Patient Facts per Visit Type

This function will loop through each site and visit type provided and execute the provided check function to compute facts stratified by visit type. Primarily intended for use in the Patient Facts module, but can be adapted for use elsewhere.

Usage

loop_through_visits(
  cohort_tbl,
  omop_or_pcornet,
  check_func,
  site_col,
  time = FALSE,
  visit_type_tbl,
  visit_tbl,
  site_list,
  visit_list = c("outpatient", "inpatient"),
  domain_tbl
)

Arguments

cohort_tbl

tabular input || required

The cohort to be used for data quality testing. This table should contain, at minimum:

site | character | the name(s) of institutions included in your cohort
person_id / patid | integer / character | the patient identifier
start_date | date | the start of the cohort period
end_date | date | the end of the cohort period

Note that the start and end dates included in this table will be used to limit the search window for the analyses in this module. It is recommended that this table has been passed through the prepare_cohort function as well.

omop_or_pcornet

string || required

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

omop: run the loop_through_visits_omop() function against an OMOP CDM instance
pcornet: run the loop_through_visits_pcnt() function against a PCORnet CDM instance

check_func

function || required

The function that should be executed within each time period in the loop. This parameter should be structured as the following, where cht is the cohort table and t is the input data for the function:

function(cht, t){check_function(param1 = cht, param2 = t, param3 = param3_input, ..., paramX = paramX_input)}

Make sure to include all parameters required for the original function where default values are not being used.

site_col

string || required

The name of the column in the cohort table that contains the site names. This will typically be either site or site_summ

time

boolean || defaults to FALSE

A boolean to indicate whether to execute a longitudinal analysis

visit_type_tbl

tabular input || required

A table that defines visit types of interest called in visit_list. This input should contain:

visit_concept_id / visit_detail_concept_id or enc_type | integer or character | the visit_(detail)_concept_id or enc_type that represents the visit type of interest (i.e. 9201 or IP)
visit_type | character | the string label to describe the visit type

visit_tbl

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

The CDM table with visit information (i.e. visit_occurrence or encounter)

site_list

list || required

A list of sites for which you would like to examine clinical facts. Can be one site (single-site) or multiple (multi-site). Ensure that all sites listed here exist in the provided cohort table.

visit_list

string or vector || defaults to c('outpatient', 'inpatient')

A string or vector of visit types by which the output should be stratified. Each visit type listed in this parameter should match an associated visit type defined in the visit_type_tbl

domain_tbl

tabular input || required

A table that defines the fact domains to be investigated in the analysis. This input should contain:

domain | character | a string label for the domain being examined (i.e. prescription drugs)
domain_tbl | character | the CDM table where information for this domain can be found (i.e. drug_exposure)
filter_logic | character | logic to be applied to the domain_tbl in order to achieve the definition of interest; should be written as if you were applying it in a dplyr::filter command in R

Value

This function will return a list of dataframes with the median number of facts per patient for all domains in domain_tbl, where each dataframe is specific to a given visit type from visit_list

Usage

Arguments

Value

Examples