any other input to create overall header labels at the specified location.

settingsColumns

A character vector with the names of settings to include in the table.

groupColumn

Columns to use as group labels. By default, the name of the new group will be the tidy* column names separated by ";". To specify a custom group name, use a named list such as: list("newGroupName" = c("variable_name", "variable_level")).

*tidy: The tidy format applied to column names replaces "_" with a space and converts to sentence case. Use rename to customize specific column names.

rename

A named vector to customize column names, e.g., c("Database name" = "cdm_name"). The function renames all column names not specified here into a tidy* format.

type

The desired format of the output table. See tableType() for allowed options.

hide

Columns to drop from the output table. By default, result_id and estimate_type are always dropped.

showMinCellCount

If TRUE, suppressed estimates will be indicated with "<{min_cell_count}", otherwise, the default na defined in .options will be used.

.options

A named list with additional formatting options. visOmopResults::tableOptions() shows allowed arguments and their default values.

split

excludeColumns

formatEstimateName

renameColumns

Value

A tibble, gt, or flextable object.

Examples

result <- mockSummarisedResult()
result |>
  visOmopTable(
    estimateName = c("N%" = "<count> (<percentage>)",
                     "N" = "<count>",
                     "Mean (SD)" = "<mean> (<sd>)"),
    header = c("group"),
    rename = c("Database name" = "cdm_name"),
    groupColumn = strataColumns(result)
  )
#> ! Results have not been suppressed.


  
Database name
      
Variable name
      
Variable level
      
Estimate name
      

        Cohort name
      
    
cohort1
      
cohort2
    
overall; overall
    
mock
number subjects
-
N
3,757,580
6,686,055

age
-
Mean (SD)
39.22 (6.09)
73.13 (1.25)

Medications
Amoxiciline
N%
20,595 (80.69)
10,504 (84.46)


Ibuprofen
N%
14,800 (60.58)
36,579 (70.03)
<40; Male
    
mock
number subjects
-
N
1,368,529
7,204,168

age
-
Mean (SD)
84.49 (6.28)
17.59 (9.18)

Medications
Amoxiciline
N%
80,943 (82.04)
34,921 (45.10)


Ibuprofen
N%
33,806 (68.42)
73,651 (59.73)
>=40; Male
    
mock
number subjects
-
N
986,021
5,419,602

age
-
Mean (SD)
88.51 (3.45)
89.05 (3.93)

Medications
Amoxiciline
N%
70,153 (60.69)
15,005 (85.40)


Ibuprofen
N%
95,087 (70.11)
64,000 (21.30)
<40; Female
    
mock
number subjects
-
N
6,423,973
3,933,305

age
-
Mean (SD)
73.61 (0.72)
92.42 (0.70)

Medications
Amoxiciline
N%
77,060 (16.22)
77,466 (95.12)


Ibuprofen
N%
31,908 (92.18)
43,092 (62.89)
>=40; Female
    
mock
number subjects
-
N
8,174,897
3,998,490

age
-
Mean (SD)
64.33 (6.00)
56.26 (6.76)

Medications
Amoxiciline
N%
41,081 (73.67)
48,826 (47.15)


Ibuprofen
N%
13,645 (75.40)
51,922 (59.68)
overall; Male
    
mock
number subjects
-
N
1,567,231
2,749,445

age
-
Mean (SD)
31.44 (2.12)
92.58 (4.66)

Medications
Amoxiciline
N%
43,455 (6.80)
73,696 (27.82)


Ibuprofen
N%
4,550 (46.81)
34,744 (61.72)
overall; Female
    
mock
number subjects
-
N
5,118,733
1,644,105

age
-
Mean (SD)
22.75 (1.04)
92.02 (4.93)

Medications
Amoxiciline
N%
56,295 (78.39)
39,168 (82.96)


Ibuprofen
N%
30,289 (79.74)
87,080 (21.79)
<40; overall
    
mock
number subjects
-
N
7,105,515
8,670,615

age
-
Mean (SD)
6.35 (6.81)
15.20 (7.08)

Medications
Amoxiciline
N%
22,634 (79.38)
63,896 (76.58)


Ibuprofen
N%
17,220 (34.67)
36,884 (31.01)
>=40; overall
    
mock
number subjects
-
N
3,634,426
6,532,899

age
-
Mean (SD)
7.86 (4.54)
65.42 (2.94)

Medications
Amoxiciline
N%
3,969 (8.16)
68,632 (35.05)


Ibuprofen
N%
39,478 (67.60)
29,888 (72.41)