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Retrieve parent or child codes

Source: R/children_parents.R
parent_child_retrieval.Rd

Returns immediate or transitive parent or child codes for the given codes by traversing the relationship graph.

Usage

CHILDREN(
  ...,
  type = getOption("codeminer.code_type"),
  lookup_version = getOption("codeminer.lookup_version", default = "latest"),
  relationship_version = getOption("codeminer.relationship_version", default = "latest"),
  preferred_description_only = TRUE,
  col_filters = "default"
)

PARENTS(
  ...,
  type = getOption("codeminer.code_type"),
  lookup_version = getOption("codeminer.lookup_version", default = "latest"),
  relationship_version = getOption("codeminer.relationship_version", default = "latest"),
  preferred_description_only = TRUE,
  col_filters = "default"
)

N_CHILDREN(
  ...,
  depth = 1,
  type = getOption("codeminer.code_type"),
  lookup_version = getOption("codeminer.lookup_version", default = "latest"),
  relationship_version = getOption("codeminer.relationship_version", default = "latest"),
  preferred_description_only = TRUE,
  col_filters = "default",
  call = rlang::caller_env()
)

N_PARENTS(
  ...,
  depth = 1,
  type = getOption("codeminer.code_type"),
  lookup_version = getOption("codeminer.lookup_version", default = "latest"),
  relationship_version = getOption("codeminer.relationship_version", default = "latest"),
  preferred_description_only = TRUE,
  col_filters = "default",
  call = rlang::caller_env()
)

Arguments

...

Codes to start from. Supports flexible input like CODES().

type

Code type (character).

lookup_version

Lookup table version (character).

relationship_version

Relationship table version (character).

preferred_description_only

Logical. If TRUE, return only preferred descriptions.

col_filters

Column filters to apply. See CODES() for details.

depth

Integer. Maximum number of steps to traverse. Use Inf for transitive closure (all ancestors/descendants). Only used by N_PARENTS() and N_CHILDREN().

call

For internal use only. The execution environment of a currently running function. Used for error reporting. Users should not need to set this parameter.

Value

A data frame of codes and descriptions.

Details

Use N_PARENTS()/N_CHILDREN() for immediate relationships (one step), and PARENTS()/CHILDREN() for transitive closure (all reachable ancestors/descendants).

See also

Other Code relationships: attributes(), relationship_types

Examples

create_dummy_database()
#> ✔ Dummy database ready to use!
#> ℹ To reconnect to your previous database:
#>   `Sys.setenv(CODEMINER_DB_PATH = "/tmp/Rtmp7fg0Bd/file1c7d4a751f5e.duckdb")`
#>   `codeminer_connect()`
PARENTS("E10", "E11", type = "ICD-10")
#> ℹ Using 'UKB v4' as latest version
#> ℹ Using 'UKB v4' as latest version
#> <codeminer_codelist>: 2 codes
#> Code type: "ICD-10"
#> 
#> # A tibble: 2 × 3
#>   code  description              code_type
#>   <chr> <chr>                    <chr>    
#> 1 E10   Type 1 diabetes mellitus ICD-10   
#> 2 E11   Type 2 diabetes mellitus ICD-10   
CHILDREN("E10", "E11", type = "ICD-10")
#> <codeminer_codelist>: 22 codes
#> Code type: "ICD-10"
#> 
#> # A tibble: 22 × 3
#>    code  description                                                   code_type
#>    <chr> <chr>                                                         <chr>    
#>  1 E10   Type 1 diabetes mellitus                                      ICD-10   
#>  2 E100  Type 1 diabetes mellitus With coma                            ICD-10   
#>  3 E101  Type 1 diabetes mellitus With ketoacidosis                    ICD-10   
#>  4 E102  Type 1 diabetes mellitus With renal complications             ICD-10   
#>  5 E103  Type 1 diabetes mellitus With ophthalmic complications        ICD-10   
#>  6 E104  Type 1 diabetes mellitus With neurological complications      ICD-10   
#>  7 E105  Type 1 diabetes mellitus With peripheral circulatory complic… ICD-10   
#>  8 E106  Type 1 diabetes mellitus With other specified complications   ICD-10   
#>  9 E107  Type 1 diabetes mellitus With multiple complications          ICD-10   
#> 10 E108  Type 1 diabetes mellitus With unspecified complications       ICD-10   
#> # ℹ 12 more rows
N_PARENTS("E10", "E11", type = "ICD-10")
#> <codeminer_codelist>: 2 codes
#> Code type: "ICD-10"
#> 
#> # A tibble: 2 × 3
#>   code  description              code_type
#>   <chr> <chr>                    <chr>    
#> 1 E10   Type 1 diabetes mellitus ICD-10   
#> 2 E11   Type 2 diabetes mellitus ICD-10   
N_CHILDREN("E10", "E11", type = "ICD-10")
#> <codeminer_codelist>: 22 codes
#> Code type: "ICD-10"
#> 
#> # A tibble: 22 × 3
#>    code  description                                                   code_type
#>    <chr> <chr>                                                         <chr>    
#>  1 E10   Type 1 diabetes mellitus                                      ICD-10   
#>  2 E100  Type 1 diabetes mellitus With coma                            ICD-10   
#>  3 E101  Type 1 diabetes mellitus With ketoacidosis                    ICD-10   
#>  4 E102  Type 1 diabetes mellitus With renal complications             ICD-10   
#>  5 E103  Type 1 diabetes mellitus With ophthalmic complications        ICD-10   
#>  6 E104  Type 1 diabetes mellitus With neurological complications      ICD-10   
#>  7 E105  Type 1 diabetes mellitus With peripheral circulatory complic… ICD-10   
#>  8 E106  Type 1 diabetes mellitus With other specified complications   ICD-10   
#>  9 E107  Type 1 diabetes mellitus With multiple complications          ICD-10   
#> 10 E108  Type 1 diabetes mellitus With unspecified complications       ICD-10   
#> # ℹ 12 more rows