Changelog

Source: NEWS.md

omopcept 0.0.6.2 2025-03-05 DEV version

• add arg nodetxtvar to omop_graph() to allow node label to be set to any column
• issue fixed in omop_cdm_read() that ID columns being read in as double not integer as needed for later joins
• omop_graph() working on raw relations table e.g. omop_concept_relationship() |> head(50) |> collect() |> omop_graph(nodecolourvar="relationship_id", nodetxtsize=3)

omopcept 0.0.6.1 2024-12-18

• add helper functions omopfreq*() for counting frequency of values in domain conceptclass relationship or vocabulary
• split out omop_graph_calc() for separate calculation of nodes & edges, either a) to enable other data to be joined on (e.g. num records) for visualisation or b) so nodes & edges can be passed to an alternative renderer (as yet unknown)
  
• split out omop_graph_vis() to enable other data to be joined on (e.g. num records) for visualisation
• omop_graph() gets separate args nodesizevar and nodesize so size can be set by a variable column and/or a sizing param
• add omop_drug_lookup_create() to create a lookup table from drugs in RxNorm or RxNorm Extension to ATC drug classes at all levels
• update omop vocabs & default location for pre-processed ones moved to Github

omopcept 0.0.6.0 2024-09-26

BREAKING CHANGES

To make use of omop_relations() easier and more intuitive * omop_relations_recursive() arg num_recurse changed to nsteps * omop_relations_recursive() renamed to omop_relations() which in turn renamed to omop_relations1step() * omop_relations() now optionally adds column step for plot colouring, replacing recurse_level

non-breaking changes

• omop_graph() gets args caption captionsize captionjust captioncolour
• repository moved from andysouth to SAFEHR-data
• issue fixed in omop_relations & omop_graph() with colouring plots by recurse_level
• omop_grap() gets nodesize arg (NOT functioning yet)
• omop_grap() gets canvas arg to set plot size, one of “A4”,“A4l”,“A3”,“A3l”,“A2”,“A2l”,“A1”,“A1l”,“A0”,“A0l”,“slide”,“slidehalf”

omopcept 0.0.5.9 2024-07-24

• omop_graph() gets args palettedirection nodetxtnudgex nodetxtnudgey titlejust backcolour

• omop_relations_recursive() gets arg add_recurse_column to add a column with recurse_level that can be used to colour

omopcept 0.0.5.8 2024-07-09

• bugfix in omop_cdm_combine(), defend against ‘non-numeric argument to binary operator’

omopcept 0.0.5.7 2024-06-12

• omop_cdm_combine() outputs msg of uniquefied fields

omopcept 0.0.5.6 2024-06-11

• omop_cdm_combine() refactored to make all IDs unique that it didn’t before
• omop_relations() gets names2avoid arg
• omop_graph() gets args nodealpha edgealpha edgewidth

omopcept 0.0.5.5 2024-05-10

• omop_cdm_combine() gets make_care_site_id_unique & add_care_site_name_to_person_id_tables arg

omopcept 0.0.5.4 2024-05-09

• omop_cdm_combine() gets make_person_id_unique arg

omopcept 0.0.5.3 2024-05-08

• omop_graph() gets args nodetxtangle legendshow
• read in omop cdm instance with omop_cdm_read() & omop_cdm_table_read()
• combine cdm instances with omop_cdm_combine()

omopcept 0.0.5.2 2024-03-13

• add to omop_codes() exact & fixed args, e.g. easier to search for loinc codes

omopcept 0.0.5.1 2024-03-01

• omop_join_name() protects against concept_id columns that are not integer

omopcept 0.0.5.0 2024-01-30

• started vignette on hierarchy, access with vignette("hierarchy-for-blood-counts")
• omop_relations() add arg itself whether to include relations to concept itself, default=FALSE
• omop_names() add an arg fixed (default=FALSE) that when true matches string as-is
• omop_domain() return domain_id s for concept_id s
• omop_id() now accepts multiple ids and can specify columns to return + a bit faster
• omop_concept_fields() omop_concept_ancestor_fields() omop_concept_relationship_fields() to get column names of omop tables, short name equivalents ocfields() ocafields() ocrfields()
• omop_join_name() made much faster by not using copy=true in join
• BREAKING CHANGE omop_join_name() & omop_join_name_all() refactor and simplify column args
• omop_join_name() arg columns=“all” to join all concept table columns

omopcept 0.0.4.0 2024-01-08

• fix bug in omop_join_names_all() - Error in class(df) == “list”

omopcept 0.0.3.0 2024-01-05

• omop_names() added argument exact= TRUE for exact string search, “start” for exact start, “end” for exact end
• omop_check_names() to check that concept names and ids match in a passed table
• fix bug in omop_join_name_all() to cope with “domain_concept_id_1” from FACT_RELATIONSHIP
• omop_join_name_all() now copes with a list of multiple tables
• update readme about vocabulary download options

omopcept 0.0.2.0 2023-12-27

• graph pkgs igraph,tidygraph,ggraph moved from imports to suggests
• num_recurse loop start at 1 rather than 0 in omop_relations_multiple() & omop_relations_recursive()

omopcept 0.0.1.1 2023-11-15

• omop_vocabs_preprocess() read in omop vocab csvs, preprocess to parquet save in package cache
• omop_vocab_table_save() renamed from omop_download()
• omop_graph() auto file naming
• omop_relations() add r_ids arg to filter by relationship_id e.g. c('Is a','Subsumes')
• omop_relations_recursive() added to recursively extract relations of a single concept

omopcept 0.0.1.0 2023-10-14

• omop_graph() working for visualising omop hierarchy with ggraph
• domain, vocabulary, concept_code & concept_class optional args added to omop_join_name() & omop_join_name_all() to be able to also join these columns
• namefull optional arg added to omop_join_name() to cope with e.g. concept_id_2 in omop_join_name_all()
• omop_relations() and omop_concept_relationship() for getting more info about immediate neighbour relationships
• bugfix, omop_ancestors() & omop_decsendants() were not filtering domin, separation etc., when concept_id not specified
• option for NULL c_id to omop_descendants() and omop_ancestors(), returns all concepts within other filters

omopcept 0.0.0.9005 2023-08-08

• optional itself argument (default FALSE) to omop_descendants() and omop_ancestors()
• optional separation argument (default NULL) to omop_descendants() and omop_ancestors() filters on min_levels_of_separation e.g. c(1,2)

omopcept 0.0.0.9003 2023-06-14

• omop_join_name_all()
• shortname copies of functions for interactive use ojoin() ojoinall()
• generalised omop_download() to get other omop tables
• omop_descendants() function to query omop hierarchy
• omop_ancestors()
• shortname function copies of above. odesc() and oance()
• added optional messages argument to query functions

omopcept 0.0.0.9002 2023-05-15

• renamed package to omopcept
• renamed package functions to make clearer, most start omop_*()
• omop_id() to search ids
• supershort name copies of functions for interactive use oid() onames() ocodes()