Generate a formatted table from a <data.table>

This function combines the functionalities of formatEstimateValue(), formatEstimateName(), formatHeader(), and formatTable() into a single function. While it does not require the input table to be a <summarised_result>, it does expect specific fields to apply some formatting functionalities.

Usage

visTable(
  result,
  estimateName = character(),
  header = character(),
  groupColumn = character(),
  rename = character(),
  type = "gt",
  hide = character(),
  .options = list()
)

Arguments

result

A table to format.

estimateName

A named list of estimate names to join, sorted by computation order. Use <...> to indicate estimate names. This argument requires that the table has estimate_name and estimate_value columns.

header

A vector specifying the elements to include in the header. The order of elements matters, with the first being the topmost header. The vector elements can be column names or labels for overall headers. The table must contain an estimate_value column to pivot the headers.

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 them 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 will rename 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.

.options

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

Value

A tibble, gt, or flextable object.

Examples

result <- mockSummarisedResult()
result |>
  visTable(
    estimateName = c("N%" = "<count> (<percentage>)",
                     "N" = "<count>",
                     "Mean (SD)" = "<mean> (<sd>)"),
    header = c("Estimate"),
    rename = c("Database name" = "cdm_name"),
    groupColumn = c("strata_name", "strata_level"),
    hide = c("additional_name", "additional_level", "estimate_type", "result_type")
  )


  Result id
      Database name
      Group name
      Group level
      Variable name
      Variable level
      Estimate name
      Estimate
    
overall; overall
    
1
mock
cohort_name
cohort1
number subjects
-
N
2,012,155



cohort2
number subjects
-
N
6,493,812



cohort1
age
-
Mean (SD)
29.15 (8.53)



cohort2
age
-
Mean (SD)
86.40 (3.18)



cohort1
Medications
Amoxiciline
N%
42,519 (81.28)



cohort2
Medications
Amoxiciline
N%
82,087 (40.21)



cohort1
Medications
Ibuprofen
N%
55,531 (87.86)



cohort2
Medications
Ibuprofen
N%
4,886 (69.78)
age_group &&& sex; <40 &&& Male
    
1
mock
cohort_name
cohort1
number subjects
-
N
4,249,537



cohort2
number subjects
-
N
2,602,081



cohort1
age
-
Mean (SD)
90.69 (8.87)



cohort2
age
-
Mean (SD)
10.65 (1.35)



cohort1
Medications
Amoxiciline
N%
83,123 (30.24)



cohort2
Medications
Amoxiciline
N%
34,727 (14.42)



cohort1
Medications
Ibuprofen
N%
4,483 (38.98)



cohort2
Medications
Ibuprofen
N%
28,574 (98.88)
age_group &&& sex; >=40 &&& Male
    
1
mock
cohort_name
cohort1
number subjects
-
N
2,110,110



cohort2
number subjects
-
N
3,232,491



cohort1
age
-
Mean (SD)
17.82 (4.57)



cohort2
age
-
Mean (SD)
74.89 (9.43)



cohort1
Medications
Amoxiciline
N%
18,203 (8.40)



cohort2
Medications
Amoxiciline
N%
84,521 (8.47)



cohort1
Medications
Ibuprofen
N%
42,031 (19.38)



cohort2
Medications
Ibuprofen
N%
85,788 (42.37)
age_group &&& sex; <40 &&& Female
    
1
mock
cohort_name
cohort1
number subjects
-
N
481,151



cohort2
number subjects
-
N
6,612,474



cohort1
age
-
Mean (SD)
91.40 (1.05)



cohort2
age
-
Mean (SD)
58.27 (5.98)



cohort1
Medications
Amoxiciline
N%
56,066 (39.76)



cohort2
Medications
Amoxiciline
N%
80,786 (85.10)



cohort1
Medications
Ibuprofen
N%
73,966 (18.56)



cohort2
Medications
Ibuprofen
N%
55,640 (52.70)
age_group &&& sex; >=40 &&& Female
    
