Added documented package data for mapping tables.

Author: eboyer221

DESCRIPTION

@@ -65,3 +65,4 @@ biocViews:
     Visualization
 URL: https://github.com/jravilab/amRshiny
 BugReports: https://github.com/jravilab/amRshiny/issues
+LazyData: true

R/data.R

@@ -0,0 +1,41 @@
+#' Drug class mapping table
+#'
+#' Maps antibiotic names to class metadata.
+#'
+#' @format A tibble with columns:
+#' \describe{
+#'   \item{drug.antibiotic_name}{Antibiotic name}
+#'   \item{drug.pubchem_cid}{PubChem compound ID (numeric)}
+#'   \item{WHO_class}{WHO classification label}
+#'   \item{AB_class}{Antibiotic class}
+#'   \item{AB_subclass}{Antibiotic subclass}
+#'   \item{drug_class}{Normalized drug class}
+#' }
+#' @source inst/extdata/drug_class_map.tsv
+"drug_class_map"
+
+#' Drug cleanup mapping table
+#'
+#' Maps misspelled drug names to predicted canonical names and classes.
+#'
+#' @format A tibble with columns:
+#' \describe{
+#'   \item{misspelled_drug}{Original, misspelled drug name}
+#'   \item{predicted_drug}{Canonical drug name}
+#'   \item{drug_classes}{Drug class name}
+#' }
+#' @source inst/extdata/drug_cleanup.csv
+"drug_cleanup"
+
+#' Isolation source mapping table
+#'
+#' Normalized isolation source values and grouped categories.
+#'
+#' @format A tibble with columns:
+#' \describe{
+#'   \item{genome.isolation_source}{Raw isolation source string}
+#'   \item{lower_cased_isolation_source}{Lower-cased version}
+#'   \item{group}{Grouped category}
+#' }
+#' @source inst/extdata/llm_gpt_amr_isolation_source_cleaned.csv
+"isolation_source_map"

data-raw/mapping-data.R

@@ -0,0 +1,12 @@
+# Generate package data (.rda) from inst/extdata files
+
+drug_class_map <- readr::read_tsv("inst/extdata/drug_class_map.tsv")
+drug_cleanup <- readr::read_csv("inst/extdata/drug_cleanup.csv")
+isolation_source_map <- readr::read_csv("inst/extdata/llm_gpt_amr_isolation_source_cleaned.csv")
+
+usethis::use_data(
+  drug_class_map,
+  drug_cleanup,
+  isolation_source_map,
+  overwrite = TRUE
+)