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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(
  codes,
  code_type = getOption("codeminer.code_type"),
  lookup_version = getOption("codeminer.lookup_version", default = "latest"),
  relationship_version = getOption("codeminer.relationship_version", default = "latest"),
  codes_only = FALSE,
  preferred_description_only = TRUE
)

PARENTS(
  codes,
  code_type = getOption("codeminer.code_type"),
  lookup_version = getOption("codeminer.lookup_version", default = "latest"),
  relationship_version = getOption("codeminer.relationship_version", default = "latest"),
  codes_only = FALSE,
  preferred_description_only = TRUE
)

N_CHILDREN(
  codes,
  depth = 1,
  code_type = getOption("codeminer.code_type"),
  lookup_version = getOption("codeminer.lookup_version", default = "latest"),
  relationship_version = getOption("codeminer.relationship_version", default = "latest"),
  codes_only = FALSE,
  preferred_description_only = TRUE
)

N_PARENTS(
  codes,
  depth = 1,
  code_type = getOption("codeminer.code_type"),
  lookup_version = getOption("codeminer.lookup_version", default = "latest"),
  relationship_version = getOption("codeminer.relationship_version", default = "latest"),
  codes_only = FALSE,
  preferred_description_only = TRUE
)

Arguments

codes

Character vector of codes to start from.

code_type

Code type (character).

lookup_version

Lookup table version (character).

relationship_version

Relationship table version (character).

codes_only

Logical. If TRUE, return only unique codes. If FALSE, return a data frame with code and description.

preferred_description_only

Logical. If TRUE, return only preferred descriptions.

depth

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

Value

A data frame of codes and descriptions, or a character vector if codes_only = TRUE.

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()
#> Creating new database at /tmp/RtmpRK6Py7/file1bd366436077.duckdb
#> Reading 17 selected tables from UKB Resource 592
#> 
#> Extending read_v2_drugs_bnf with BNF hierarchy and descriptions
#> Extending read_v2_icd10 by expanding ICD-10 code ranges
#> Adding tables to database
#> ✔ Lookup table BNF_UKB v4 added successfully.
#> ✔ Relationship table BNF_relationship_UKB v4 added successfully.
#> ✔ Lookup table DM+D_UKB v4 added successfully.
#> ✔ Lookup table ICD-9_UKB v4 added successfully.
#> ✔ Relationship table ICD-9_relationship_UKB v4 added successfully.
#> ✔ Lookup table ICD-10_UKB v4 added successfully.
#> ✔ Relationship table ICD-10_relationship_UKB v4 added successfully.
#> ✔ Mapping table ICD-9_ICD-10_UKB v4 added successfully.
#> ✔ Lookup table Read 2_UKB v4 added successfully.
#> ✔ Relationship table Read 2_relationship_UKB v4 added successfully.
#> ✔ Lookup table Read 2, drugs_UKB v4 added successfully.
#> ✔ Mapping table Read 2, drugs_BNF_UKB v4 added successfully.
#> ✔ Mapping table Read 2_ICD-9_UKB v4 added successfully.
#> ✔ Mapping table Read 2_ICD-10_UKB v4 added successfully.
#> ✔ Mapping table Read 2_OPCS4_UKB v4 added successfully.
#> ✔ Mapping table Read 2_Read 3_UKB v4 added successfully.
#> ✔ Lookup table Read 3_UKB v4 added successfully.
#> ✔ Mapping table Read 3_ICD-9_UKB v4 added successfully.
#> ✔ Mapping table Read 3_ICD-10_UKB v4 added successfully.
#> ✔ Mapping table Read 3_OPCS4_UKB v4 added successfully.
#> ✔ Mapping table Read 3_Read 2_UKB v4 added successfully.
#> ✔ Dummy database ready to use!
PARENTS(c("E10", "E11"), code_type = "ICD-10")
#> Error in N_PARENTS(codes, depth = Inf, code_type = code_type, lookup_version = lookup_version,     relationship_version = relationship_version, codes_only = codes_only,     preferred_description_only = preferred_description_only): Code type 'ICD-10' not found in relationship metadata.
#> ℹ Did you add the relationship table with
#>   `codeminer::add_relationship_table()`?
CHILDREN(c("E10", "E11"), code_type = "ICD-10")
#> Error in N_CHILDREN(codes, depth = Inf, code_type = code_type, lookup_version = lookup_version,     relationship_version = relationship_version, codes_only = codes_only,     preferred_description_only = preferred_description_only): Code type 'ICD-10' not found in relationship metadata.
#> ℹ Did you add the relationship table with
#>   `codeminer::add_relationship_table()`?
N_PARENTS(c("E10", "E11"), code_type = "ICD-10")
#> Error in N_PARENTS(c("E10", "E11"), code_type = "ICD-10"): Code type 'ICD-10' not found in relationship metadata.
#> ℹ Did you add the relationship table with
#>   `codeminer::add_relationship_table()`?
N_CHILDREN(c("E10", "E11"), code_type = "ICD-10")
#> Error in N_CHILDREN(c("E10", "E11"), code_type = "ICD-10"): Code type 'ICD-10' not found in relationship metadata.
#> ℹ Did you add the relationship table with
#>   `codeminer::add_relationship_table()`?