Package index

All functions

check_c_id()

check c_id arg to omop_ancestors() and omop_descendants() TODO want to not export but couldn't get to work when not exported

dynamic_by()

Produces a list from string variables suitable for use in join expressions

get_plot_dims()

set plot dimensions from a string e.g. "A4" "A4l" etc.

omop_ancestors() oance()

find omop concept ancestors of one passed

omop_cdm_combine()

combine two omop cdm (Common Data Model) instances initially works on lists NOTE these omop_cdm* functions are for omop extracts rather than the concepts and may be best moved to another package TODO could be modified relatively easily to work on >2 extracts up to 9 :-) TODO get it to work on folder names by calling omop_cdm_read()

omop_cdm_read()

read all omop tables from a folder containing parquet or csv files into a list advantage that you don't need to specify table names NOTE these omop_cdm* functions are for omop extracts rather than the concepts and may be best moved to another package

omop_cdm_table_read()

read single omop table from parquet or csv file NOTE these omop_cdm* functions are for omop extracts rather than the concepts and may be best moved to another package

omop_check_names() ochecknames()

check that concept names and ids match in a passed table

omop_codes() ocodes()

string search of concept_code in omop concepts table

omop_concept() oc()

open a reference to omop concept file(s) from provided location

omop_concept_ancestor() oca()

open a reference to omop concept ancestor file from provided location

omop_concept_ancestor_fields() ocafields()

field names of omop concept ancestor table

omop_concept_fields() ocfields()

field names of omop concept table

omop_concept_relationship() ocr()

open a reference to omop concept relationship file from provided location

omop_concept_relationship_fields() ocrfields()

field names of omop concept relationship table

omop_descendants() odesc()

find omop concept descendants of one passed

omop_domain()

return domain_id s for concept_id s

omop_drug_lookup_create()

create a lookup table from drug concepts in vocabs RxNorm and/or RxNorm Extension to ATC drug classes

omop_filter_concepts()

filter omop concepts by standard attributes

omop_graph() omgr()

graph omop hierarchy accepts output from either omop_ancestors(), omop_descendants() or omop_relations

omop_graph_calc()

calculate nodes and edges from omop hierarchy accepts output from either omop_ancestors(), omop_descendants() or omop_relations used by omop_graph(), you are only likely to want to use on it's own to a) separate calculation & visualisation so that you can join attributes for visualisation b) pass the nodes and edges to a different graph rendering package

omop_graph_vis()

visualise graph of omop hierarchy called by omop_graph()

omop_id() oid()

query concept records by concept_id from omop concepts table

omop_join_name() ojoin()

join omop concept name and other concept columns onto a dataframe with a *_concept_id column

omop_join_name_all() ojoinall()

join omop concept names onto all *_concept_id columns in a dataframe

omop_names() onames()

string search of concept_name in omop concepts table

omop_relations() orels()

recursively extract omop concept relations of one passed - immediate relations with indication of relationship

omop_relations1step()

find immediate omop concept relations of one passed ADVISORY instead to use omop_relations() with default nsteps=1 arg.

omop_relations_multiple()

extract omop concept relations of a vector of concept_ids - immediate relations with indication of relationship

omop_relations_names() ornames()

string search of concepts by name in the CONCEPT_RELATIONSHIP table

omop_vocab_table_save()

save omop vocabulary parquet file from provided location to local package cache

omop_vocabs_preprocess()

read in omop vocabulary csvs downloaded from Athena, preprocess and write out as binary parquet files for better performance.

omopfreqconceptclass() ofreqcc()

count freq of values in an omop field EXPERIMENTAL may change

omopfreqdomain() ofreqd()

count freq of values in an omop field EXPERIMENTAL may change

omopfreqrelationship() ofreqr()

count freq of values in an omop field EXPERIMENTAL may change

omopfreqvocabulary() ofreqv()

count freq of values in an omop field EXPERIMENTAL may change

pipe_if()

conditionally apply a pipe