Date Plausibility

This function will iterate through the provided input table to identify the proportion of rows in each fact type that have an implausible date. Implausibility is defined as a date that falls before the associated visit start date, after the associated visit end date, before the patient's birth date, or after the patient's death date + the defined buffer period.

Usage

check_dp(
  dp_tbl,
  omop_or_pcornet = "omop",
  visit_tbl = cdm_tbl("visit_occurrence"),
  dob_tbl = cdm_tbl("person"),
  death_tbl = cdm_tbl("death"),
  post_death_buffer = 30L,
  check_string = "dp"
)

Arguments

dp_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 clinical fact types that should be evaluated for date plausibility. see ?dp_input_omop or ?dp_input_pcornet for examples of the input structure

omop_or_pcornet

string || defaults to omop

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

visit_tbl

tabular input || defaults to cdm_tbl(visit_occurrence)

A table with visit information, including identifiers that can link back to facts and start & end dates. This argument will most likely be the visit_occurrence table for OMOP or the encounter table for PCORnet. Custom tables with specific visit subsets (i.e. a table with only nephrology specialist visits) can also be provided.

dob_tbl

tabular input || defaults to cdm_tbl('person')

A table with patient identifiers that can link back to facts and birth dates. This argument will most likely be the person table for OMOP or the demographic table for PCORnet.

death_tbl

tabular input || defaults to cdm_tbl('death')

A table with patient identifiers that can link back to facts and death dates. This argument will most likely be the death table for OMOP or the death table for PCORnet.

post_death_buffer

integer || defaults to 30

An integer reflecting the number of days after death where the function should begin counting facts as implausible. This allows the user to capture autopsy results or other expected post-death facts to occur within the plausible window.

check_string

string || defaults to dp

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

Value

This function will return a table with the count & proportion of rows with an implausible date value, with one column for each of the 3 implausibility definitions. These will indicate the proportion of facts falling before the associated visit start date, after the associated visit end date, or before the patient birth date

Examples

# First create input file with desired checks to be executed
# You can access examples for both OMOP & PCORnet here:
ndq::dp_input_omop
#> # A tibble: 3 × 6
#>   check_id check_description schema table                date_field filter_logic
#>   <chr>    <chr>             <chr>  <chr>                <chr>      <lgl>       
#> 1 pr       procedures        cdm    procedure_occurrence procedure… NA          
#> 2 co       conditions        cdm    condition_occurrence condition… NA          
#> 3 dr       drugs             cdm    drug_exposure        drug_expo… NA          
ndq::dp_input_pcornet
#> # A tibble: 4 × 6
#>   check_id check_description         schema table       date_field  filter_logic
#>   <chr>    <chr>                     <chr>  <chr>       <chr>       <lgl>       
#> 1 pr       procedures                cdm    procedures  px_date     NA          
#> 2 co       conditions                cdm    diagnosis   admit_date  NA          
#> 3 rx       prescribed drugs          cdm    prescribing rx_start_d… NA          
#> 4 admin    inpatient administrations cdm    med_admin   med_admin_… NA          

# Use this as your input to the DP function
if (FALSE) { # \dontrun{
my_dp_rslt <- check_dp(dp_tbl = ndq::dp_input_omop,
                       omop_or_pcornet = 'omop',
                       visit_tbl = cdm_tbl('visit_occurrence'), ## table with visit/encounter dates
                       dob_tbl = cdm_tbl('person'), ## table with dates of birth
                       check_string = 'dp')
} # }