Data Cycle Changes — check

This function will compute row & patient counts in the specified tables for both the current data model version and a previous data model version in order to assess changes across data extractions. If you have previously executed this function, you have the option to point to a previous result set instead of recomputing the counts from the CDM.

Usage

check_dc(
  dc_tbl,
  omop_or_pcornet = "omop",
  prev_db_string = "v1",
  current_db_string = "v2",
  prev_ct_src = "cdm",
  prev_db = config("db_src"),
  prev_rslt_tbl = "dc_output",
  prev_rslt_schema = config("results_schema"),
  check_string = "dc"
)

Arguments

dc_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 CDM elements that should be compared between the current and previous data model versions. see ?dc_input_omop or ?dc_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

prev_db_string

string || defaults to v1

A string label indicating the previous CDM version

If prev_ct_src is set to result, make sure this matches the appropriate database label in the last set of results

current_db_string

string || defaults to v2

A string label indicating the current CDM version

prev_ct_src

string || defaults to cdm

A string indicating the source from which the counts from the previous data model should be extracted:

cdm will compute the counts based on the previous CDM tables
result will pull existing counts from a previous instance of check_dc output

prev_db

database connection || defaults to config('db_src')

A database connection object that will connect the function to the previous CDM instance or the defined result table

prev_rslt_tbl

string || defaults to dc_output

If prev_ct_src is set to result, this string should reflect name of the table where previous results are stored on the database

prev_rslt_schema

string || defaults to config('results_schema')

If prev_ct_src is set to result, this string should reflect name of the schema where previous results are stored on the database

check_string

string || defaults to dc

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

Value

This function will return a list with two dataframes:

dc_cts: A table containing the row and (where applicable) person counts for each CDM element specified by the user
dc_meta: A table containing the metadata associated with each check that appears in dc_cts

Examples

# First create input file with desired checks to be executed
# You can access examples for both OMOP & PCORnet here:
ndq::dc_input_omop
#> # A tibble: 26 × 8
#>    schema_current table_current schema_prev table_prev filter_logic check_domain
#>    <chr>          <chr>         <chr>       <chr>      <chr>        <chr>       
#>  1 cdm            person        cdm         person     NA           person      
#>  2 cdm            drug_exposure cdm         drug_expo… NA           drug_exposu…
#>  3 cdm            condition_oc… cdm         condition… NA           condition_o…
#>  4 cdm            device_expos… cdm         device_ex… NA           device_expo…
#>  5 cdm            visit_occurr… cdm         visit_occ… NA           visit_occur…
#>  6 cdm            condition_oc… cdm         condition… condition_t… condition_o…
#>  7 cdm            condition_oc… cdm         condition… condition_t… condition_i…
#>  8 cdm            condition_oc… cdm         condition… condition_t… condition_ed
#>  9 cdm            condition_oc… cdm         condition… condition_t… condition_o…
#> 10 cdm            condition_oc… cdm         condition… condition_t… condition_o…
#> # ℹ 16 more rows
#> # ℹ 2 more variables: check_id <chr>, check_description <chr>
ndq::dc_input_pcornet
#> # A tibble: 22 × 8
#>    schema_current table_current schema_prev table_prev filter_logic check_domain
#>    <chr>          <chr>         <chr>       <chr>      <chr>        <chr>       
#>  1 cdm            demographic   cdm         demograph… NA           person      
#>  2 cdm            diagnosis     cdm         diagnosis  NA           diagnosis   
#>  3 cdm            encounter     cdm         encounter  NA           encounter   
#>  4 cdm            diagnosis     cdm         diagnosis  enc_type %i… diagnosis_o…
#>  5 cdm            diagnosis     cdm         diagnosis  enc_type %i… diagnosis_i…
#>  6 cdm            diagnosis     cdm         diagnosis  enc_type %i… diagnosis_ed
#>  7 cdm            diagnosis     cdm         diagnosis  enc_type %i… diagnosis_o…
#>  8 cdm            diagnosis     cdm         diagnosis  enc_type %i… diagnosis_o…
#>  9 cdm            diagnosis     cdm         diagnosis  enc_type %i… diagnosis_i…
#> 10 cdm            diagnosis     cdm         diagnosis  enc_type %i… diagnosis_i…
#> # ℹ 12 more rows
#> # ℹ 2 more variables: check_id <chr>, check_description <chr>

# Use this as your input to the DC function

## If you would like to retrieve counts from a previous CDM instance,
## configure the function like so:
if (FALSE) { # \dontrun{
my_dc_rslt <- check_dc(dc_tbl = ndq::dc_input_omop,
                       omop_or_pcornet = 'omop',
                       prev_db_string = 'my_previous_data',
                       current_db_string = 'my_current_data',
                       prev_ct_src = 'cdm', ## looking in previous CDM instance
                       prev_db = my_prev_db_connection,
                       check_string = 'dc')
} # }

## If you would like to reference previously executed counts from a prior
## run of check_dc, configure the function like so:
if (FALSE) { # \dontrun{
my_dc_rslt <- check_dc(dc_tbl = ndq::dc_input_omop,
                       omop_or_pcornet = 'omop',
                       prev_db_string = 'my_previous_data',
                       current_db_string = 'my_current_data',
                       prev_ct_src = 'result', ## looking in previous results
                       prev_db = my_prev_db_connection,
                       prev_rslt_tbl = 'my_dc_rslt',
                       prev_rslt_schema = 'my_previous_schema',
                       check_string = 'dc')
} # }