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.
Arguments
- result
A table to format.
- 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 vector elements can be column names or labels for overall headers. The table must contain an
estimate_valuecolumn to pivot the headers.- 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
renameto customise specific column names.- rename
A named vector to customise 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.
- style
Named list that specifies how to style the different parts of the table generated. It can either be a pre-defined style ("default" or "darwin" - the latter just for gt and flextable), NULL to get the table default style, or custom. Keep in mind that styling code is different for all table styles. To see the different styles use
tableStyle().- .options
A named list with additional formatting options.
visOmopResults::tableOptions()shows allowed arguments and their default values.
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 | 2,655,087 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | number subjects | - | N | 617,863 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | age | - | Mean (SD) | 38.00 (7.94) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | age | - | Mean (SD) | 38.24 (7.89) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Amoxiciline | N% | 7,068 (34.67) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Amoxiciline | N% | 33,239 (71.25) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Ibuprofen | N% | 23,963 (92.41) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Ibuprofen | N% | 60,493 (10.32) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | **age_group &&& sex; <40 &&& Male** |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | 1 | mock | cohort_name | cohort1 | number subjects | - | N | 3,721,239 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | number subjects | - | N | 2,059,746 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | age | - | Mean (SD) | 77.74 (1.08) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | age | - | Mean (SD) | 86.97 (0.23) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Amoxiciline | N% | 9,947 (33.38) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Amoxiciline | N% | 65,087 (40.00) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Ibuprofen | N% | 5,893 (59.88) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Ibuprofen | N% | 65,472 (44.63) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | **age_group &&& sex; >=40 &&& Male** |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | 1 | mock | cohort_name | cohort1 | number subjects | - | N | 5,728,534 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | number subjects | - | N | 1,765,568 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | age | - | Mean (SD) | 93.47 (7.24) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | age | - | Mean (SD) | 34.03 (4.77) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Amoxiciline | N% | 31,627 (47.64) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Amoxiciline | N% | 25,802 (32.54) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Ibuprofen | N% | 64,229 (97.62) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Ibuprofen | N% | 35,320 (64.01) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | **age_group &&& sex; <40 &&& Female** |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | 1 | mock | cohort_name | cohort1 | number subjects | - | N | 9,082,078 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | number subjects | - | N | 6,870,228 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | age | - | Mean (SD) | 21.21 (4.11) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | age | - | Mean (SD) | 48.21 (7.32) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Amoxiciline | N% | 51,863 (89.22) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Amoxiciline | N% | 47,855 (75.71) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Ibuprofen | N% | 87,627 (73.18) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Ibuprofen | N% | 27,026 (99.18) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | **age_group &&& sex; >=40 &&& Female** |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | 1 | mock | cohort_name | cohort1 | number subjects | - | N | 2,016,819 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | number subjects | - | N | 3,841,037 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | age | - | Mean (SD) | 65.17 (8.21) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | age | - | Mean (SD) | 59.96 (6.93) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Amoxiciline | N% | 66,201 (86.43) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Amoxiciline | N% | 76,631 (20.27) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Ibuprofen | N% | 77,891 (35.67) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Ibuprofen | N% | 99,268 (49.56) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | **sex; Male** |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | 1 | mock | cohort_name | cohort1 | number subjects | - | N | 8,983,897 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | number subjects | - | N | 7,698,414 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | age | - | Mean (SD) | 12.56 (6.47) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | age | - | Mean (SD) | 49.35 (4.78) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Amoxiciline | N% | 40,683 (39.00) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Amoxiciline | N% | 8,425 (71.11) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Ibuprofen | N% | 79,731 (43.15) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Ibuprofen | N% | 63,349 (48.43) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | **sex; Female** |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | 1 | mock | cohort_name | cohort1 | number subjects | - | N | 9,446,753 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | number subjects | - | N | 4,976,992 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | age | - | Mean (SD) | 26.72 (7.83) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | age | - | Mean (SD) | 18.62 (8.61) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Amoxiciline | N% | 91,288 (77.73) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Amoxiciline | N% | 87,532 (12.17) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Ibuprofen | N% | 45,527 (14.82) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Ibuprofen | N% | 21,321 (17.34) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | **age_group; <40** |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | 1 | mock | cohort_name | cohort1 | number subjects | - | N | 6,607,978 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | number subjects | - | N | 7,176,185 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | age | - | Mean (SD) | 38.61 (5.53) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | age | - | Mean (SD) | 82.74 (4.38) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Amoxiciline | N% | 29,360 (96.06) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Amoxiciline | N% | 33,907 (24.55) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Ibuprofen | N% | 41,008 (1.31) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Ibuprofen | N% | 12,937 (75.48) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | **age_group; >=40** |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | 1 | mock | cohort_name | cohort1 | number subjects | - | N | 6,291,140 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | number subjects | - | N | 9,919,061 |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | age | - | Mean (SD) | 1.34 (5.30) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | age | - | Mean (SD) | 66.85 (2.45) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Amoxiciline | N% | 45,907 (43.47) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Amoxiciline | N% | 83,944 (14.33) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort1 | Medications | Ibuprofen | N% | 81,087 (71.56) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+
#> | | | | cohort2 | Medications | Ibuprofen | N% | 47,812 (45.39) |
#> +---------------+-------------------+----------------+-----------------+-------------------+--------------------+-------------------+----------------+