Utility functions • visOmopResults

In this vignette we will present the column retrieval and unite functionalities which provide useful tools to work with visOmopResults functions and managing <summarised_result> objects.

Column retrieval functions

Column retrieval functions are designed to simplify the extraction of specific columns or variables within name-level columns from <summarised_result> objects. In this section, we will review the different column functions and provide a use-case example.

Variables in name-level columns

The following functions are useful for identifying variables stored in name-level pairs:

For example, let’s see which strata are included in a mock <summarised_result>:

# Set-up
library(visOmopResults)
library(dplyr)

# Create a mock summarized result
result <- mockSummarisedResult()
head(result)
#> # A tibble: 6 × 13
#>   result_id cdm_name group_name  group_level strata_name       strata_level   
#>       <int> <chr>    <chr>       <chr>       <chr>             <chr>          
#> 1         1 mock     cohort_name cohort1     overall           overall        
#> 2         1 mock     cohort_name cohort1     age_group &&& sex <40 &&& Male   
#> 3         1 mock     cohort_name cohort1     age_group &&& sex >=40 &&& Male  
#> 4         1 mock     cohort_name cohort1     age_group &&& sex <40 &&& Female 
#> 5         1 mock     cohort_name cohort1     age_group &&& sex >=40 &&& Female
#> 6         1 mock     cohort_name cohort1     sex               Male           
#> # ℹ 7 more variables: variable_name <chr>, variable_level <chr>,
#> #   estimate_name <chr>, estimate_type <chr>, estimate_value <chr>,
#> #   additional_name <chr>, additional_level <chr>

# Get strata columns
strataColumns(result)
#> [1] "age_group" "sex"

This function returns the strata columns that would be generated if result were split by strata.

Settings

The settingsColumns() function returns which settings are linked to a <summarised_result>:

# Display settings tibble
settings(result)
#> # A tibble: 1 × 4
#>   result_id result_type            package_name   package_version
#>       <int> <chr>                  <chr>          <chr>          
#> 1         1 mock_summarised_result visOmopResults 0.4.1

# Get which settings are present using `settingsColumns()`
settingsColumns(result)
#> [1] "result_type"     "package_name"    "package_version"

Tidy columns

The tidyColumns() function provides the columns that the will have in its tidy format:

# Show tidy result:
tidy(result) |> head()
#> # A tibble: 6 × 13
#>   cdm_name cohort_name age_group sex   variable_name variable_level  count  mean
#>   <chr>    <chr>       <chr>     <chr> <chr>         <chr>           <int> <dbl>
#> 1 mock     cohort1     overall   over… number subje… NA             8.08e5    NA
#> 2 mock     cohort1     <40       Male  number subje… NA             8.34e6    NA
#> 3 mock     cohort1     >=40      Male  number subje… NA             6.01e6    NA
#> 4 mock     cohort1     <40       Fema… number subje… NA             1.57e6    NA
#> 5 mock     cohort1     >=40      Fema… number subje… NA             7.40e4    NA
#> 6 mock     cohort1     overall   Male  number subje… NA             4.66e6    NA
#> # ℹ 5 more variables: sd <dbl>, percentage <dbl>, result_type <chr>,
#> #   package_name <chr>, package_version <chr>

# Get the tidy columns with `tidyColumns()`
tidyColumns(result)
#>  [1] "cdm_name"        "cohort_name"     "age_group"       "sex"            
#>  [5] "variable_name"   "variable_level"  "count"           "mean"           
#>  [9] "sd"              "percentage"      "result_type"     "package_name"   
#> [13] "package_version"

Use-case

These functionalities can be used in table and plot functions. For instance, let’s plot the number of subjects in each cohort and strata from our mock result.

We’ll first filter the result to focus on the variable of interest, and then use barPlot() (see vignette on plots for more information on how to use plotting functions).

result <- result |>
  filter(variable_name == "number subjects")

barPlot(
  result = result, 
  x = groupColumns(result), 
  y = "count", 
  facet = strataColumns(result), 
  colour = groupColumns(result)
)

Unite functions

The unite functions serve as the complementary tools to the split functions (see vignette on tidying <summarised_result>), allowing you to generate name-level pair columns from targeted columns within a <dataframe>.

There are three unite functions that allow to create group, strata, and additional name-level columns from specified sets of columns:

For example, to create group_name and group_level columns from a tibble, you can use:

# Create and show mock data
data <- tibble(
  denominator_cohort_name = c("general_population", "older_than_60", "younger_than_60"),
  outcome_cohort_name = c("stroke", "stroke", "stroke")
)
head(data)
#> # A tibble: 3 × 2
#>   denominator_cohort_name outcome_cohort_name
#>   <chr>                   <chr>              
#> 1 general_population      stroke             
#> 2 older_than_60           stroke             
#> 3 younger_than_60         stroke

# Unite into group name-level columns
data |>
  uniteGroup(cols = c("denominator_cohort_name", "outcome_cohort_name"))
#> # A tibble: 3 × 2
#>   group_name                                      group_level                  
#>   <chr>                                           <chr>                        
#> 1 denominator_cohort_name &&& outcome_cohort_name general_population &&& stroke
#> 2 denominator_cohort_name &&& outcome_cohort_name older_than_60 &&& stroke     
#> 3 denominator_cohort_name &&& outcome_cohort_name younger_than_60 &&& stroke

This functions can be helpful when creating your own <summarised_result>.