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
2,202,471



cohort2
number subjects
-
N
4,513,757



cohort1
age
-
Mean (SD)
44.81 (7.83)



cohort2
age
-
Mean (SD)
26.89 (7.36)



cohort1
Medications
Amoxiciline
N%
62,237 (92.84)



cohort2
Medications
Amoxiciline
N%
33,863 (63.98)



cohort1
Medications
Ibuprofen
N%
24,332 (61.44)



cohort2
Medications
Ibuprofen
N%
16,482 (1.81)
age_group &&& sex; <40 &&& Male
    
1
mock
cohort_name
cohort1
number subjects
-
N
371,822



cohort2
number subjects
-
N
7,942,700



cohort1
age
-
Mean (SD)
82.39 (6.22)



cohort2
age
-
Mean (SD)
88.35 (9.41)



cohort1
Medications
Amoxiciline
N%
55,533 (41.34)



cohort2
Medications
Amoxiciline
N%
76,968 (88.25)



cohort1
Medications
Ibuprofen
N%
51,505 (19.24)



cohort2
Medications
Ibuprofen
N%
18,098 (38.20)
age_group &&& sex; >=40 &&& Male
    
1
mock
cohort_name
cohort1
number subjects
-
N
6,980,541



cohort2
number subjects
-
N
8,246,223



cohort1
age
-
Mean (SD)
96.94 (8.66)



cohort2
age
-
Mean (SD)
67.06 (8.61)



cohort1
Medications
Amoxiciline
N%
96,107 (13.10)



cohort2
Medications
Amoxiciline
N%
30,134 (94.62)



cohort1
Medications
Ibuprofen
N%
86,319 (7.18)



cohort2
Medications
Ibuprofen
N%
99,645 (51.36)
age_group &&& sex; <40 &&& Female
    
1
mock
cohort_name
cohort1
number subjects
-
N
1,498,340



cohort2
number subjects
-
N
2,090,516



cohort1
age
-
Mean (SD)
29.54 (9.20)



cohort2
age
-
Mean (SD)
7.43 (3.64)



cohort1
Medications
Amoxiciline
N%
91,564 (6.12)



cohort2
Medications
Amoxiciline
N%
62,964 (70.94)



cohort1
Medications
Ibuprofen
N%
4,056 (30.62)



cohort2
Medications
Ibuprofen
N%
64,511 (4.72)
age_group &&& sex; >=40 &&& Female
    
1
mock
cohort_name
cohort1
number subjects
-
N
5,424,376



cohort2
number subjects
-
N
1,682,065



cohort1
age
-
Mean (SD)
23.27 (3.25)



cohort2
age
-
Mean (SD)
68.53 (9.13)



cohort1
Medications
Amoxiciline
N%
60,328 (88.61)



cohort2
Medications
Amoxiciline
N%
80,250 (92.36)



cohort1
Medications
Ibuprofen
N%
46,003 (17.46)



cohort2
Medications
Ibuprofen
N%
91,810 (80.31)
sex; Male
    
1
mock
cohort_name
cohort1
number subjects
-
N
7,967,724



cohort2
number subjects
-
N
9,802,742



cohort1
age
-
Mean (SD)
32.55 (9.16)



cohort2
age
-
Mean (SD)
60.08 (7.53)



cohort1
Medications
Amoxiciline
N%
31,155 (59.22)



cohort2
Medications
Amoxiciline
N%
54,224 (1.62)



cohort1
Medications
Ibuprofen
N%
16,600 (88.78)



cohort2
Medications
Ibuprofen
N%
79,507 (63.41)
sex; Female
    
1
mock
cohort_name
cohort1
number subjects
-
N
7,196,247



cohort2
number subjects
-
N
6,006,700



cohort1
age
-
Mean (SD)
10.04 (0.81)



cohort2
age
-
Mean (SD)
70.61 (6.41)



cohort1
Medications
Amoxiciline
N%
55,515 (72.24)



cohort2
Medications
Amoxiciline
N%
63,100 (17.15)



cohort1
Medications
Ibuprofen
N%
91,538 (49.78)



cohort2
Medications
Ibuprofen
N%
91,310 (77.13)
age_group; <40
    
1
mock
cohort_name
cohort1
number subjects
-
N
7,281,897



cohort2
number subjects
-
N
1,516,763



cohort1
age
-
Mean (SD)
33.02 (8.56)



cohort2
age
-
Mean (SD)
46.82 (7.95)



cohort1
Medications
Amoxiciline
N%
93,760 (51.24)



cohort2
Medications
Amoxiciline
N%
18,979 (21.40)



cohort1
Medications
Ibuprofen
N%
40,942 (69.39)



cohort2
Medications
Ibuprofen
N%
39,056 (50.18)
age_group; >=40
    
1
mock
cohort_name
cohort1
number subjects
-
N
478,162



cohort2
number subjects
-
N
2,927,387



cohort1
age
-
Mean (SD)
19.26 (3.05)



cohort2
age
-
Mean (SD)
1.10 (9.85)



cohort1
Medications
Amoxiciline
N%
36,504 (29.61)



cohort2
Medications
Amoxiciline
N%
20,345 (84.51)



cohort1
Medications
Ibuprofen
N%
64,053 (87.42)



cohort2
Medications
Ibuprofen
N%
35,740 (71.13)

