Make messages to console optional

R/align_taxa.R

@@ -14,6 +14,7 @@
 #' @param full Parameter to determine how many columns are output
 #' @param resources the taxonomic resources used to align the taxa names. Loading this can be slow,
 #' so call \code{\link{load_taxonomic_resources}} separately to greatly speed this function up and pass the resources in.
+#' @param quiet Logical to indicate whether to display messages while aligning taxa.
 #' @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`
@@ -69,17 +70,20 @@ align_taxa <- function(original_name,
                        output = NULL,
                        full = FALSE,
                        resources = load_taxonomic_resources(),
+                       quiet = FALSE,
                        fuzzy_abs_dist = 3, 
                        fuzzy_rel_dist = 0.2, 
                        fuzzy_matches = TRUE, 
                        imprecise_fuzzy_matches = FALSE, 
                        APNI_matches = TRUE,
                        identifier = NA_character_) {
 
-  message("Checking alignments of ", dplyr::n_distinct(original_name, na.rm = TRUE), " taxa\n")
+  if(!quiet)
+    message("Checking alignments of ", dplyr::n_distinct(original_name, na.rm = TRUE), " taxa\n")
 
   if (!is.null(output) && file.exists(output)) {
-    message("  - reading existing data from ", output)
+    if(!quiet)
+      message("  - reading existing data from ", output)
 
     taxa_raw <-
       readr::read_csv(
@@ -158,17 +162,18 @@ align_taxa <- function(original_name,
     dplyr::filter(!duplicated(original_name))
 
   if (all(taxa$tocheck$checked)|all(is.na(taxa$tocheck$checked))) {
-    message("  - all taxa are already checked, yay!")
+    if(!quiet)
+      message("  - all taxa are already checked, yay!")
     return(invisible(taxa$tocheck))
   }
 
   # move all checked taxa to "checked"
   taxa <- redistribute(taxa)
 
   # messages if there is an saved list being added to
-  if (!is.null(output) && file.exists(output) && !all(taxa$tocheck$checked)) {
-  # check unknown taxa
-  message(
+  if (!is.null(output) && file.exists(output) && !all(taxa$tocheck$checked) && !quiet) {
+    # check unknown taxa
+    message(
     "  -> ",
     crayon::blue(sum(!is.na(taxa$checked$accepted_name), na.rm = T)),
     " names already matched; ",
@@ -190,12 +195,13 @@ align_taxa <- function(original_name,
     filter(original_name %in% resources$`APC list (accepted)`$canonical_name) %>%
     distinct() %>%
     nrow()
-
-  message(
-    "  -> of these ",
-    crayon::blue(perfect_matches),
-    " names have a perfect match to a scientific name in the APC. Alignments being sought for remaining names."
-  )
+
+  if(!quiet)
+    message(
+      "  -> of these ",
+      crayon::blue(perfect_matches),
+      " names have a perfect match to a scientific name in the APC. Alignments being sought for remaining names."
+    )
   }
 
   # do the actual matching
@@ -228,7 +234,8 @@ align_taxa <- function(original_name,
     taxa$checked<-TRUE
     taxa$known<-!is.na(taxa$aligned_name)
     readr::write_csv(taxa, output)
-    #message("  - output saved in file: ", output)
+    if(!quiet)
+      message("  - output saved in file: ", output)
   }
 
   return(taxa)

R/create_taxonomic_update_lookup.R

@@ -15,6 +15,7 @@
 #' @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 are turned on as a default.
 #' @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.
@@ -58,6 +59,7 @@ create_taxonomic_update_lookup <- function(taxa,
                                            imprecise_fuzzy_matches = FALSE, 
                                            identifier = NA_character_,
                                            resources = load_taxonomic_resources(),
+                                           quiet = FALSE,
                                            output = NULL) {
 
   validate_taxonomic_splits_input(taxonomic_splits)
@@ -67,12 +69,14 @@ create_taxonomic_update_lookup <- function(taxa,
                APNI_matches = APNI_matches, 
                identifier = identifier, 
                imprecise_fuzzy_matches = imprecise_fuzzy_matches,
+               quiet = quiet,
                output=output)
 
   updated_data <- 
     update_taxonomy(aligned_data, 
       taxonomic_splits = taxonomic_splits,
-      resources = resources, 
+      resources = resources,
+      quiet = quiet,
       output = output)
 
   if (!full) {

R/update_taxonomy.R

@@ -17,7 +17,7 @@
 #'    most_likely_species, which returns the species name in use before the split; alternative names are returned in a separate column
 #'    return_all, which returns all possible names
 #'    collapse_to_higher_taxon, which declares that an ambiguous name cannot be aligned to an accepted species/infraspecific name and the name is demoted to genus rank
-#' 
+#' @param quiet Logical to indicate whether to display messages while updating taxa.
 #' @param output (optional) Name of the file where results are saved. The default is NULL and no file is created.
 #' If specified, the output will be saved in a CSV file with the given name.
 #'
@@ -66,6 +66,7 @@
 
 update_taxonomy <- function(aligned_data,
                             taxonomic_splits = "most_likely_species",
+                            quiet = TRUE,
                             output = NULL,
                             resources = load_taxonomic_resources()) {
 
@@ -194,7 +195,8 @@ update_taxonomy <- function(aligned_data,
     taxa_out$checked<-TRUE
     taxa_out$known<-!is.na(taxa_out$accepted_name)
     readr::write_csv(taxa_out, output)
-    message("  - output saved in file: ", output)
+    if(!quiet)
+      message("  - output saved in file: ", output)
   }
 
   taxa_out