DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.2.9129
-Date: 2023-02-15
+Version: 1.8.2.9126
+Date: 2023-02-14
 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 1.8.2.9129
+# AMR 1.8.2.9126
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 

R/aa_helper_functions.R

@@ -889,36 +889,34 @@ get_current_data <- function(arg_name, call) {
   valid_df <- function(x) {
     !is.null(x) && is.data.frame(x)
   }
+  # try dplyr::cur_data_all() first to support dplyr groups
+  # only useful for e.g. dplyr::filter(), dplyr::mutate() and dplyr::summarise()
+  # not useful (throws error) with e.g. dplyr::select(), dplyr::across(), or dplyr::vars(),
+  # but that will be caught later on in this function
+  cur_data_all <- import_fn("cur_data_all", "dplyr", error_on_fail = FALSE)
+  if (!is.null(cur_data_all)) {
+    out <- tryCatch(cur_data_all(), error = function(e) NULL)
+    if (valid_df(out)) {
+      return(out)
+    }
+  }
 
   # try a manual (base R) method, by going over all underlying environments with sys.frames()
   for (env in sys.frames()) {
-
-    # dplyr support ----
-    if (!is.null(env$mask) && is.function(env$mask$current_rows) && (valid_df(env$data) || valid_df(env$`.data`))) {
-      # an element `.data` or `data` (containing all data) and `mask` (containing functions) will be in the environment when using dplyr verbs
-      # we use their mask$current_rows() to get the group rows, since dplyr::cur_data_all() is deprecated and will be removed in the future
-      # e.g. for `example_isolates %>% group_by(ward) %>% mutate(first = first_isolate(.))`
-      if (valid_df(env$data)) {
-        # support for dplyr 1.1.x
-        return(env$data[env$mask$current_rows(), , drop = FALSE])
-      } else {
-        # support for dplyr 1.0.x
-        return(env$`.data`[env$mask$current_rows(), , drop = FALSE])
-      }
-
-      # base R support ----
-    } else if (!is.null(env$`.Generic`)) {
+    if (!is.null(env$`.Generic`)) {
       # don't check `".Generic" %in% names(env)`, because in R < 3.2, `names(env)` is always NULL
 
-      if (valid_df(env$xx)) {
-        # an element `xx` will be in the environment for rows + cols in base R, e.g. `example_isolates[c(1:3), carbapenems()]`
+      if (valid_df(env$`.data`)) {
+        # an element `.data` will be in the environment when using `dplyr::select()`
+        # (but not when using `dplyr::filter()`, `dplyr::mutate()` or `dplyr::summarise()`)
+        return(env$`.data`)
+      } else if (valid_df(env$xx)) {
+        # an element `xx` will be in the environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
         return(env$xx)
       } else if (valid_df(env$x)) {
-        # an element `x` will be in the environment for only cols in base R, e.g. `example_isolates[, carbapenems()]`
+        # an element `x` will be in the environment for only cols, e.g. `example_isolates[, carbapenems()]`
         return(env$x)
       }
-      
-      # scoped dplyr support ----
     } else if (!is.null(names(env)) && all(c(".tbl", ".vars", ".cols") %in% names(env), na.rm = TRUE) && valid_df(env$`.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()`)

R/antibiogram.R

@@ -102,7 +102,7 @@
 #'                                           "Study Group", "Control Group"))
 #'    ```
 #'
-#' All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using [ggplot2::autoplot()] or base \R [plot()]/[barplot()]) or printed into R Markdown / Quarto formats for reports using `print()`. Use functions from specific 'table reporting' packages to transform the output of [antibiogram()] to your needs, e.g. `flextable::as_flextable()` or `gt::gt()`.
+#' All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using [ggplot2::autoplot()] or base \R [plot()]/[barplot()]) or printed into R Markdown / Quarto formats for reports. Use functions from specific 'table reporting' packages to transform the output of [antibiogram()] to your needs, e.g. `flextable::as_flextable()` or `gt::gt()`.
 #'
 #' Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the `only_all_tested` argument (defaults to `FALSE`). See this example for two antibiotics, Drug A and Drug B, about how [antibiogram()] works to calculate the %SI:
 #'

