updates to taxonomy functions

R/taxonomy.R

@@ -93,25 +93,40 @@ taxonomy_changelog <- function(taxonomy_code = NULL) {
 #' @param taxonomy_code `<chr>`  Health Care Provider Taxonomy code, a unique
 #'   alphanumeric code, ten characters in length
 #'
+#' @param taxonomy_level `<chr>`  Taxonomy level; options are `"I. Section"`,
+#'   `"II. Grouping"`, `"III. Classification"` and `"IV. Specialization"`
+#'
+#' @param taxonomy_level_title `<chr>`  Taxonomy level title
+#'
 #' @returns `<tibble>` of search results
 #'
 #' @examples
 #' taxonomy_hierarchy(taxonomy_code = "101Y00000X")
 #'
 #' taxonomy_hierarchy(taxonomy_code = "103TA0400X")
 #'
+#' taxonomy_hierarchy(taxonomy_level = "I. Section")
+#'
+#' taxonomy_hierarchy(taxonomy_level_title = "Allopathic & Osteopathic Physicians")
+#'
 #' @importFrom fuimus search_in_if
 #'
 #' @autoglobal
 #'
 #' @export
-taxonomy_hierarchy <- function(taxonomy_code = NULL) {
+taxonomy_hierarchy <- function(taxonomy_code = NULL,
+                               taxonomy_level = NULL,
+                               taxonomy_level_title = NULL) {
 
   check_nchar(taxonomy_code, 10)
 
   pin <- get_pin("tax_hierarchy")
 
-  search_in_if(pin, pin[["code"]], taxonomy_code)
+  pin <- search_in_if(pin, pin[["taxonomy_code"]], taxonomy_code)
+  pin <- search_in_if(pin, pin[["taxonomy_level"]], taxonomy_level)
+  pin <- search_in_if(pin, pin[["taxonomy_level_title"]], taxonomy_level_title)
+
+  return(pin)
 }
 
 #' Taxonomy Display Names
@@ -137,7 +152,7 @@ taxonomy_display <- function(taxonomy_code = NULL) {
 
   pin <- get_pin("tax_display")
 
-  search_in_if(pin, pin[["code"]], taxonomy_code)
+  search_in_if(pin, pin[["taxonomy_code"]], taxonomy_code)
 }
 
 #' Taxonomy Definitions
@@ -161,7 +176,7 @@ taxonomy_definition <- function(taxonomy_code = NULL) {
 
   check_nchar(taxonomy_code, 10)
 
-  pin <- get_pin("tax_definitions")
+  pin <- get_pin("tax_definition")
 
-  search_in_if(pin, pin[["code"]], taxonomy_code)
+  search_in_if(pin, pin[["taxonomy_code"]], taxonomy_code)
 }

data-raw/02_nucc_pins.R

@@ -75,9 +75,7 @@ readr::read_csv(
   name_repair = janitor::make_clean_names)
 
 deactivated <- ark_spt |>
-  dplyr::filter(
-    codex::not_na(deactivated)
-    ) |>
+  dplyr::filter(codex::not_na(deactivated)) |>
   dplyr::pull(code)
 
 ark_spt
@@ -150,19 +148,12 @@ ark_long <- ark_long |>
   tidyr::fill(nlevels, nyears)
 
 
-hierarchy <- get_pin("ark_long") |>
+hierarchy <- get_pin("tax_hierarchy") |>
   dplyr::mutate(id = dplyr::consecutive_id(level), .by = code) |>
   dplyr::filter(id != dplyr::lag(id, default = 0)) |>
   dplyr::select(-id)
 
-pin_update(
-  hierarchy,
-  name = "hierarchy",
-  title = "NUCC Taxonomy Gierarchy",
-  description = "Health Care Provider Taxonomy Code Set Archive 2009-2024 (Hierarchy)"
-)
-
-get_pin("ark_long") |>
+get_pin("tax_hierarchy") |>
   dplyr::count(code, level, sort = TRUE) |>
   dplyr::filter(n > 1) |>
   dplyr::pull(code)

data-raw/03_nucc_split.R

@@ -189,15 +189,15 @@ pin_update(
 #--------- Comparing raw dates to the updates
 updates |> dplyr::filter(type == "modified")
 
