Create a visual table from a summariseClinicalRecord() output

Create a visual table from a summariseClinicalRecord() output

Usage

tableClinicalRecords(result, type = NULL, style = NULL)

Arguments

result

A summarised_result object (output of summariseClinicalRecords()).

type

Character string specifying the desired output table format. See visOmopResults::tableType() for supported table types. If type = NULL, global options (set via visOmopResults::setGlobalTableOptions()) will be used if available; otherwise, a default 'gt' table is created.

style

Defines the visual formatting of the table. This argument can be provided in one of the following ways:

1. Pre-defined style: Use the name of a built-in style (e.g., "darwin"). See visOmopResults::tableStyle() for available options.

2. YAML file path: Provide the path to an existing .yml file defining a new style.

3. List of custome R code: Supply a block of custom R code or a named list describing styles for each table section. This code must be specific to the selected table type.

If style = NULL, the function will use global options (seevisOmopResults::setGlobalTableOptions()) or a _brand.yml file (if found); otherwise, the default style is applied.

Value

A formatted table visualisation.

Examples

# \donttest{
library(OmopSketch)
library(omock)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
#> ℹ Reading GiBleed tables.
#> ℹ Adding drug_strength table.
#> ℹ Creating local <cdm_reference> object.
#> ℹ Inserting <cdm_reference> into duckdb.

summarisedResult <- summariseClinicalRecords(
  cdm = cdm,
  omopTableName = c("condition_occurrence", "drug_exposure"),
  recordsPerPerson = c("mean", "sd"),
  inObservation = TRUE,
  standardConcept = TRUE,
  sourceVocabulary = TRUE,
  domainId = TRUE,
  typeConcept = TRUE
)
#> Warning: The `inObservation` argument of `summariseClinicalRecords()` is deprecated as
#> of OmopSketch 1.0.0.
#> ℹ Please use the `quality` argument instead.
#> Warning: The `standardConcept` argument of `summariseClinicalRecords()` is deprecated as
#> of OmopSketch 1.0.0.
#> ℹ Please use the `conceptSummary` argument instead.
#> Warning: The `sourceVocabulary` argument of `summariseClinicalRecords()` is deprecated
#> as of OmopSketch 1.0.0.
#> ℹ Please use the `conceptSummary` argument instead.
#> Warning: The `domainId` argument of `summariseClinicalRecords()` is deprecated as of
#> OmopSketch 1.0.0.
#> ℹ Please use the `conceptSummary` argument instead.
#> Warning: The `typeConcept` argument of `summariseClinicalRecords()` is deprecated as of
#> OmopSketch 1.0.0.
#> ℹ Please use the `conceptSummary` argument instead.
#> ℹ Adding variables of interest to condition_occurrence.
#> ℹ Summarising records per person in condition_occurrence.
#> ℹ Summarising subjects not in person table in condition_occurrence.
#> ℹ Summarising records in observation in condition_occurrence.
#> ℹ Summarising records with start before birth date in condition_occurrence.
#> ℹ Summarising records with end date before start date in condition_occurrence.
#> ℹ Summarising domains in condition_occurrence.
#> ℹ Summarising standard concepts in condition_occurrence.
#> ℹ Summarising source vocabularies in condition_occurrence.
#> ℹ Summarising concept types in condition_occurrence.
#> ℹ Summarising missing data in condition_occurrence.
#> ℹ Adding variables of interest to drug_exposure.
#> ℹ Summarising records per person in drug_exposure.
#> ℹ Summarising subjects not in person table in drug_exposure.
#> ℹ Summarising records in observation in drug_exposure.
#> ℹ Summarising records with start before birth date in drug_exposure.
#> ℹ Summarising records with end date before start date in drug_exposure.
#> ℹ Summarising domains in drug_exposure.
#> ℹ Summarising standard concepts in drug_exposure.
#> ℹ Summarising source vocabularies in drug_exposure.
#> ℹ Summarising concept types in drug_exposure.
#> ℹ Summarising concept class in drug_exposure.
#> ℹ Summarising missing data in drug_exposure.

summarisedResult |>
  suppress(minCellCount = 5) |>
  tableClinicalRecords()


  
Summary of condition_occurrence, drug_exposure tables

  
Variable name
      
Variable level
      
Estimate name
      

        
Database name
      
    
GiBleed
    
condition_occurrence
    
Number records
–
N
65,332
Number subjects
–
N (%)
2,694 (100.00%)
Subjects not in person table
–
N (%)
0 (0.00%)
Records per person
–
Mean (SD)
24.25 (7.41)
In observation
No
N (%)
450 (0.69%)

Yes
N (%)
64,882 (99.31%)
Domain
Condition
N (%)
65,332 (100.00%)
Source vocabulary
Icd10cm
N (%)
479 (0.73%)

No matching concept
N (%)
27 (0.04%)

