Add line breaks (#224)

Have greatly reduced number of lines > 80 characters, in all R files except in the file match_taxa.R which we will likely refactor - as this is the one file with lots of longer lines within the code itself.

Closes #188

R/APCalign-package.R

@@ -10,7 +10,8 @@
 #' @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)
+#' submit an issue at our 
+#' [GitHub repository](https://github.com/traitecoevo/APCalign/issues)
 #' @keywords internal
 #' @section Functions:
 #' **Standarise taxon names**

R/create_species_state_origin_matrix.R

@@ -1,13 +1,17 @@
-#' Use the taxon distribution data from the APC to determine state level native and introduced origin status
+#' Use the taxon distribution data from the APC to determine state level
+#'  native and introduced origin status
 #'
 #' This function processes the geographic data available in the APC and 
 #' returns state level native, introduced and more complicated origins status for all taxa.
 #'
 #'
 #' @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.
+#' @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 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.
+#' @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.
 #'
 #' 
 #' @export

R/create_taxonomic_update_lookup.R

@@ -1,49 +1,93 @@
-#' Create a lookup table with the best-possible scientific name match for a list of Australian plant names
+#' Create a lookup table with the best-possible scientific name match for a
+#'  list of Australian plant names
 #'
-#' This function takes a list of Australian plant names that need to be reconciled with current taxonomy and 
-#' generates a lookup table of the best-possible scientific name match for each input name. 
-#' It uses first the function `align_taxa`, then the function `update_taxonomy` to achieve the output.
+#' This function takes a list of Australian plant names that need to be
+#'  reconciled with current taxonomy and 
+#' generates a lookup table of the best-possible scientific name match for
+#'  each input name. 
+#' It uses first the function `align_taxa`, then the function `update_taxonomy`
+#'  to achieve the output.
 #'
 #' @family taxonomic alignment functions
 #'
-#' @param taxa A list of Australian plant species that needs to be reconciled with current taxonomy.
-#' @param stable_or_current_data either "stable" for a consistent version, or "current" for the leading edge version.
+#' @param taxa A list of Australian plant species that needs to be reconciled
+#'  with current taxonomy.
+#' @param stable_or_current_data either "stable" for a consistent version,
+#'  or "current" for the leading edge version.
 #' @param version The version number of the dataset to use.
-#' @param taxonomic_splits How to handle one_to_many taxonomic matches.  Default is "return_all".  The other options are "collapse_to_higher_taxon" and "most_likely_species". most_likely_species defaults to the original_name if that name is accepted by the APC; this will be right for certain species subsets, but make errors in other cases, use with caution.
-#' @param full logical for whether the full lookup table is returned or just key columns 
-#' @param fuzzy_abs_dist The number of characters allowed to be different for a fuzzy match.
-#' @param fuzzy_rel_dist The proportion of characters allowed to be different for a fuzzy match. 
-#' @param fuzzy_matches Fuzzy matches are turned on as a default. The relative and absolute distances allowed for fuzzy matches to species and infraspecific taxon names are defined by the parameters `fuzzy_abs_dist` and `fuzzy_rel_dist`
-#' @param resources These are the taxonomic resources used for cleaning, this will default to loading them from a local place on your computer.  If this is to be called repeatedly, it's much faster to load the resources using \code{\link{load_taxonomic_resources}} separately and pass the data in.
-#' @param APNI_matches Name matches to the APNI (Australian Plant Names Index) are turned off as a default. 
-#' @param imprecise_fuzzy_matches Imprecise fuzzy matches uses the fuzzy matching function
-#' with lenient levels set (absolute distance of 5 characters; relative distance = 0.25). 
-#' It offers a way to get a wider range of possible names, possibly corresponding to very distant spelling mistakes. 
-#' This is FALSE as default and all outputs should be checked as it often makes erroneous matches.
-#' @param identifier A dataset, location or other identifier, which defaults to NA.
-#' @param quiet Logical to indicate whether to display messages while aligning taxa.
-#' @param output file path to save the output. If this file already exists, this function will check if it's a subset of the species passed in and try to add to this file. This can be useful for large and growing projects. 
-#' @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. 
+#' @param taxonomic_splits How to handle one_to_many taxonomic matches.
+#'  Default is "return_all".  The other options are "collapse_to_higher_taxon"
+#'  and "most_likely_species". most_likely_species defaults to the original_name
+#'  if that name is accepted by the APC; this will be right for certain species
+#'  subsets, but make errors in other cases, use with caution.
+#' @param full logical for whether the full lookup table is returned or
+#'  just key columns 
+#' @param fuzzy_abs_dist The number of characters allowed to be different for
+#'  a fuzzy match.
+#' @param fuzzy_rel_dist The proportion of characters allowed to be different
+#'  for a fuzzy match. 
+#' @param fuzzy_matches Fuzzy matches are turned on as a default. The relative
+#'  and absolute distances allowed for fuzzy matches to species and
+#'  infraspecific taxon names are defined by the parameters `fuzzy_abs_dist`
+#'  and `fuzzy_rel_dist`.
+#' @param resources These are the taxonomic resources used for cleaning, this
+#'  will default to loading them from a local place on your computer. If this is
+#'  to be called repeatedly, it's much faster to load the resources using