1
mock
cohort_name
cohort1
number subjects
-
N
4,739,725



cohort2
number subjects
-
N
2,370,871



cohort1
age
-
Mean (SD)
58.30 (2.80)



cohort2
age
-
Mean (SD)
51.23 (7.25)



cohort1
Medications
Amoxiciline
N%
63,604 (4.93)



cohort2
Medications
Amoxiciline
N%
70,355 (48.39)



cohort1
Medications
Ibuprofen
N%
51,352 (86.25)



cohort2
Medications
Ibuprofen
N%
45,659 (51.15)
sex; Male
    
1
mock
cohort_name
cohort1
number subjects
-
N
9,722,978



cohort2
number subjects
-
N
8,282,743



cohort1
age
-
Mean (SD)
40.14 (6.56)



cohort2
age
-
Mean (SD)
29.35 (3.14)



cohort1
Medications
Amoxiciline
N%
22,084 (37.14)



cohort2
Medications
Amoxiciline
N%
13,769 (85.68)



cohort1
Medications
Ibuprofen
N%
15,981 (55.44)



cohort2
Medications
Ibuprofen
N%
63,828 (64.55)
sex; Female
    
1
mock
cohort_name
cohort1
number subjects
-
N
921,884



cohort2
number subjects
-
N
6,662,380



cohort1
age
-
Mean (SD)
54.66 (3.76)



cohort2
age
-
Mean (SD)
99.11 (6.79)



cohort1
Medications
Amoxiciline
N%
66,826 (28.75)



cohort2
Medications
Amoxiciline
N%
16,167 (66.33)



cohort1
Medications
Ibuprofen
N%
64,206 (67.12)



cohort2
Medications
Ibuprofen
N%
97,123 (64.00)
age_group; <40
    
1
mock
cohort_name
cohort1
number subjects
-
N
2,069,944



cohort2
number subjects
-
N
5,409,234



cohort1
age
-
Mean (SD)
33.55 (8.25)



cohort2
age
-
Mean (SD)
91.82 (2.68)



cohort1
Medications
Amoxiciline
N%
91,820 (52.93)



cohort2
Medications
Amoxiciline
N%
27,483 (75.63)



cohort1
Medications
Ibuprofen
N%
83,243 (22.69)



cohort2
Medications
Ibuprofen
N%
76,411 (54.85)
age_group; >=40
    
1
mock
cohort_name
cohort1
number subjects
-
N
2,437,146



cohort2
number subjects
-
N
1,210,301



cohort1
age
-
Mean (SD)
91.09 (6.83)



cohort2
age
-
Mean (SD)
99.51 (2.28)



cohort1
Medications
Amoxiciline
N%
9,427 (1.49)



cohort2
Medications
Amoxiciline
N%
88,254 (57.99)



cohort1
Medications
Ibuprofen
N%
54,962 (0.52)



cohort2
Medications
Ibuprofen
N%
12,776 (48.84)

