From 1029aa2fdc25962908c997929c1e611e3fbf2e1d Mon Sep 17 00:00:00 2001
From: Matthijs Berends <berendsms@gmail.com>
Date: Sat, 7 Jan 2023 14:53:14 +0100
Subject: [PATCH] algorithm improvement

---
 DESCRIPTION        |  2 +-
 NEWS.md            |  2 +-
 R/mo.R             | 10 +++++++++-
 R/mo_property.R    | 16 ++++++++--------
 man/mo_property.Rd | 16 ++++++++--------
 5 files changed, 27 insertions(+), 19 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d091855e..2dc0e60e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9088
+Version: 1.8.2.9089
 Date: 2023-01-07
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 436c3797..e943c346 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.2.9088
+# AMR 1.8.2.9089
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 
diff --git a/R/mo.R b/R/mo.R
index 35f6a516..27d6982c 100755
--- a/R/mo.R
+++ b/R/mo.R
@@ -236,6 +236,9 @@ as.mo <- function(x,
     x[trimws2(x) %like% translate_into_language("no .*growth", language = language)] <- NA_character_
     x[trimws2(x) %like% paste0("^(", translate_into_language("no|not", language = language), ") ")] <- NA_character_
 
+    # groups are in our taxonomic table with a capital G
+    x <- gsub(" group ", " Group ", x, fixed = TRUE)
+
     # run over all unique leftovers
     x_unique <- unique(x[is.na(out) & !is.na(x)])
 
@@ -782,7 +785,7 @@ rep.mo <- function(x, ...) {
 #' @noRd
 print.mo_uncertainties <- function(x, ...) {
   if (NROW(x) == 0) {
-    cat(word_wrap("No uncertainties to show. Only uncertainties of the last call of `as.mo()` or any `mo_*()` function are stored.\n", add_fn = font_blue))
+    cat(word_wrap("No uncertainties to show. Only uncertainties of the last call of `as.mo()` or any `mo_*()` function are stored.\n\n", add_fn = font_blue))
     return(invisible(NULL))
   }
 
@@ -925,6 +928,11 @@ convert_colloquial_input <- function(x) {
     x[x %like_case% "strepto[ck]o[ck].* [abcdfghkl]$"],
     perl = TRUE
   )
+  out[x %like_case% "strep[a-z]* group [abcdfghkl]$"] <- gsub(".* ([abcdfghkl])$",
+    "B_STRPT_GRP\\U\\1",
+    x[x %like_case% "strep[a-z]* group [abcdfghkl]$"],
+    perl = TRUE
+  )
   out[x %like_case% "group [abcdfghkl] strepto[ck]o[ck]"] <- gsub(".*group ([abcdfghkl]) strepto[ck]o[ck].*",
     "B_STRPT_GRP\\U\\1",
     x[x %like_case% "group [abcdfghkl] strepto[ck]o[ck]"],
diff --git a/R/mo_property.R b/R/mo_property.R
index b6c0fce4..dca10b53 100755
--- a/R/mo_property.R
+++ b/R/mo_property.R
@@ -137,18 +137,18 @@
 #' \donttest{
 #' # Becker classification, see ?as.mo ----------------------------------------
 #'
-#' mo_fullname("Staph. epidermidis")
-#' mo_fullname("Staph. epidermidis", Becker = TRUE)
-#' mo_shortname("Staph. epidermidis")
-#' mo_shortname("Staph. epidermidis", Becker = TRUE)
+#' mo_fullname("Staph epidermidis")
+#' mo_fullname("Staph epidermidis", Becker = TRUE)
+#' mo_shortname("Staph epidermidis")
+#' mo_shortname("Staph epidermidis", Becker = TRUE)
 #'
 #'
 #' # Lancefield classification, see ?as.mo ------------------------------------
 #'
-#' mo_fullname("Strep Group B")
-#' mo_fullname("Strep Group B", Lancefield = TRUE)
-#' mo_shortname("Strep Group B")
-#' mo_shortname("Strep Group B", Lancefield = TRUE)
+#' mo_fullname("Strep agalactiae")
+#' mo_fullname("Strep agalactiae", Lancefield = TRUE)
+#' mo_shortname("Strep agalactiae")
+#' mo_shortname("Strep agalactiae", Lancefield = TRUE)
 #'
 #'
 #' # language support  --------------------------------------------------------
diff --git a/man/mo_property.Rd b/man/mo_property.Rd
index c7c40fd6..fb4c0993 100644
--- a/man/mo_property.Rd
+++ b/man/mo_property.Rd
@@ -409,18 +409,18 @@ mo_shortname("K. pneu rh")
 \donttest{
 # Becker classification, see ?as.mo ----------------------------------------
 
-mo_fullname("Staph. epidermidis")
-mo_fullname("Staph. epidermidis", Becker = TRUE)
-mo_shortname("Staph. epidermidis")
-mo_shortname("Staph. epidermidis", Becker = TRUE)
+mo_fullname("Staph epidermidis")
+mo_fullname("Staph epidermidis", Becker = TRUE)
+mo_shortname("Staph epidermidis")
+mo_shortname("Staph epidermidis", Becker = TRUE)
 
 
 # Lancefield classification, see ?as.mo ------------------------------------
 
-mo_fullname("Strep Group B")
-mo_fullname("Strep Group B", Lancefield = TRUE)
-mo_shortname("Strep Group B")
-mo_shortname("Strep Group B", Lancefield = TRUE)
+mo_fullname("Strep agalactiae")
+mo_fullname("Strep agalactiae", Lancefield = TRUE)
+mo_shortname("Strep agalactiae")
+mo_shortname("Strep agalactiae", Lancefield = TRUE)
 
 
 # language support  --------------------------------------------------------