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

defaults to package cache used by omop_vocab_table_save()

Usage

omop_concept(location = tools::R_user_dir("omopcept", which = "cache"))

oc(location = tools::R_user_dir("omopcept", which = "cache"))

Arguments

location

url of file location, defaults to package cache

Examples

# open reference, query and collect data to dataframe
omop_concept() |> head() |> dplyr::collect()
#> # A tibble: 6 × 10
#>   concept_id concept_name               domain_id vocabulary_id concept_class_id
#>        <int> <chr>                      <chr>     <chr>         <chr>           
#> 1   45756805 Pediatric Cardiology       Provider  ABMS          Physician Speci…
#> 2   45756804 Pediatric Anesthesiology   Provider  ABMS          Physician Speci…
#> 3   45756803 Pathology-Anatomic / Path… Provider  ABMS          Physician Speci…
#> 4   45756802 Pathology - Pediatric      Provider  ABMS          Physician Speci…
#> 5   45756801 Pathology - Molecular Gen… Provider  ABMS          Physician Speci…
#> 6   45756800 Microbiology               Provider  ABMS          Physician Speci…
#> # ℹ 5 more variables: standard_concept <chr>, concept_code <chr>,
#> #   valid_start_date <date>, valid_end_date <date>, invalid_reason <chr>
# count rows per vocab
omop_concept() |> dplyr::count(vocabulary_id, sort=TRUE) |> dplyr::collect()
#> # A tibble: 69 × 2
#>    vocabulary_id          n
#>    <chr>              <int>
#>  1 RxNorm Extension 2145325
#>  2 SNOMED           1079403
#>  3 dm+d              405431
#>  4 RxNorm            308709
#>  5 OMOP Genomic      289889
#>  6 LOINC             269552
#>  7 Read              108945
#>  8 ICDO3              64471
#>  9 UK Biobank         19337
#> 10 ICD10              16638
#> # ℹ 59 more rows

oc() |> head() |> dplyr::collect()
#> # A tibble: 6 × 10
#>   concept_id concept_name               domain_id vocabulary_id concept_class_id
#>        <int> <chr>                      <chr>     <chr>         <chr>           
#> 1   45756805 Pediatric Cardiology       Provider  ABMS          Physician Speci…
#> 2   45756804 Pediatric Anesthesiology   Provider  ABMS          Physician Speci…
#> 3   45756803 Pathology-Anatomic / Path… Provider  ABMS          Physician Speci…
#> 4   45756802 Pathology - Pediatric      Provider  ABMS          Physician Speci…
#> 5   45756801 Pathology - Molecular Gen… Provider  ABMS          Physician Speci…
#> 6   45756800 Microbiology               Provider  ABMS          Physician Speci…
#> # ℹ 5 more variables: standard_concept <chr>, concept_code <chr>,
#> #   valid_start_date <date>, valid_end_date <date>, invalid_reason <chr>