fix for scoped dplyr verbs

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.2.9024
+Version: 1.8.2.9027
-Date: 2022-10-20
+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

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

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$`.tbl`)) {
+    } else if (!is.null(names(env)) && all(c(".tbl", ".vars", ".cols") %in% names(env), na.rm = TRUE) && valid_df(env$`.tbl`)) {
-      # an element `.tbl` will be in the environment when using `dplyr::vars()`
+      # an element `.tbl` will be in the environment when using scoped dplyr variants, with or without `dplyr::vars()`
-      # (e.g. in `dplyr::summarise_at()` or `dplyr::mutate_at()`)
+      # (e.g. `dplyr::summarise_at()` or `dplyr::mutate_at()`)
       return(env$`.tbl`)
     }
   }

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(

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")) {