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Create a visual table of the most common concepts from summariseConceptIdCounts() output

Source: R/tableTopConceptCounts.R
tableTopConceptCounts.Rd

This function takes a summarised_result object and generates a formatted table highlighting the most frequent concepts.

Usage

tableTopConceptCounts(
  result,
  top = 10,
  countBy = NULL,
  type = NULL,
  style = NULL
)

Arguments

result

A summarised_result object (output of summariseConceptIdCounts()).

top

Integer. The number of top concepts to display. Defaults to 10.

countBy

Either 'person' or 'record'. If NULL whatever is in the data is used.

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.

result <- summariseConceptIdCounts(cdm = cdm, omopTableName = "condition_occurrence")

tableTopConceptCounts(result = result, top = 5)



  
Top 5 concepts in condition_occurrence table
  
Top
      
        
Cdm name

      		
    
GiBleed
    
condition_occurrence
    
1
Standard: Viral sinusitis (40481087) 
 Source: Viral sinusitis (40481087) 
 17268
2
Standard: Acute viral pharyngitis (4112343) 
 Source: Acute viral pharyngitis (4112343) 
 10217
3
Standard: Acute bronchitis (260139) 
 Source: Acute bronchitis (260139) 
 8184
4
Standard: Otitis media (372328) 
 Source: Otitis media (372328) 
 3605
5
Standard: Osteoarthritis (80180) 
 Source: Osteoarthritis (80180) 
 2694

cdmDisconnect(cdm = cdm)
# }