From ba81220aed6fab2ec6d03d4c00ecb5f4fe1f5ff0 Mon Sep 17 00:00:00 2001
From: Will Cornwell <wcornwell@gmail.com>
Date: Thu, 27 Jul 2023 14:20:05 +1000
Subject: [PATCH] Cran prep (#67)

* fixing notes from devtools::check() with fonti's knowledge and tricks
---
 R/ausflora-package.R   | 58 ++++++++++++++++++++++++++++++++++++------
 R/clean_names.R        |  2 ++
 man/update_taxonomy.Rd |  2 ++
 3 files changed, 54 insertions(+), 8 deletions(-)

diff --git a/R/ausflora-package.R b/R/ausflora-package.R
index 669ba7d4..15d5631f 100644
--- a/R/ausflora-package.R
+++ b/R/ausflora-package.R
@@ -2,32 +2,74 @@
 #'
 #' @description
 #' The process of standardising taxon names is necessary when working with
-#' biodiversity data. 'ausflora' uses the Australian Plant Name Index (APNI) 
-#' and the Australian Plant Census (APC) to align and update plant taxon names 
+#' biodiversity data. 'ausflora' uses the Australian Plant Name Index (APNI)
+#' and the Australian Plant Census (APC) to align and update plant taxon names
 #' to current, accepted standards. 'ausflora' can also supply information about
 #' the established status of plant taxa across different states/territories.
-#' 
+#'
 #' @name ausflora
 #' @docType package
-#' @references If you have any questions, comments or suggestions, please 
+#' @references If you have any questions, comments or suggestions, please
 #' submit an issue at our [GitHub repository](https://github.com/traitecoevo/ausflora/issues)
 #' @keywords internal
 #' @section Functions:
 #' **Standarise taxon names**
-#' 
+#'
 #' * [load_taxonomic_resources]
 #' * [create_taxonomic_update_lookup]
 #' * [align_taxa]
 #' * [update_taxonomy]
-#' 
+#'
 #' **Established status by region**
-#' 
+#'
 #' * [state_diversity_counts]
 #' * [create_species_state_origin_matrix]
 #' * [native_anywhere_in_australia]
-#' 
+#'
 "_PACKAGE"
 
 ## usethis namespace: start
 ## usethis namespace: end
 NULL
+utils::globalVariables(
+  c(
+    ".",
+    "acceptedNameUsage",
+    "acceptedNameUsageID",
+    "aligned_name",
+    "aligned_reason",
+    "alternativeTaxonomicStatusClean",
+    "binomial",
+    "canonicalName",
+    "canonical_name",
+    "ccAttributionIRI",
+    "checked",
+    "cleaned_name",
+    "family",
+    "fuzzy_match_genus",
+    "fuzzy_match_genus_APNI",
+    "fuzzy_match_genus_known",
+    "genus",
+    "my_order",
+    "nameElement", 
+    "nameType",
+    "native_anywhere", 
+    "original_name",
+    "scientificName",
+    "scientificNameAuthorship",
+    "scientificNameID",
+    "stripped_canonical",
+    "stripped_canonical2",
+    "stripped_name",
+    "stripped_name2",
+    "subclass",
+    "taxonDistribution",
+    "taxonID",
+    "taxonIDClean",
+    "taxonRank",
+    "taxonomicStatus",
+    "taxonomicStatusClean",
+    "taxonomic_ref",
+    "trinomial"
+  )
+)
diff --git a/R/clean_names.R b/R/clean_names.R
index 6c286dd6..9fdda0fa 100644
--- a/R/clean_names.R
+++ b/R/clean_names.R
@@ -200,7 +200,9 @@ redistribute <- function(data) {
 #' update_taxonomy(c("Eucalyptus pauciflora", "Acacia victoriae"))
 #'
 #' # Update taxonomy for two plant names and save the result to a CSV file
+#' \dontrun{
 #' update_taxonomy(c("Eucalyptus pauciflora", "Acacia victoriae"), output = "updated_taxonomy.csv")
+#' }
 update_taxonomy <- function(aligned_names,
                             output = NULL,
                             resources = load_taxonomic_resources()) {
diff --git a/man/update_taxonomy.Rd b/man/update_taxonomy.Rd
index a532f022..5cdfa665 100644
--- a/man/update_taxonomy.Rd
+++ b/man/update_taxonomy.Rd
@@ -49,8 +49,10 @@ to their current accepted name.
 update_taxonomy(c("Eucalyptus pauciflora", "Acacia victoriae"))
 
 # Update taxonomy for two plant names and save the result to a CSV file
+\dontrun{
 update_taxonomy(c("Eucalyptus pauciflora", "Acacia victoriae"), output = "updated_taxonomy.csv")
 }
+}
 \seealso{
 load_taxonomic_resources