Minor documentation changes

R/align_taxa.R

@@ -18,9 +18,7 @@
 #' @param APNI_matches Name matches to the APNI (Australian Plant Names Index) are turned off as a default.
 #' @param identifier A dataset, location or other identifier, which defaults to NA.
 #'
-#' @return A tibble with columns that include original_name, aligned_name, taxonomic_dataset, taxon_rank, aligned_reason, alignment_code. See Details
-#' 
-#' @details 
+#' @return A tibble with columns that include original_name, aligned_name, taxonomic_dataset, taxon_rank, aligned_reason, alignment_code. 
 #' - original_name: the original plant name input.
 #' - aligned_name: the original plant name after the function standardise_names has standardised the syntax of infraspecific taxon designations.
 #' - taxonomic_dataset: the source of the aligned names (APC or APNI).

R/create_species_state_origin_matrix.R

@@ -6,7 +6,7 @@
 #' @family diversity methods
 #' @param resources the taxonomic resources required to make the summary statistics.  Loading this can be slow, so call load_taxonomic_resources separately to greatly speed this function up and pass the resources in.
 #'
-#' @return A data frame with columns representing each state and rows representing each species. The values in each cell represent the origin of the species in that state.
+#' @return A tibble with columns representing each state and rows representing each species. The values in each cell represent the origin of the species in that state.
 #'
 #' @import dplyr
 #' @import stringr

R/create_taxonomic_update_lookup.R

@@ -14,9 +14,7 @@
 #' @param imprecise_fuzzy_matches Imprecise fuzzy matches are turned off as a default.
 #' @param identifier A dataset, location or other identifier, which defaults to NA.
 #' @param output file path to save the intermediate output to
-#' @return A lookup table containing the accepted and suggested names for each original name input, and additional taxonomic information such as taxon rank, taxonomic status, taxon IDs and genera. See Details.
-#' 
-#' @details
+#' @return A lookup table containing the accepted and suggested names for each original name input, and additional taxonomic information such as taxon rank, taxonomic status, taxon IDs and genera. 
 #' - original_name: the original plant name.
 #' - aligned_name: the input plant name that has been aligned to a taxon name in the APC or APNI by the align_taxa function.
 #' - accepted_name: the APC-accepted plant name, when available.

R/data.R

@@ -4,7 +4,7 @@
 #' 
 #'
 #' @format `gbif_lite`
-#' A data frame with 129 rows and 7 columns:
+#' A tibble with 129 rows and 7 columns:
 #' \describe{
 #'   \item{species}{The name of the first or species of scientificname}
 #'   \item{infraspecificepithet}{	The name of the lowest or terminal infraspecific epithet of the scientificname}

R/load_taxonomic_resources.R

@@ -1,6 +1,6 @@
 #' Load taxonomic resources from either stable or current versions of APC and APNI
 #'
-#' Loads taxonomic resources into the global environment. This function accesses taxonomic data from a dataset using the provided version number or the default version. The loaded data contains two lists: APC and APNI, which contain taxonomic information about plant species in Australia. The function creates several data frames by filtering and selecting data from the loaded lists.
+#' Loads taxonomic resources into the global environment. This function accesses taxonomic data from a dataset using the provided version number or the default version. The loaded data contains two lists: APC and APNI, which contain taxonomic information about plant species in Australia. The function creates several tibbles by filtering and selecting data from the loaded lists.
 #'
 #' @param stable_or_current_data Type of dataset to access. The default is "stable", which loads the
 #'   dataset from a github archived file. If set to "current", the dataset will be loaded from

R/update_taxonomy.R

@@ -24,31 +24,6 @@
 #'
 #'
 #' @return A tibble with updated taxonomy for the specified plant names. The tibble contains the following columns:
-#' \itemize{
-#'   \item \code{original_name}: the original plant name.
-#'   \item \code{aligned_name}: the input plant name.
-#'   \item \code{accepted_name}: the APC-accepted plant name, when available.
-#'   \item \code{suggested_name}: the suggested plant name to use. Identical to the accepted_name, when an accepted_name exists.
-#'   \item \code{taxonomic_dataset}: the source of the updated taxonomic information (APC or APNI).
-#'   \item \code{accepted_name_usage_ID}: the unique identifier for the accepted name of the input name.
-#'   \item \code{canonical_name}: the accepted (or known) scientific name for the input name.
-#'   \item \code{scientific_name}: the full scientific name, with authorship.
-#'   \item \code{taxon_rank}: the taxonomic rank of the accepted (or known) name.
-#'   \item \code{taxonomic_status}: the taxonomic status of the accepted (or known) name.
-#'   \item \code{taxonomic_status_aligned}: for taxa where there is ambiguity due to a taxon split, the taxonomic status of each possible match.
-#'   \item \code{aligned_reason}: the explanation of a specific taxon name alignment (from an original name to an aligned name).
-#'   \item \code{update_reason}: the explanation of a specific taxon name update (from an aligned name to an accepted name).
-#'   \item \code{genus}: the genus of the accepted (or known) name.
-#'   \item \code{family}: the family of the accepted (or known) name.
-#'   \item \code{subclass}: the subclass of the accepted name.
-#'   \item \code{taxon_distribution}: the distribution of the accepted name.
-#'   \item \code{taxon_ID}: an identifier for a specific taxon concept.
-#'   \item \code{taxon_ID_genus}: an identifier for the genus.
-#'   \item \code{scientific_name_ID}: an identifier for the nomenclatural (not taxonomic) details of a scientific name.
-#'   \item \code{row_number}: the row number of a specific original_name in the input.
-#' }
-#' 
-#' @details
 #' - original_name: the original plant name.
 #' - aligned_name: the input plant name that has been aligned to a taxon name in the APC or APNI by the align_taxa function.
 #' - accepted_name: the APC-accepted plant name, when available.