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Create a plot from the output of summariseObservationPeriod()

Source: R/plotObservationPeriod.R
plotObservationPeriod.Rd

Create a plot from the output of summariseObservationPeriod()

Usage

plotObservationPeriod(
  result,
  variableName = "Number subjects",
  plotType = "barplot",
  facet = NULL,
  colour = NULL,
  style = NULL,
  type = NULL
)

Arguments

result

A summarised_result object (output of summariseObservationPeriod()).

variableName

The variable to plot it can be: "Number subjects", "Records per person", "Duration in days" or "Days to next observation period".

plotType

The plot type, it can be: "barplot", "boxplot" or "densityplot".

facet

Columns to face by. Formula format can be provided. See possible columns to face by with: visOmopResults::tidyColumns().

colour

Columns to colour by. See possible columns to colour by with: visOmopResults::tidyColumns().

style

Visual theme to apply. Character, or NULL. If a character, this may be either the name of a built-in style (see visOmopResults::plotStyle()), or a path to a .yml file that defines a custom style. If NULL, the function will use the explicit default style, unless a global style option is set (see visOmopResults::setGlobalPlotOptions()) or a _brand.yml file is present (in that order).

type

Character string indicating the output plot format. See visOmopResults::plotType() for the list of supported plot types. If type = NULL, the function will use the global setting defined via visOmopResults::setGlobalPlotOptions() (if available); otherwise, a standard ggplot2 plot is produced by default.

Value

A plot 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]
13,868.00 [7,102.50 - 20,955.50]



Range [min to max]
[1.00 to 40,349.00]

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]
13,868.00 [7,102.50 - 20,955.50]



Range [min to max]
[1.00 to 40,349.00]

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


cdmDisconnect(cdm = cdm)
# }