Result id	Database name	Group name	Group level	Variable name	Variable level	Estimate name	Estimate
overall; overall
1	mock	cohort_name	cohort1	number subjects	-	N	2,012,155
			cohort2	number subjects	-	N	6,493,812
			cohort1	age	-	Mean (SD)	29.15 (8.53)
			cohort2	age	-	Mean (SD)	86.40 (3.18)
			cohort1	Medications	Amoxiciline	N%	42,519 (81.28)
			cohort2	Medications	Amoxiciline	N%	82,087 (40.21)
			cohort1	Medications	Ibuprofen	N%	55,531 (87.86)
			cohort2	Medications	Ibuprofen	N%	4,886 (69.78)
age_group &&& sex; <40 &&& Male
1	mock	cohort_name	cohort1	number subjects	-	N	4,249,537
			cohort2	number subjects	-	N	2,602,081
			cohort1	age	-	Mean (SD)	90.69 (8.87)
			cohort2	age	-	Mean (SD)	10.65 (1.35)
			cohort1	Medications	Amoxiciline	N%	83,123 (30.24)
			cohort2	Medications	Amoxiciline	N%	34,727 (14.42)
			cohort1	Medications	Ibuprofen	N%	4,483 (38.98)
			cohort2	Medications	Ibuprofen	N%	28,574 (98.88)
age_group &&& sex; >=40 &&& Male
1	mock	cohort_name	cohort1	number subjects	-	N	2,110,110
			cohort2	number subjects	-	N	3,232,491
			cohort1	age	-	Mean (SD)	17.82 (4.57)
			cohort2	age	-	Mean (SD)	74.89 (9.43)
			cohort1	Medications	Amoxiciline	N%	18,203 (8.40)
			cohort2	Medications	Amoxiciline	N%	84,521 (8.47)
			cohort1	Medications	Ibuprofen	N%	42,031 (19.38)
			cohort2	Medications	Ibuprofen	N%	85,788 (42.37)
age_group &&& sex; <40 &&& Female
1	mock	cohort_name	cohort1	number subjects	-	N	481,151
			cohort2	number subjects	-	N	6,612,474
			cohort1	age	-	Mean (SD)	91.40 (1.05)
			cohort2	age	-	Mean (SD)	58.27 (5.98)
			cohort1	Medications	Amoxiciline	N%	56,066 (39.76)
			cohort2	Medications	Amoxiciline	N%	80,786 (85.10)
			cohort1	Medications	Ibuprofen	N%	73,966 (18.56)
			cohort2	Medications	Ibuprofen	N%	55,640 (52.70)
age_group &&& sex; >=40 &&& Female
1	mock	cohort_name	cohort1	number subjects	-	N	4,739,725
			cohort2	number subjects	-	N	2,370,871
			cohort1	age	-	Mean (SD)	58.30 (2.80)
			cohort2	age	-	Mean (SD)	51.23 (7.25)
			cohort1	Medications	Amoxiciline	N%	63,604 (4.93)
			cohort2	Medications	Amoxiciline	N%	70,355 (48.39)
			cohort1	Medications	Ibuprofen	N%	51,352 (86.25)
			cohort2	Medications	Ibuprofen	N%	45,659 (51.15)
sex; Male
1	mock	cohort_name	cohort1	number subjects	-	N	9,722,978
			cohort2	number subjects	-	N	8,282,743
			cohort1	age	-	Mean (SD)	40.14 (6.56)
			cohort2	age	-	Mean (SD)	29.35 (3.14)
			cohort1	Medications	Amoxiciline	N%	22,084 (37.14)
			cohort2	Medications	Amoxiciline	N%	13,769 (85.68)
			cohort1	Medications	Ibuprofen	N%	15,981 (55.44)
			cohort2	Medications	Ibuprofen	N%	63,828 (64.55)
sex; Female
1	mock	cohort_name	cohort1	number subjects	-	N	921,884
			cohort2	number subjects	-	N	6,662,380
			cohort1	age	-	Mean (SD)	54.66 (3.76)
			cohort2	age	-	Mean (SD)	99.11 (6.79)
			cohort1	Medications	Amoxiciline	N%	66,826 (28.75)
			cohort2	Medications	Amoxiciline	N%	16,167 (66.33)
			cohort1	Medications	Ibuprofen	N%	64,206 (67.12)
			cohort2	Medications	Ibuprofen	N%	97,123 (64.00)
age_group; <40
1	mock	cohort_name	cohort1	number subjects	-	N	2,069,944
			cohort2	number subjects	-	N	5,409,234
			cohort1	age	-	Mean (SD)	33.55 (8.25)
			cohort2	age	-	Mean (SD)	91.82 (2.68)
			cohort1	Medications	Amoxiciline	N%	91,820 (52.93)
			cohort2	Medications	Amoxiciline	N%	27,483 (75.63)
			cohort1	Medications	Ibuprofen	N%	83,243 (22.69)
			cohort2	Medications	Ibuprofen	N%	76,411 (54.85)
age_group; >=40
1	mock	cohort_name	cohort1	number subjects	-	N	2,437,146
			cohort2	number subjects	-	N	1,210,301
			cohort1	age	-	Mean (SD)	91.09 (6.83)
			cohort2	age	-	Mean (SD)	99.51 (2.28)
			cohort1	Medications	Amoxiciline	N%	9,427 (1.49)
			cohort2	Medications	Amoxiciline	N%	88,254 (57.99)
			cohort1	Medications	Ibuprofen	N%	54,962 (0.52)
			cohort2	Medications	Ibuprofen	N%	12,776 (48.84)