-arktax::retrieve_ark(which = "wide") |>
+arktax::taxonomy_raw() |>
   dplyr::select(code, modified) |>
   dplyr::filter(codex::not_na(modified)) |>
   dplyr::distinct() |>
   print(n = 200)
 
 updates |> dplyr::filter(type == "effective")
 
-arktax::retrieve_ark(which = "wide") |>
+arktax::taxonomy_raw() |>
   dplyr::select(code, effective) |>
   dplyr::filter(codex::not_na(effective)) |>
   dplyr::distinct()
@@ -206,35 +206,7 @@ updates |>
   dplyr::filter(type == "deactivated") |>
   print(n = 30)
 
-arktax::retrieve_ark(which = "wide") |>
+arktax::taxonomy_raw() |>
   dplyr::select(code, deactivated) |>
   dplyr::filter(codex::not_na(deactivated)) |>
   dplyr::distinct()
-
-
-#-------DISPLAY NAME
-display <- arktax::taxonomy_raw(year = 2024, version = 1) |>
-  dplyr::select(code, display_name)
-
-pin_update(
-  display,
-  "display",
-  "NUCC Taxonomy Display Names 2009-2024",
-  "Health Care Provider Taxonomy Code Set Display Names 2009-2024"
-)
-
-#-------DEFINITION
-definitions <- arktax::taxonomy_raw(year = 2024, version = 1) |>
-  dplyr::select(code, definition) |>
-  dplyr::mutate(
-    definition = dplyr::if_else(
-      codex::na(definition),
-      "None",
-      definition))
-
-pin_update(
-  definitions,
-  "definitions",
-  "NUCC Taxonomy Definitions 2009-2024",
-  "Health Care Provider Taxonomy Code Set Definitions 2009-2024"
-)

data-raw/04_nucc_display.R

@@ -0,0 +1,29 @@
+source(here::here("data-raw", "pins_internal.R"))
+
+raw_display <- arktax::taxonomy_raw() |>
+  dplyr::select(code, year, version, display_name)
+
+no_display <- raw_display |>
+  dplyr::filter(is.na(display_name)) |>
+  dplyr::pull(code) |>
+  fuimus::uniq_rmna()
+
+raw_display |>
+  dplyr::filter(!is.na(display_name)) |>
+  # dplyr::filter(code %in% no_display) |>
+  dplyr::filter(.by = code,
+                year == max(year),
+                version == max(version)) |>
+  dplyr::count(code, sort = TRUE)
+
+tax_display <- get_pin("tax_display") |>
+  dplyr::select(
+    taxonomy_code = code,
+    taxonomy_display = display_name)
+
+pin_update(
+  tax_display,
+  "tax_display",
+  "NUCC Taxonomy Display Names 2009-2024",
+  "Health Care Provider Taxonomy Code Set Display Names 2009-2024"
+)

data-raw/05_nucc_definition.R

@@ -0,0 +1,47 @@
+source(here::here("data-raw", "pins_internal.R"))
+
+raw_definition <- arktax::taxonomy_raw() |>
+  dplyr::select(code, year, version, definition) |>
+  dplyr::mutate(definition = stringr::str_replace_all(definition, notes_regs) |>
+                  stringr::str_squish())
+
+no_definition <- raw_definition |>
+  dplyr::filter(is.na(definition)) |>
+  dplyr::pull(code) |>
+  fuimus::uniq_rmna()
+
+has_definition <- raw_definition |>
+  dplyr::filter(code %in% no_definition) |>
+  dplyr::filter(!is.na(definition)) |>
+  dplyr::pull(code) |>
+  fuimus::uniq_rmna()
+
+vctrs::vec_slice(no_definition, vctrs::vec_in(no_definition, has_definition))
+vctrs::vec_slice(has_definition, vctrs::vec_in(has_definition, no_definition))
+
+raw_definition |>
+  dplyr::filter(.by = code,
+                !is.na(definition),
+                year == max(year),
+                version == max(version)) |>
+  dplyr::arrange(code, year, version) |>
+  dplyr::filter(year < 2024)
+  print(n = 200)
+  dplyr::filter(is.na(definition))
+  dplyr::select(code, definition)
+
+
+
+definitions <- get_pin("tax_definitions") |>
+    dplyr::reframe(
+      taxonomy_code = code,
+      taxonomy_definition = dplyr::if_else(definition == "None", NA_character_, definition)
+    )
+
+
+pin_update(
+  definitions,
+  "tax_definition",
+  "NUCC Taxonomy Definitions 2009-2024",
+  "Health Care Provider Taxonomy Code Set Definitions 2009-2024"
+)