Snomed
N (%)
64,826 (99.23%)
Standard concept
S
N (%)
65,332 (100.00%)
Type concept id
Ehr encounter diagnosis
N (%)
65,332 (100.00%)
Start date before birth date
–
N (%)
0 (0.00%)
End date before start date
–
N (%)
0 (0.00%)
Column name
Condition concept id
N missing data (%)
0 (0.00%)


N zeros (%)
0 (0.00%)

Condition end date
N missing data (%)
8,652 (13.24%)

Condition end datetime
N missing data (%)
8,652 (13.24%)

Condition occurrence id
N missing data (%)
0 (0.00%)


N zeros (%)
0 (0.00%)

Condition source concept id
N missing data (%)
0 (0.00%)


N zeros (%)
0 (0.00%)

Condition source value
N missing data (%)
0 (0.00%)

Condition start date
N missing data (%)
0 (0.00%)

Condition start datetime
N missing data (%)
0 (0.00%)

Condition status concept id
N missing data (%)
0 (0.00%)


N zeros (%)
65,332 (100.00%)

Condition status source value
N missing data (%)
65,332 (100.00%)

Condition type concept id
N missing data (%)
0 (0.00%)


N zeros (%)
0 (0.00%)

Person id
N missing data (%)
0 (0.00%)


N zeros (%)
0 (0.00%)

Provider id
N missing data (%)
65,332 (100.00%)


N zeros (%)
0 (0.00%)

Stop reason
N missing data (%)
65,332 (100.00%)

Visit detail id
N missing data (%)
0 (0.00%)


N zeros (%)
65,332 (100.00%)

Visit occurrence id
N missing data (%)
64 (0.10%)


N zeros (%)
0 (0.00%)
drug_exposure
    
Number records
–
N
67,713
Number subjects
–
N (%)
2,694 (100.00%)
Subjects not in person table
–
N (%)
0 (0.00%)
Records per person
–
Mean (SD)
25.13 (5.25)
In observation
No
N (%)
251 (0.37%)

Yes
N (%)
67,462 (99.63%)
Domain
Drug
N (%)
67,713 (100.00%)
Source vocabulary
Cvx
N (%)
25,713 (37.97%)

Ndc
N (%)
2,694 (3.98%)

No matching concept
N (%)
35 (0.05%)

Rxnorm
N (%)
39,271 (58.00%)
Standard concept
S
N (%)
67,713 (100.00%)
Type concept id
Dispensed in outpatient office
N (%)
25,713 (37.97%)

Prescription written
N (%)
42,000 (62.03%)
Concept class
Branded drug
N (%)
68 (0.10%)

Branded drug comp
N (%)
145 (0.21%)

Branded pack
N (%)
1,640 (2.42%)

Clinical drug
N (%)
36,221 (53.49%)

Clinical drug comp
N (%)
137 (0.20%)

Cvx
N (%)
25,713 (37.97%)

Ingredient
N (%)
2,764 (4.08%)

Quant branded drug
N (%)
6 (0.01%)

Quant clinical drug
N (%)
1,019 (1.50%)
Start date before birth date
–
N (%)
<5
End date before start date
–
N (%)
0 (0.00%)
Column name
Days supply
N missing data (%)
0 (0.00%)

Dose unit source value
N missing data (%)
67,707 (100.00%)

Drug concept id
N missing data (%)
0 (0.00%)


N zeros (%)
0 (0.00%)

Drug exposure end date
N missing data (%)
0 (0.00%)

Drug exposure end datetime
N missing data (%)
0 (0.00%)

Drug exposure id
N missing data (%)
0 (0.00%)


N zeros (%)
0 (0.00%)

Drug exposure start date
N missing data (%)
0 (0.00%)

Drug exposure start datetime
N missing data (%)
0 (0.00%)

Drug source concept id
N missing data (%)
0 (0.00%)


N zeros (%)
0 (0.00%)

Drug source value
N missing data (%)
0 (0.00%)

Drug type concept id
N missing data (%)
0 (0.00%)


N zeros (%)
0 (0.00%)

Lot number
N missing data (%)
0 (0.00%)

Person id
N missing data (%)
0 (0.00%)


N zeros (%)
0 (0.00%)

Provider id
N missing data (%)
0 (0.00%)


N zeros (%)
67,707 (100.00%)

Quantity
N missing data (%)
0 (0.00%)

Refills
N missing data (%)
0 (0.00%)

Route concept id
N missing data (%)
0 (0.00%)


N zeros (%)
67,707 (100.00%)

Route source value
N missing data (%)
67,707 (100.00%)

Sig
N missing data (%)
67,707 (100.00%)

Stop reason
N missing data (%)
67,707 (100.00%)

Verbatim end date
N missing data (%)
5,763 (8.51%)

Visit detail id
N missing data (%)
0 (0.00%)


N zeros (%)
67,707 (100.00%)

Visit occurrence id
N missing data (%)
520 (0.77%)


N zeros (%)
0 (0.00%)

cdmDisconnect(cdm = cdm)
# }