R/APCalign-package.R

In APCalign: Resolving Plant Taxon Names Using the Australian Plant Census

#' @title Standardising Taxonomic Names in Australian Plants
#'
#' @description
#' The process of standardising taxon names is necessary when working with
#' biodiversity data. 'APCalign' uses the Australian Plant Name Index (APNI)
#' and the Australian Plant Census (APC) to align and update plant taxon names
#' to current, accepted standards. 'APCalign' can also supply information about
#' the established status of plant taxa across different states/territories.
#'
#' @name APCalign
#' @docType package
#' @references If you have any questions, comments or suggestions, please
#' submit an issue at our 
#' [GitHub repository](https://github.com/traitecoevo/APCalign/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(
    ".",
    "accepted_name",
    "accepted_name_usage",
    "accepted_name_usage_ID",
    "accepted_name_usage_ID_genus",
    "aligned_name",
    "aligned_minus_genus",
    "aligned_reason",
    "alignment_code",
    "alternative_accepted_name",
    "alternative_possible_names",
    "binomial",
    "canonical_name",
    "canonicalName",
    "ccAttributionIRI",
    "checked",
    "cleaned_name",
    "family",
    "family_accepted",
    "fuzzy_match_genus",
    "fuzzy_match_genus_APNI",
    "fuzzy_match_genus_synonym",
    "fuzzy_match_family",
    "fuzzy_match_family_synonym",
    "genus",
    "genus_accepted",
    "known",
    "my_order",
    "name_element", 
    "name_type",
    "native_anywhere",
    "number_of_collapsed_taxa",
    "original_name",
    "scientific_name",
    "scientific_name_authorship",
    "scientific_name_ID",
    "stripped_canonical",
    "stripped_canonical2",
    "stripped_name",
    "stripped_name2",
    "subclass",
    "taxon_distribution",
    "taxon_ID",
    "taxon_ID_aligned",
    "taxon_rank",
    "txtProgressBar",
    "setTxtProgressBar",
    "taxonomic_status",
    "taxonomic_status_aligned",
    "taxonomic_status_genus",
    "taxonomic_dataset",
    "taxonomic_dataset_genus",
    "trinomial",
    "aligned_name_tmp",
    "identifier_string",
    "identifier_string2",
    "suggested_name",
    "update_reason",
    "taxon_ID_genus",
    "possible_names_collapsed",
    "number_of_collapsed_taxa",
    "row_number",
    "accepted_name_2",
    "alternative_accepted_name_tmp",
    "pro_parte",
    "suggested_collapsed_name"
  )
)