From 61c0bdb7af2e2b0c5b00428d08c4c66606d3b670 Mon Sep 17 00:00:00 2001
From: Matthijs Berends <berendsms@gmail.com>
Date: Wed, 28 Dec 2022 15:04:59 +0100
Subject: [PATCH] documentation

---
 DESCRIPTION                      | 2 +-
 NEWS.md                          | 2 +-
 R/add_custom_microorganisms.R    | 5 +++--
 R/mo.R                           | 2 +-
 man/add_custom_microorganisms.Rd | 4 +++-
 5 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 391816c7..55d22b7d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9072
+Version: 1.8.2.9073
 Date: 2022-12-28
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index fb432123..b91ba92f 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.2.9072
+# AMR 1.8.2.9073
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 
diff --git a/R/add_custom_microorganisms.R b/R/add_custom_microorganisms.R
index ecf27866..296011f5 100644
--- a/R/add_custom_microorganisms.R
+++ b/R/add_custom_microorganisms.R
@@ -29,7 +29,7 @@
 
 #' Add Custom Microorganisms to This Package
 #'
-#' With [add_custom_microorganisms()] you can add your own custom antimicrobial drug codes to the `AMR` package.
+#' With [add_custom_microorganisms()] you can add your own custom microorganisms to the `AMR` package, such the non-taxonomic outcome of laboratory analysis.
 #' @param x a [data.frame] resembling the [microorganisms] data set, at least containing columns "genus" and "species"
 #' @details This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see *Examples*.
 #' 
@@ -86,9 +86,10 @@
 #'
 #' # E. asburiae/cloacae is now a new microorganism:
 #' mo_name("Enterobacter asburiae/cloacae")
+#' 
 #' # its code:
 #' as.mo("Enterobacter asburiae/cloacae")
-
+#' 
 #' # all internal algorithms will work as well:
 #' mo_name("Ent asburia cloacae")
 #' 
diff --git a/R/mo.R b/R/mo.R
index f1f52dca..b9173223 100755
--- a/R/mo.R
+++ b/R/mo.R
@@ -371,7 +371,7 @@ as.mo <- function(x,
         }
         msg <- c(msg, paste0(
           "Microorganism translation was uncertain for ", examples,
-          ". Run `mo_uncertainties()` to review ", plural[2], "."
+          ". Run `mo_uncertainties()` to review ", plural[2], ", or use `add_custom_microorganisms()` to add own entries."
         ))
 
         for (m in msg) {
diff --git a/man/add_custom_microorganisms.Rd b/man/add_custom_microorganisms.Rd
index 7b764a76..891db595 100644
--- a/man/add_custom_microorganisms.Rd
+++ b/man/add_custom_microorganisms.Rd
@@ -13,7 +13,7 @@ clear_custom_microorganisms()
 \item{x}{a \link{data.frame} resembling the \link{microorganisms} data set, at least containing columns "genus" and "species"}
 }
 \description{
-With \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} you can add your own custom antimicrobial drug codes to the \code{AMR} package.
+With \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} you can add your own custom microorganisms to the \code{AMR} package, such the non-taxonomic outcome of laboratory analysis.
 }
 \details{
 This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see \emph{Examples}.
@@ -67,8 +67,10 @@ add_custom_microorganisms(
 
 # E. asburiae/cloacae is now a new microorganism:
 mo_name("Enterobacter asburiae/cloacae")
+
 # its code:
 as.mo("Enterobacter asburiae/cloacae")
+
 # all internal algorithms will work as well:
 mo_name("Ent asburia cloacae")