From 0461a17b305653f70febede70953c3677ee08b99 Mon Sep 17 00:00:00 2001
From: Will Cornwell <w.cornwell@unsw.edu.au>
Date: Thu, 15 Dec 2022 14:51:43 +1100
Subject: [PATCH] updating documentation a bit, more needed

---
 DESCRIPTION       | 2 +-
 NAMESPACE         | 1 +
 R/clean_names.R   | 6 +++---
 man/align_taxa.Rd | 9 ++++++---
 4 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1bf31c58..2e74c61c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -27,5 +27,5 @@ Remotes:
     traitecoevo/datastorr
 Suggests:
     testthat (>= 3.0.0)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.2
 Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
index b5f34529..0491db31 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -12,3 +12,4 @@ export(standardise_names)
 export(strip_names)
 export(update_taxonomy)
 importFrom(magrittr,"%>%")
+
diff --git a/R/clean_names.R b/R/clean_names.R
index 67d75e61..c1829f88 100644
--- a/R/clean_names.R
+++ b/R/clean_names.R
@@ -18,9 +18,9 @@ default_version <- function() {
 #' @param original_name list of names to query
 #' @param output (optional) name of file to save results
 #' @param fuzzy_matching option to turn off fuzzy matching
-#' @param max_distance_abs 
-#' @param max_distance_rel 
-#' @param ver 
+#' @param max_distance_abs absolute distance in substitution space
+#' @param max_distance_rel relative distance in substitution space
+#' @param ver version number for flora resource
 #'
 #' @return
 #' @export
diff --git a/man/align_taxa.Rd b/man/align_taxa.Rd
index 47a4acce..77a62014 100644
--- a/man/align_taxa.Rd
+++ b/man/align_taxa.Rd
@@ -7,6 +7,7 @@
 align_taxa(
   original_name,
   output = NULL,
+  fuzzy_matching = TRUE,
   max_distance_abs = 3,
   max_distance_rel = 0.2,
   ver = default_version()
@@ -17,11 +18,13 @@ align_taxa(
 
 \item{output}{(optional) name of file to save results}
 
-\item{max_distance_abs}{}
+\item{fuzzy_matching}{option to turn off fuzzy matching}
 
-\item{max_distance_rel}{}
+\item{max_distance_abs}{absolute distance in substitution space}
 
-\item{ver}{}
+\item{max_distance_rel}{relative distance in substitution space}
+
+\item{ver}{version number for flora resource}
 }
 \description{
 Use APC & APNI to find taxonomic alignments for a list of names