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

Source: R/visOmopTable.R
visOmopTable.Rd

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(),
  settingsColumn = character(),
  groupColumn = character(),
  rename = character(),
  type = "gt",
  hide = character(),
  columnOrder = character(),
  factor = list(),
  showMinCellCount = TRUE,
  .options = list(),
  settingsColumns = 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. Elements in header can be:

  • Any of the columns returned by tableColumns(result) to create a header for these columns.

  • Any other input to create an overall header.

settingsColumn

A character vector with the names of settings to include in the table. To see options use settingsColumns(result).

groupColumn

Columns to use as group labels, to see options use tableColumns(result). 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.

columnOrder

Character vector establishing the position of the columns in the formatted table. Columns in either header, groupColumn, or hide will be ignored.

factor

A named list where names refer to columns (see available columns in tableColumns()) and list elements are the level order of that column to arrange the results. The column order in the list will be used for arranging the result.

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.

settingsColumns

[Deprecated]

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)
  )



  
Database name
      Variable name
      Variable level
      Estimate name
      
        
Cohort name

      		
    
cohort1
      cohort2
    
overall; overall
    
mock
number subjects
-
N
2,009,283
3,012,543

age
-
Mean (SD)
27.92 (5.88)
33.71 (6.72)

Medications
Amoxiciline
N%
82,683 (49.14)
20,832 (29.82)


Ibuprofen
N%
90,252 (24.88)
54,539 (58.02)
<40; Male
    
mock
number subjects
-
N
8,141,156
7,204,667

age
-
Mean (SD)
67.27 (4.92)
14.12 (8.20)

Medications
Amoxiciline
N%
61,938 (84.54)
22,826 (38.13)


Ibuprofen
N%
43,803 (74.80)
72,510 (38.57)
>=40; Male
    
mock
number subjects
-
N
6,537,801
2,614,054

age
-
Mean (SD)
6.01 (2.86)
35.26 (9.15)

Medications
Amoxiciline
N%
84,105 (2.51)
5,044 (24.78)


Ibuprofen
N%
80,676 (40.72)
52,548 (23.65)
<40; Female
    
mock
number subjects
-
N
3,532,520
1,076,963

age
-
Mean (SD)
98.85 (0.08)
40.14 (6.90)

Medications
Amoxiciline
N%
42,725 (54.84)
56,182 (34.50)


Ibuprofen
N%
48,150 (56.17)
61,894 (51.95)
>=40; Female
    
mock
number subjects
-
N
5,965,949
2,624,227

age
-
Mean (SD)
28.23 (5.51)
88.89 (4.92)

Medications
Amoxiciline
N%
76,929 (95.55)
69,425 (41.98)


Ibuprofen
N%
25,804 (75.05)
17,896 (64.12)
overall; Male
    
mock
number subjects
-
N
7,277,044
1,867,062

age
-
Mean (SD)
55.41 (8.13)
31.26 (6.47)

Medications
Amoxiciline
N%
71,214 (14.05)
22,794 (65.91)


Ibuprofen
N%
17,014 (55.12)
76,772 (82.99)
overall; Female
    
mock
number subjects
-
N
9,955,685
5,424,417

age
-
Mean (SD)
89.01 (6.44)
6.17 (4.57)

Medications
Amoxiciline
N%
6,337 (71.03)
96,031 (95.40)


Ibuprofen
N%
16,061 (47.33)
81,629 (91.91)
<40; overall
    
mock
number subjects
-
N
4,980,553
655,185

age
-
Mean (SD)
2.28 (0.69)
67.95 (1.25)

Medications
Amoxiciline
N%
42,601 (12.64)
49,284 (46.99)


Ibuprofen
N%
66,139 (6.26)
19,458 (92.94)
>=40; overall
    
mock
number subjects
-
N
2,302,948
8,803,851

age
-
Mean (SD)
67.77 (7.29)
37.82 (6.04)

Medications
Amoxiciline
N%
8,828 (83.57)
72,321 (15.06)


Ibuprofen
N%
46,855 (9.39)
21,251 (64.53)