From 05dcb436601e6b1490ed312588f65169aad59cb2 Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Sun, 25 Aug 2019 23:25:12 +0200
Subject: [PATCH] (v0.7.1.9060) globals

---
 DESCRIPTION               | 2 +-
 NEWS.md                   | 2 +-
 R/bug_drug_combinations.R | 6 +++---
 R/globals.R               | 1 +
 4 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 2c44bec9..0e511b56 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 0.7.1.9059
+Version: 0.7.1.9060
 Date: 2019-08-25
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
diff --git a/NEWS.md b/NEWS.md
index 37cb658c..a2d59f54 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 0.7.1.9059
+# AMR 0.7.1.9060
 
 ### Breaking
 * Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). The `freq()` function still works, since it is re-exported from the `clean` package to this `AMR` package. Creating frequency tables is actually not the scope of this package (never was) and this function has matured  a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R
index 8f418abf..ef32b5b4 100644
--- a/R/bug_drug_combinations.R
+++ b/R/bug_drug_combinations.R
@@ -78,9 +78,9 @@ format.bugdrug <- function(x, combine_SI = TRUE, add_ab_group = TRUE, ...) {
   }
   y <- x %>%
     mutate(mo = mo_name(mo),
-           txt = paste0(AMR:::percent(isolates / total, force_zero = TRUE), 
-                            " (", trimws(format(isolates, big.mark = ",")), "/", 
-                            trimws(format(total, big.mark = ",")), ")")) %>% 
+           txt = paste0(percent(isolates / total, force_zero = TRUE), 
+                        " (", trimws(format(isolates, big.mark = ",")), "/", 
+                        trimws(format(total, big.mark = ",")), ")")) %>% 
     select(ab, mo, txt) %>% 
     spread(mo, txt) %>%
     mutate_all(~ifelse(is.na(.), "", .)) %>% 
diff --git a/R/globals.R b/R/globals.R
index 46f68624..a61399b6 100755
--- a/R/globals.R
+++ b/R/globals.R
@@ -86,6 +86,7 @@ globalVariables(c(".",
                   "species_id",
                   "subspecies",
                   "synonyms",
+                  "total",
                   "txt",
                   "value",
                   "xdr",