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string search of concept_code in omop concepts table

Source: R/omop_codes.R
omop_codes.Rd

string search of concept_code in omop concepts table

super short name func to search concepts by concept_code

Usage

omop_codes(
  findstring,
  ignore_case = TRUE,
  exact = TRUE,
  fixed = FALSE,
  c_ids = NULL,
  d_ids = NULL,
  v_ids = NULL,
  cc_ids = NULL,
  standard = NULL,
  messages = TRUE
)

ocodes(
  findstring,
  ignore_case = TRUE,
  exact = TRUE,
  fixed = FALSE,
  c_ids = NULL,
  d_ids = NULL,
  v_ids = NULL,
  cc_ids = NULL,
  standard = NULL,
  messages = TRUE
)

Arguments

findstring

string to search for or regex

ignore_case

ignore case in string comparison, default TRUE

exact

TRUE for exact string search, "start" for exact start, "end" for exact end, default=TRUE because user likely to look for whole code

fixed

default FALSE allows regex,TRUE uses grepl exact matching

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

messages

whether to print info messages, default=TRUE

Examples

omop_codes("81752-8")
#> returning 1 concepts
#> # A tibble: 1 × 10
#>   concept_id concept_name               domain_id vocabulary_id concept_class_id
#>        <int> <chr>                      <chr>     <chr>         <chr>           
#> 1   21494134 Chromosome region 1q21 du… Measurem… LOINC         Lab Test        
#> # ℹ 5 more variables: standard_concept <chr>, concept_code <chr>,
#> #   valid_start_date <date>, valid_end_date <date>, invalid_reason <chr>
omop_codes("AJCC/UICC-Stage",exact=FALSE)
#> returning 720 concepts
#> # A tibble: 720 × 10
#>    concept_id concept_name            domain_id   vocabulary_id concept_class_id
#>         <int> <chr>                   <chr>       <chr>         <chr>           
#>  1    1635658 AJCC/UICC 6th Stage 0   Measurement Cancer Modif… Staging/Grading 
#>  2    1633642 AJCC/UICC 6th Stage 0a  Measurement Cancer Modif… Staging/Grading 
#>  3    1635189 AJCC/UICC 6th Stage 0is Measurement Cancer Modif… Staging/Grading 
#>  4    1634888 AJCC/UICC 6th Stage 1   Measurement Cancer Modif… Staging/Grading 
#>  5    1634027 AJCC/UICC 6th Stage 1A  Measurement Cancer Modif… Staging/Grading 
#>  6    1633734 AJCC/UICC 6th Stage 1A1 Measurement Cancer Modif… Staging/Grading 
#>  7    1634553 AJCC/UICC 6th Stage 1A2 Measurement Cancer Modif… Staging/Grading 
#>  8    1634171 AJCC/UICC 6th Stage 1A3 Measurement Cancer Modif… Staging/Grading 
#>  9    1634604 AJCC/UICC 6th Stage 1B  Measurement Cancer Modif… Staging/Grading 
#> 10    1635608 AJCC/UICC 6th Stage 1B1 Measurement Cancer Modif… Staging/Grading 
#> # ℹ 710 more rows
#> # ℹ 5 more variables: standard_concept <chr>, concept_code <chr>,
#> #   valid_start_date <date>, valid_end_date <date>, invalid_reason <chr>
ocodes("AJCC/UICC-Stage")
#> returning 0 concepts
#> # A tibble: 0 × 10
#> # ℹ 10 variables: concept_id <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>