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find omop concept ancestors of one passed

Source: R/omop_ancestors.R
omop_ancestors.Rd

find omop concept ancestors of one passed

super short name func to find ancestors

Usage

omop_ancestors(
  c_id = NULL,
  c_ids = NULL,
  d_ids = NULL,
  v_ids = NULL,
  cc_ids = NULL,
  standard = NULL,
  separation = NULL,
  itself = FALSE,
  messages = TRUE
)

oance(
  c_id = NULL,
  c_ids = NULL,
  d_ids = NULL,
  v_ids = NULL,
  cc_ids = NULL,
  standard = NULL,
  separation = NULL,
  itself = FALSE,
  messages = TRUE
)

Arguments

c_id

single omop concept_id or exact concept_name to get ancestors of, default NULL returns all

c_ids

one or more concept_id to filter by, default NULL for all

d_ids

one or more domain_id to filter by, default NULL for all

v_ids

one or more vocabulary_id to filter by, default NULL for all

cc_ids

one or more concept_class_id to filter by, default NULL for all

standard

one or more standard_concept to filter by, default NULL for all, S,C

separation

levels of separation to filter by, default NULL for all

itself

whether to include passed concept in returned table (min_levels_of_separation==0), default=FALSE

messages

whether to print info messages, default=TRUE

Value

a dataframe of concepts and attributes

Examples

omop_ancestors(1633308)
#> querying concept ancestors of: AJCC/UICC Stage 4 - may take a few seconds
#> Warning: downloading a subset of omop vocab files, pre-processed.
#> If you want to make sure you have the vocabs you need, download from Athena, save locally & call `omop_vocabs_preprocess()`
#> downloading concept_ancestor file, may take a few minutes, this only needs to be repeated if the package is re-installed
#> returning 2 concepts
#> # A tibble: 2 × 14
#>   concept_id descendant_concept_id descendant_concept_n…¹ min_levels_of_separa…²
#>        <int>                 <int> <chr>                                   <int>
#> 1     734320               1633308 AJCC/UICC Stage 4                           1
#> 2    1633987               1633308 AJCC/UICC Stage 4                           1
#> # ℹ abbreviated names: ¹​descendant_concept_name, ²​min_levels_of_separation
#> # ℹ 10 more variables: max_levels_of_separation <int>, concept_name <chr>,
#> #   domain_id <chr>, vocabulary_id <chr>, concept_class_id <chr>,
#> #   standard_concept <chr>, concept_code <chr>, valid_start_date <date>,
#> #   valid_end_date <date>, invalid_reason <chr>
#omop_ancestors("Non-invasive blood pressure")
#omop_ancestors("Non-invasive blood pressure",separation=c(1,2))
#epoch_ance <- omop_ancestors("EPOCH, dose-escalated")
#no filtering by ancestors
#cman <- omop_ancestors(v_ids="Cancer Modifier")
# because of R argument matching, you can just use the first unique letters of
# arguments e.g. v for v_ids, cc for cc_ids
chemodrugs <- odesc("Cytotoxic chemotherapeutic", v="HemOnc", d="Regimen")
#> querying concept descendants of: Cytotoxic chemotherapeutic - may take a few seconds
#> returning 357 concepts