Sensitivity to Selection Criteria – OMOP

Sensitivity to Selection Criteria – OMOP

Usage

ssc_process_omop(
  base_cohort,
  alt_cohorts,
  multi_or_single_site = "single",
  anomaly_or_exploratory = "exploratory",
  person_tbl = cdm_tbl("person"),
  visit_tbl = cdm_tbl("visit_occurrence"),
  provider_tbl = cdm_tbl("provider"),
  care_site_tbl = cdm_tbl("care_site"),
  demographic_mappings = sensitivityselectioncriteria::ssc_omop_demographics,
  specialty_concepts = NULL,
  outcome_concepts = NULL,
  domain_tbl = sensitivityselectioncriteria::ssc_domain_file,
  domain_select = sensitivityselectioncriteria::ssc_domain_file %>% distinct(domain)
    %>% pull()
)

Arguments

base_cohort

a dataframe including all patients who meet the base cohort definition should have the columns site | person_id | start_date | end_date

alt_cohorts

a list or named list of dataframes with patients meeting alternative cohort definitions; if names are not provided, numbers will be assigned to each cohort definition for labelling purposes

multi_or_single_site

direction to determine what kind of check to run string that is either multi or single

anomaly_or_exploratory

direction to determine what kind of check to run; a string that is either anomaly or exploratory

person_tbl

CDM person table

visit_tbl

CDM visit_occurrence table

provider_tbl

the CDM table with provider & provider specialty information only used if specialty_concepts are provided if provider_tbl & care_site_tbl are both not null, provider specialty is prioritized

care_site_tbl

the CDM table with care site / facility & care site / facility specialty information only used if specialty_concepts are provided if provider_tbl & care_site_tbl are both not null, provider specialty is prioritized

demographic_mappings

table defining how demographic elements should be defined if NULL, the default demographic mappings for the CDM will be used (ssc_omop_demographics) otherwise, the user provided table will be used

specialty_concepts

a concept set with provider specialty concepts of interest to be used to identify specialty visits

outcome_concepts

a concept set with the following columns: concept_id | concept_code | concept_name | vocabulary_id | variable | domain

                    where domain matches a domain listed in the `domain_defs` table

domain_tbl

a table with domain definitions with the following columns: domain, domain_tbl, concept_field, date_field, filter_logic

domain_select

a vector of domain names that should be used in the computation of facts per domain per year of follow up

                 this vector does NOT need to include domains used in the computation for
                 outcomes, as those will be accessed from the table directly

Value

a dataframe summarizing fact and demographic distributions for each of the provided cohort definitions; for both anomaly detection outputs, the standardized mean difference between the base cohort and each alternate cohort definition is computed for each of the variables of interest