Get class(es) in an ontology

get_class(..., regex = FALSE, external = FALSE, ontology = NULL)

Arguments

...: combination of column name and value to filter that column by. The value to filter by can be provided as regular expression, if regex = TRUE.
regex: logical(1)
whether or not the value in ... shall be matched in full, or whether any partial match should be returned.
external: logical(1)
whether or not the external classes (TRUE), or the harmonized classes should be returned (FALSE, default).
ontology: ontology(1)
either a path where the ontology is stored, or an already loaded ontology.

Value

A table of the class(es) in the ontology according to the values in ...

Examples

ontoDir <- system.file("extdata", "crops.rds", package = "ontologics")
onto <- load_ontology(path = ontoDir)

# exact classes from a loaded ontology ...
get_class(label = "class", ontology = onto)
#> # A tibble: 1 × 8
#>   label id     has_broader description        has_close_match has_narrower_match
#>   <chr> <chr>  <chr>       <chr>              <chr>           <chr>             
#> 1 class .xx.xx group       Classes of crop o… NA              NA                
#> # ℹ 2 more variables: has_broader_match <chr>, has_exact_match <chr>

# ... or one stored on the harddisc
get_class(id = ".xx.xx", ontology = ontoDir)
#> # A tibble: 1 × 8
#>   label id     has_broader description        has_close_match has_narrower_match
#>   <chr> <chr>  <chr>       <chr>              <chr>           <chr>             
#> 1 class .xx.xx group       Classes of crop o… NA              NA                
#> # ℹ 2 more variables: has_broader_match <chr>, has_exact_match <chr>

# use regular expressions ...
get_class(label = "ro", regex = TRUE, ontology = onto)
#> # A tibble: 2 × 8
#>   label id        has_broader description     has_close_match has_narrower_match
#>   <chr> <chr>     <chr>       <chr>           <chr>           <chr>             
#> 1 group .xx       NA          Groups of crop… NA              NA                
#> 2 crop  .xx.xx.xx class       Crop or livest… NA              NA                
#> # ℹ 2 more variables: has_broader_match <chr>, has_exact_match <chr>

# get all sources
get_class(ontology = onto)
#> # A tibble: 3 × 8
#>   label id        has_broader description     has_close_match has_narrower_match
#>   <chr> <chr>     <chr>       <chr>           <chr>           <chr>             
#> 1 group .xx       NA          Groups of crop… NA              NA                
#> 2 class .xx.xx    group       Classes of cro… NA              NA                
#> 3 crop  .xx.xx.xx class       Crop or livest… NA              NA                
#> # ℹ 2 more variables: has_broader_match <chr>, has_exact_match <chr>