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Patient Facts per Visit Type – OMOP

Source: R/fact_loops.R
loop_through_visits_omop.Rd

Patient Facts per Visit Type – OMOP

Usage

loop_through_visits_omop(
  cohort_tbl,
  check_func,
  site_col,
  time = FALSE,
  visit_type_tbl,
  visit_tbl = cdm_tbl("visit_occurrence"),
  site_list,
  visit_list = c("inpatient", "outpatient"),
  domain_tbl
)

Arguments

cohort_tbl

a table with members of the cohort that has been run through prepare_cohort()

check_func

the base function for the check that needs to be executed across time; this argument should be structured as the following, where cht is the cohort and t is the input data for the function:

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

              all parameters for the base check function should be included if any defaults are not being
              used

site_col

the column in the data where the site variable can be found

time

a logical indicating whether the analysis is being conducted longitudinally

visit_type_tbl

a table that defines available visit types that are called in visit_types.:

  • visit_concept_id / visit_detail_concept_id: the visit_(detail)_concept_id that represents the visit type of interest (i.e. 9201 or IP)

  • visit_type: the string label to describe the visit type; this label can be used multiple times within the file if multiple visit_concept_ids/enc_types represent the visit type

visit_tbl

the cdm visit_occurrence or visit_detail tbl

site_list

the sites to iterate through

visit_list

the list of visit types to iterate through

domain_tbl

a table that defines the domains where facts should be identified with the following columns:

  • domain: a string label for the domain being examined (i.e. prescription drugs)

  • domain_tbl: the CDM table where information for this domain can be found (i.e. drug_exposure)

  • filter_logic: an optional string to be parsed as logic to filter the domain_tbl as needed to best represent the domain

Value

a list of dataframes with 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