data-raw/06_nucc_hierarchy.R

@@ -0,0 +1,15 @@
+source(here::here("data-raw", "pins_internal.R"))
+
+hierarchy <- get_pin("tax_hierarchy") |>
+  dplyr::select(
+    taxonomy_code = code,
+    taxonomy_level = level,
+    taxonomy_level_title = description
+  )
+
+pin_update(
+  hierarchy,
+  name = "tax_hierarchy",
+  title = "NUCC Taxonomy Hierarchy",
+  description = "Health Care Provider Taxonomy Code Set Hierarchy 2009-2024"
+)

inst/extdata/pins/_pins.yaml

@@ -6,12 +6,12 @@ cross_tax:
 - cross_tax/20241202T105926Z-6e97a/
 tax_changelog:
 - tax_changelog/20241202T101138Z-342e2/
-tax_definitions:
-- tax_definitions/20241202T101218Z-79f37/
+tax_definition:
+- tax_definition/20241202T165819Z-5bf90/
 tax_display:
-- tax_display/20241202T101342Z-6657b/
+- tax_display/20241202T170112Z-8d652/
 tax_hierarchy:
-- tax_hierarchy/20241202T101433Z-582c1/
+- tax_hierarchy/20241202T170833Z-7cc99/
 tax_raw:
 - tax_raw/20241202T101525Z-05252/
 tax_sources:

inst/extdata/pins/tax_definitions/20241202T101218Z-79f37/data.txt → inst/extdata/pins/tax_definition/20241202T165819Z-5bf90/data.txt

@@ -1,10 +1,10 @@
-file: tax_definitions.qs
-file_size: 75021
-pin_hash: 79f378e9d0fd77bd
+file: tax_definition.qs
+file_size: 75008
+pin_hash: 5bf90ad3e935769f
 type: qs
 title: NUCC Taxonomy Definitions 2009-2024
 description: Health Care Provider Taxonomy Code Set Definitions 2009-2024
 tags: ~
 urls: ~
-created: 20241202T101218Z
+created: 20241202T165819Z
 api_version: 1

inst/extdata/pins/tax_display/20241202T101342Z-6657b/data.txt → inst/extdata/pins/tax_display/20241202T170112Z-8d652/data.txt

@@ -1,10 +1,10 @@
 file: tax_display.qs
-file_size: 11358
-pin_hash: 6657beed09bdcfc0
+file_size: 11365
+pin_hash: 8d652affb5c85d60
 type: qs
 title: NUCC Taxonomy Display Names 2009-2024
 description: Health Care Provider Taxonomy Code Set Display Names 2009-2024
 tags: ~
 urls: ~
-created: 20241202T101342Z
+created: 20241202T170112Z
 api_version: 1

inst/extdata/pins/tax_hierarchy/20241202T101433Z-582c1/data.txt → inst/extdata/pins/tax_hierarchy/20241202T170833Z-7cc99/data.txt

@@ -1,10 +1,10 @@
 file: tax_hierarchy.qs
-file_size: 13373
-pin_hash: 582c1ecdec65c40d
+file_size: 13384
+pin_hash: 7cc99691802694b7
 type: qs
-title: NUCC Taxonomy Hierarchy 2009-2024
+title: NUCC Taxonomy Hierarchy
 description: Health Care Provider Taxonomy Code Set Hierarchy 2009-2024
 tags: ~
 urls: ~
-created: 20241202T101433Z
+created: 20241202T170833Z
 api_version: 1