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	2,202,471
			cohort2	number subjects	-	N	4,513,757
			cohort1	age	-	Mean (SD)	44.81 (7.83)
			cohort2	age	-	Mean (SD)	26.89 (7.36)
			cohort1	Medications	Amoxiciline	N%	62,237 (92.84)
			cohort2	Medications	Amoxiciline	N%	33,863 (63.98)
			cohort1	Medications	Ibuprofen	N%	24,332 (61.44)
			cohort2	Medications	Ibuprofen	N%	16,482 (1.81)
age_group &&& sex; <40 &&& Male
1	mock	cohort_name	cohort1	number subjects	-	N	371,822
			cohort2	number subjects	-	N	7,942,700
			cohort1	age	-	Mean (SD)	82.39 (6.22)
			cohort2	age	-	Mean (SD)	88.35 (9.41)
			cohort1	Medications	Amoxiciline	N%	55,533 (41.34)
			cohort2	Medications	Amoxiciline	N%	76,968 (88.25)
			cohort1	Medications	Ibuprofen	N%	51,505 (19.24)
			cohort2	Medications	Ibuprofen	N%	18,098 (38.20)
age_group &&& sex; >=40 &&& Male
1	mock	cohort_name	cohort1	number subjects	-	N	6,980,541
			cohort2	number subjects	-	N	8,246,223
			cohort1	age	-	Mean (SD)	96.94 (8.66)
			cohort2	age	-	Mean (SD)	67.06 (8.61)
			cohort1	Medications	Amoxiciline	N%	96,107 (13.10)
			cohort2	Medications	Amoxiciline	N%	30,134 (94.62)
			cohort1	Medications	Ibuprofen	N%	86,319 (7.18)
			cohort2	Medications	Ibuprofen	N%	99,645 (51.36)
age_group &&& sex; <40 &&& Female
1	mock	cohort_name	cohort1	number subjects	-	N	1,498,340
			cohort2	number subjects	-	N	2,090,516
			cohort1	age	-	Mean (SD)	29.54 (9.20)
			cohort2	age	-	Mean (SD)	7.43 (3.64)
			cohort1	Medications	Amoxiciline	N%	91,564 (6.12)
			cohort2	Medications	Amoxiciline	N%	62,964 (70.94)
			cohort1	Medications	Ibuprofen	N%	4,056 (30.62)
			cohort2	Medications	Ibuprofen	N%	64,511 (4.72)
age_group &&& sex; >=40 &&& Female
1	mock	cohort_name	cohort1	number subjects	-	N	5,424,376
			cohort2	number subjects	-	N	1,682,065
			cohort1	age	-	Mean (SD)	23.27 (3.25)
			cohort2	age	-	Mean (SD)	68.53 (9.13)
			cohort1	Medications	Amoxiciline	N%	60,328 (88.61)
			cohort2	Medications	Amoxiciline	N%	80,250 (92.36)
			cohort1	Medications	Ibuprofen	N%	46,003 (17.46)
			cohort2	Medications	Ibuprofen	N%	91,810 (80.31)
sex; Male
1	mock	cohort_name	cohort1	number subjects	-	N	7,967,724
			cohort2	number subjects	-	N	9,802,742
			cohort1	age	-	Mean (SD)	32.55 (9.16)
			cohort2	age	-	Mean (SD)	60.08 (7.53)
			cohort1	Medications	Amoxiciline	N%	31,155 (59.22)
			cohort2	Medications	Amoxiciline	N%	54,224 (1.62)
			cohort1	Medications	Ibuprofen	N%	16,600 (88.78)
			cohort2	Medications	Ibuprofen	N%	79,507 (63.41)
sex; Female
1	mock	cohort_name	cohort1	number subjects	-	N	7,196,247
			cohort2	number subjects	-	N	6,006,700
			cohort1	age	-	Mean (SD)	10.04 (0.81)
			cohort2	age	-	Mean (SD)	70.61 (6.41)
			cohort1	Medications	Amoxiciline	N%	55,515 (72.24)
			cohort2	Medications	Amoxiciline	N%	63,100 (17.15)
			cohort1	Medications	Ibuprofen	N%	91,538 (49.78)
			cohort2	Medications	Ibuprofen	N%	91,310 (77.13)
age_group; <40
1	mock	cohort_name	cohort1	number subjects	-	N	7,281,897
			cohort2	number subjects	-	N	1,516,763
			cohort1	age	-	Mean (SD)	33.02 (8.56)
			cohort2	age	-	Mean (SD)	46.82 (7.95)
			cohort1	Medications	Amoxiciline	N%	93,760 (51.24)
			cohort2	Medications	Amoxiciline	N%	18,979 (21.40)
			cohort1	Medications	Ibuprofen	N%	40,942 (69.39)
			cohort2	Medications	Ibuprofen	N%	39,056 (50.18)
age_group; >=40
1	mock	cohort_name	cohort1	number subjects	-	N	478,162
			cohort2	number subjects	-	N	2,927,387
			cohort1	age	-	Mean (SD)	19.26 (3.05)
			cohort2	age	-	Mean (SD)	1.10 (9.85)
			cohort1	Medications	Amoxiciline	N%	36,504 (29.61)
			cohort2	Medications	Amoxiciline	N%	20,345 (84.51)
			cohort1	Medications	Ibuprofen	N%	64,053 (87.42)
			cohort2	Medications	Ibuprofen	N%	35,740 (71.13)