From 4bebba361022ec46e07ef47eb8d0895fc121fac4 Mon Sep 17 00:00:00 2001
From: Matthijs Berends <berendsms@gmail.com>
Date: Fri, 21 Oct 2022 15:13:19 +0200
Subject: [PATCH] fix for scoped dplyr verbs

---
 DESCRIPTION             |  4 ++--
 NEWS.md                 |  4 ++--
 R/aa_helper_functions.R |  6 +++---
 R/proportion.R          | 12 ++++++++++++
 man/proportion.Rd       | 12 ++++++++++++
 5 files changed, 31 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6aa8d876..4dd863a2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.2.9024
-Date: 2022-10-20
+Version: 1.8.2.9027
+Date: 2022-10-21
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
     data analysis and to work with microbial and antimicrobial properties by
diff --git a/NEWS.md b/NEWS.md
index 470a1530..0bcd4481 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.2.9024
+# AMR 1.8.2.9027
 
 This version will eventually become v2.0! We're happy to reach a new major milestone soon!
 
@@ -27,7 +27,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
 * Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The `AMR` package is now available in 16 languages. The automatic language determination will give a note at start-up on systems in supported languages.
 * Our data sets are now also continually exported to Apache Feather and Apache Parquet formats. You can find more info [in this article on our website](https://msberends.github.io/AMR/articles/datasets.html).
 * Added confidence intervals in AMR calculation. This is now included in `rsi_df()` and `proportion_df()` and manually available as `rsi_confidence_interval()`
-* Support for using antibiotic selectors in `dplyr::vars()`, such as in: `... %>% summarise_at(vars(aminoglycosides()), resistance)`
+* Support for using antibiotic selectors in scoped `dplyr` verbs (worh or without `vars()`), such as in: `... %>% summarise_at(aminoglycosides(), resistance)`
 
 ### Changed
 * Fix for using `as.rsi()` on certain EUCAST breakpoints for MIC values
diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R
index b1a456c3..478c2371 100755
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@@ -882,9 +882,9 @@ get_current_data <- function(arg_name, call) {
         return(env$x)
       }
       
-    } else if (!is.null(names(env)) && all(c(".tbl", ".vars", ".env") %in% names(env), na.rm = TRUE) && valid_df(env$`.tbl`)) {
-      # an element `.tbl` will be in the environment when using `dplyr::vars()`
-      # (e.g. in `dplyr::summarise_at()` or `dplyr::mutate_at()`)
+    } else if (!is.null(names(env)) && all(c(".tbl", ".vars", ".cols") %in% names(env), na.rm = TRUE) && valid_df(env$`.tbl`)) {
+      # an element `.tbl` will be in the environment when using scoped dplyr variants, with or without `dplyr::vars()`
+      # (e.g. `dplyr::summarise_at()` or `dplyr::mutate_at()`)
       return(env$`.tbl`)
     }
   }
diff --git a/R/proportion.R b/R/proportion.R
index ece78e0a..920fb89a 100755
--- a/R/proportion.R
+++ b/R/proportion.R
@@ -143,6 +143,18 @@
 #' }
 #' if (require("dplyr")) {
 #' 
+#'   # scoped dplyr verbs with antibiotic selectors
+#'   # (you could also use across() of course)
+#'   example_isolates %>%
+#'     group_by(ward) %>%
+#'     summarise_at(
+#'       c(aminoglycosides(), carbapenems()),
+#'       resistance
+#'     )
+#' 
+#' }
+#' if (require("dplyr")) {
+#' 
 #'   example_isolates %>%
 #'     group_by(ward) %>%
 #'     summarise(
diff --git a/man/proportion.Rd b/man/proportion.Rd
index 09c8b735..7b2a5df8 100644
--- a/man/proportion.Rd
+++ b/man/proportion.Rd
@@ -201,6 +201,18 @@ if (require("dplyr")) {
       ci_max = rsi_confidence_interval(CIP, side = "max"),
     )
     
+}
+if (require("dplyr")) {
+
+  # scoped dplyr verbs with antibiotic selectors
+  # (you could also use across() of course)
+  example_isolates \%>\%
+    group_by(ward) \%>\%
+    summarise_at(
+      c(aminoglycosides(), carbapenems()),
+      resistance
+    )
+
 }
 if (require("dplyr")) {