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Create a visual table from a summariseObservationPeriod() result

Source: R/tableObservationPeriod.R
tableObservationPeriod.Rd

Create a visual table from a summariseObservationPeriod() result

Usage

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

Arguments

result

A summarised_result object (output of summariseObservationPeriod()).

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(dplyr, warn.conflicts = FALSE)
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 <- summariseObservationPeriod(cdm = cdm)
#> Warning: ! There are 2649 individuals not included in the person table.

tableObservationPeriod(result = result)



  
Summary of observation_period table
  
Observation period ordinal
      Variable name
      Variable level
      Estimate name
      
        
CDM name

      		
    
GiBleed
    
all
Number records
–
N
5,343

Number subjects
–
N
5,343

Subjects not in person table
–
N (%)
2,649 (49.58%)

Records per person
–
Mean (SD)
1.00 (0.00)



Median [Q25 - Q75]
1 [1 - 1]



Range [min to max]
[1 to 1]

Duration in days
–
Mean (SD)
14,402.00 (8,725.34)



Median [Q25 - Q75]
13,868 [7,102 - 20,956]



Range [min to max]
[1 to 40,349]

Type concept id
Period covering healthcare encounters
N (%)
5,343 (100.00%)

Start date before birth date
–
N (%)
0 (0.00%)

End date before start date
–
N (%)
0 (0.00%)

Column name
Observation period end date
N missing data (%)
0 (0.00%)


Observation period id
N missing data (%)
0 (0.00%)



N zeros (%)
0 (0.00%)


Observation period start date
N missing data (%)
0 (0.00%)


Period 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%)
1st
Number subjects
–
N
5,343

Duration in days
–
Mean (SD)
14,402.00 (8,725.34)



Median [Q25 - Q75]
13,868 [7,102 - 20,956]



Range [min to max]
[1 to 40,349]

plotObservationPeriod(
  result = result,
  variableName = "Duration in days",
  plotType = "boxplot"
)


cdmDisconnect(cdm = cdm)
# }