+#'  \code{\link{load_taxonomic_resources}} separately and pass the data in.
+#' @param APNI_matches Name matches to the APNI (Australian Plant Names Index)
+#'  are turned off as a default. 
+#' @param imprecise_fuzzy_matches Imprecise fuzzy matches uses the fuzzy
+#'  matching function with lenient levels set (absolute distance of
+#'  5 characters; relative distance = 0.25). 
+#'  It offers a way to get a wider range of possible names, possibly
+#'  corresponding to very distant spelling mistakes. 
+#'  This is FALSE as default and all outputs should be checked as it often
+#'  makes erroneous matches.
+#' @param identifier A dataset, location or other identifier,
+#'  which defaults to NA.
+#' @param quiet Logical to indicate whether to display messages while
+#'  aligning taxa.
+#' @param output file path to save the output. If this file already exists,
+#'  this function will check if it's a subset of the species passed in and try
+#'  to add to this file. This can be useful for large and growing projects. 
+#' @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.
+#' - 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.
-#' - suggested_name: the suggested plant name to use. Identical to the accepted_name, when an accepted_name exists; otherwise the the suggested_name is the aligned_name.
-#' - genus: the genus of the accepted (or suggested) name; only APC-accepted genus names are filled in.
-#' - family: the family of the accepted (or suggested) name; only APC-accepted family names are filled in.
+#' - suggested_name: the suggested plant name to use. Identical to the
+#'   accepted_name, when an accepted_name exists;
+#'   otherwise the the suggested_name is the aligned_name.
+#' - genus: the genus of the accepted (or suggested) name; 
+#'  only APC-accepted genus names are filled in.
+#' - family: the family of the accepted (or suggested) name;
+#'   only APC-accepted family names are filled in.
 #' - taxon_rank: the taxonomic rank of the suggested (and accepted) name.
-#' - taxonomic_dataset: the source of the suggested (and accepted) names (APC or APNI).
+#' - taxonomic_dataset: the source of the suggested (and accepted) names
+#'   (APC or APNI).
 #' - taxonomic_status: the taxonomic status of the suggested (and accepted) name.
-#' - taxonomic_status_aligned: the taxonomic status of the aligned name, before any taxonomic updates have been applied.
-#' - aligned_reason: the explanation of a specific taxon name alignment (from an original name to an aligned name).
-#' - update_reason: the explanation of a specific taxon name update (from an aligned name to an accepted or suggested name).
+#' - taxonomic_status_aligned: the taxonomic status of the aligned name,
+#'   before any taxonomic updates have been applied.
+#' - aligned_reason: the explanation of a specific taxon name alignment
+#'   (from an original name to an aligned name).
+#' - update_reason: the explanation of a specific taxon name update
+#'   (from an aligned name to an accepted or suggested name).
 #' - subclass: the subclass of the accepted name.
-#' - taxon_distribution: the distribution of the accepted name; only filled in if an APC accepted_name is available.
-#' - scientific_name_authorship: the authorship information for the accepted (or synonymous) name; available for both APC and APNI names.
-#' - taxon_ID: the unique taxon concept identifier for the accepted_name; only filled in if an APC accepted_name is available.
-#' - taxon_ID_genus: an identifier for the genus; only filled in if an APC-accepted genus name is available.
-#' - scientific_name_ID: an identifier for the nomenclatural (not taxonomic) details of a scientific name; available for both APC and APNI names.
+#' - taxon_distribution: the distribution of the accepted name;
+#'   only filled in if an APC accepted_name is available.
+#' - scientific_name_authorship: the authorship information for the accepted
+#'   (or synonymous) name; available for both APC and APNI names.
+#' - taxon_ID: the unique taxon concept identifier for the accepted_name;
+#'   only filled in if an APC accepted_name is available.
+#' - taxon_ID_genus: an identifier for the genus;
+#'   only filled in if an APC-accepted genus name is available.
+#' - scientific_name_ID: an identifier for the nomenclatural (not taxonomic)
+#'   details of a scientific name; available for both APC and APNI names.
 #' - row_number: the row number of a specific original_name in the input.
-#' - number_of_collapsed_taxa: when taxonomic_splits == "collapse_to_higher_taxon", the number of possible taxon names that have been collapsed.
+#' - number_of_collapsed_taxa: when taxonomic_splits == "collapse_to_higher_taxon",
+#'   the number of possible taxon names that have been collapsed.
 #' 
 #' @export
 #'
@@ -96,8 +140,11 @@ create_taxonomic_update_lookup <- function(taxa,
       updated_data %>%
         dplyr::select(
           dplyr::any_of(c(
-            "original_name", "aligned_name", "accepted_name", "suggested_name", "genus", "taxon_rank", "taxonomic_dataset", "taxonomic_status", "scientific_name", "aligned_reason", "update_reason", 
-            "alternative_possible_names", "possible_names_collapsed", "number_of_collapsed_taxa"
+            "original_name", "aligned_name", "accepted_name", "suggested_name",
+            "genus", "taxon_rank", "taxonomic_dataset", "taxonomic_status",
+            "scientific_name", "aligned_reason", "update_reason", 
+            "alternative_possible_names", "possible_names_collapsed",
+            "number_of_collapsed_taxa"
           ))
         )        
   }
@@ -117,7 +164,8 @@ validate_taxonomic_splits_input <- function(taxonomic_splits) {
       paste(
         "Invalid input:",
         taxonomic_splits,
-        ". Valid inputs are 'return_all', 'collapse_to_higher_taxon', or 'most_likely_species'."
+        ". Valid inputs are 'return_all', 'collapse_to_higher_taxon', or
+         'most_likely_species'."
       )
     )
 }