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Create a visual table from a summariseClinicalRecord() output.

Source: R/tableClinicalRecords.R
tableClinicalRecords.Rd

Create a visual table from a summariseClinicalRecord() output.

Usage

tableClinicalRecords(result, type = "gt")

Arguments

result

Output from summariseClinicalRecords().

type

Type of formatting output table, either "gt" or "flextable".

Value

A gt or flextable object with the summarised data.

Examples

# \donttest{
cdm <- mockOmopSketch()

summarisedResult <- summariseClinicalRecords(
  cdm = cdm,
  omopTableName = c("condition_occurrence", "drug_exposure"),
  recordsPerPerson = c("mean", "sd"),
  inObservation = TRUE,
  standardConcept = TRUE,
  sourceVocabulary = TRUE,
  domainId = TRUE,
  typeConcept = TRUE
)
#> ℹ Summarising table counts
#> ℹ The following estimates will be computed:
#> → Start summary of data, at 2024-09-26 11:49:24.588711
#> ✔ Summary finished, at 2024-09-26 11:49:24.716322
#> ℹ Summarising records per person
#> ℹ The following estimates will be computed:
#> • records_per_person: mean, sd
#> → Start summary of data, at 2024-09-26 11:49:25.464836
#> ✔ Summary finished, at 2024-09-26 11:49:25.654862
#> ℹ Summarising in_observation, standard, domain_id, source, and type information
#> ℹ Summarising table counts
#> ℹ The following estimates will be computed:
#> → Start summary of data, at 2024-09-26 11:49:29.178223
#> ✔ Summary finished, at 2024-09-26 11:49:29.312913
#> ℹ Summarising records per person
#> ℹ The following estimates will be computed:
#> • records_per_person: mean, sd
#> → Start summary of data, at 2024-09-26 11:49:30.051484
#> ✔ Summary finished, at 2024-09-26 11:49:30.240484
#> ℹ Summarising in_observation, standard, domain_id, source, and type information

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



  
Variable name
      Variable level
      Estimate name
      
        Database name
      
    
mockOmopSketch
    
condition_occurrence
    
Number records
-
N
1,900
Number subjects
-
N (%)
100 (100.00%)
Records per person
-
Mean (SD)
19.00 (4.71)
In observation
Yes
N (%)
1,900 (100.00%)
Standard concept
Source
N (%)
1,900 (100.00%)
Source vocabulary
No matching concept
N (%)
1,900 (100.00%)
Domain
Condition
N (%)
1,900 (100.00%)
Type concept id
1
N (%)
1,900 (100.00%)
drug_exposure
    
Number records
-
N
5,600
Number subjects
-
N (%)
100 (100.00%)
Records per person
-
Mean (SD)
56.00 (6.20)
In observation
Yes
N (%)
5,600 (100.00%)
Standard concept
Source
N (%)
5,600 (100.00%)
Source vocabulary
No matching concept
N (%)
5,600 (100.00%)
Domain
Drug
N (%)
5,600 (100.00%)
Type concept id
1
N (%)
5,600 (100.00%)

PatientProfiles::mockDisconnect(cdm)
# }