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Valueset Conformance

Source: R/valueset_conformance.R
check_vs.Rd

This function will intake a limited valueset that is expected to make up the entire contents of a field (minus the specified null_values) and identify if any non-permitted values exist in the field (and how often).

Usage

check_vs(
  vs_tbl,
  omop_or_pcornet = "omop",
  concept_tbl = NULL,
  null_values = c(44814650L, 0L, 44814653L, 44814649L),
  check_string = "vs"
)

Arguments

vs_tbl

tabular input || required

The primary input table that contains descriptive information about the checks to be executed by the function. It should include definitions for the fields and associated valuesets of interest. see ?vs_input_omop or ?vs_input_pcornet for examples of the input structure

omop_or_pcornet

omop_or_pcornet string || defaults to omop

A string, either omop or pcornet, indicating the CDM format of the data

concept_tbl

tabular input || defaults to NULL

An optional parameter used to define a vocabulary table with concept definitions (for example, the OHDSI concept table). If left NULL, the concepts as they exist in the fact table will be returned to the user.

null_values

string / vector || defaults to 44814650, 0, 44814653, & 44814649

A string or vector listing the concept(s) that indicate a NULL value, which will be excluding when assessing for the presence of values not present in the valueset.

check_string

string || defaults to vs

An abbreviated identifier that will be used to label all output from this module

Value

This function will return a dataframe with summary information about each value that appears in the data but does not comply with the valueset definition. If no violations are identified for a particular check, a placeholder row will dummy information will be inserted instead.

Examples

# First create input file with desired checks to be executed
# You can access examples for both OMOP & PCORnet here:
ndq::vs_input_omop
#> # A tibble: 2 × 6
#>   check_id    schema table  valueset_name      concept_field        filter_logic
#>   <chr>       <chr>  <chr>  <chr>              <chr>                <lgl>       
#> 1 pd_race_cid cdm    person valueset_race      race_concept_id      NA          
#> 2 pd_eth_cid  cdm    person valueset_ethnicity ethnicity_concept_id NA          
ndq::vs_input_pcornet
#> # A tibble: 2 × 7
#>   check_id    schema table       valueset_name    concept_field vocabulary_field
#>   <chr>       <chr>  <chr>       <chr>            <chr>         <lgl>           
#> 1 pd_race_cid cdm    demographic valueset_race    race          NA              
#> 2 pd_eth_cid  cdm    demographic valueset_ethnic… hispanic      NA              
#> # ℹ 1 more variable: filter_logic <lgl>

# Use this as your input to the VS function
if (FALSE) { # \dontrun{
my_vs_rslt <- check_vs(vs_tbl = ndq::vs_input_omop,
                       omop_or_pcornet = 'omop',
                       concept_tbl = vocabulary_tbl("concept"), ## points to OHDSI concept table
                       null_values = c(44814650L,0L,
                                       44814653L,44814649L), # ignored illegal values
                       check_string = 'vs')
} # }