R/first_isolate.R

@@ -177,7 +177,7 @@ first_isolate <- function(x = NULL,
                           include_untested_sir = TRUE,
                           ...) {
   if (is_null_or_grouped_tbl(x)) {
-    # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
+    # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
     x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
   }
@@ -634,7 +634,7 @@ filter_first_isolate <- function(x = NULL,
                                  method = c("phenotype-based", "episode-based", "patient-based", "isolate-based"),
                                  ...) {
   if (is_null_or_grouped_tbl(x)) {
-    # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
+    # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
     x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
   }

R/key_antimicrobials.R

@@ -138,7 +138,7 @@ key_antimicrobials <- function(x = NULL,
                                only_sir_columns = FALSE,
                                ...) {
   if (is_null_or_grouped_tbl(x)) {
-    # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
+    # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
     x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
   }
@@ -250,7 +250,7 @@ all_antimicrobials <- function(x = NULL,
                                only_sir_columns = FALSE,
                                ...) {
   if (is_null_or_grouped_tbl(x)) {
-    # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
+    # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also fix for using a grouped df as input (a dot as first argument)
     x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
   }

R/mdro.R

@@ -178,7 +178,7 @@ mdro <- function(x = NULL,
                  only_sir_columns = FALSE,
                  ...) {
   if (is_null_or_grouped_tbl(x)) {
-    # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
+    # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
     # is also a fix for using a grouped df as input (i.e., a dot as first argument)
     x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
   }

index.md

@@ -78,7 +78,7 @@ This base R snippet will work in any version of R since April 2013 (R-3.0).
 
 The `AMR` package supports generating traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA).
 
-If used inside R Markdown or Quarto, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.) when using `print()` on an antibiogram object.
+If used inside R Markdown or Quarto, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.).
 
 ```r
 antibiogram(example_isolates,
@@ -111,21 +111,6 @@ antibiogram(example_isolates,
 |Gram-negative (641-693)  |  88|        99|        98|
 |Gram-positive (345-1044) |  86|        98|        95|
 
-Like many other functions in this package, `antibiograms()` comes with support for 20 languages that are often detected automatically based on system language:
-
-```r
-antibiogram(example_isolates,
-            antibiotics = c("CIP", "TOB", "GEN"),
-            mo_transform = "gramstain",
-            ab_transform = "name",
-            language = "uk") # Ukrainian
-```
-
-|Збудник (N min-max)      | Гентаміцин| Тобраміцин| Ципрофлоксацин|
-|:------------------------|----------:|----------:|--------------:|
-|Грамнегативні (684-686)  |         96|         96|             91|
-|Грампозитивні (665-1170) |         63|         34|             77|
-
 
 #### Calculating resistance per group
 

man/antibiogram.Rd

@@ -124,7 +124,7 @@ your_data \%>\%
 }\if{html}{\out{</div>}}
 }
 
-All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using \code{\link[ggplot2:autoplot]{ggplot2::autoplot()}} or base \R \code{\link[=plot]{plot()}}/\code{\link[=barplot]{barplot()}}) or printed into R Markdown / Quarto formats for reports using \code{print()}. Use functions from specific 'table reporting' packages to transform the output of \code{\link[=antibiogram]{antibiogram()}} to your needs, e.g. \code{flextable::as_flextable()} or \code{gt::gt()}.
+All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using \code{\link[ggplot2:autoplot]{ggplot2::autoplot()}} or base \R \code{\link[=plot]{plot()}}/\code{\link[=barplot]{barplot()}}) or printed into R Markdown / Quarto formats for reports. Use functions from specific 'table reporting' packages to transform the output of \code{\link[=antibiogram]{antibiogram()}} to your needs, e.g. \code{flextable::as_flextable()} or \code{gt::gt()}.
 
 Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the \code{only_all_tested} argument (defaults to \code{FALSE}). See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=antibiogram]{antibiogram()}} works to calculate the \%SI:
 

pkgdown/extra.css

@@ -54,13 +54,10 @@ mark, .mark {
   background: rgba(17, 143, 118, 0.25) !important;
 }
 
-/* smaller tables */
-.table {
-  font-size: 0.9em !important;
-}
 
 /* SYNTAX */
 /* These are simple changes for the syntax highlighting */
+
 pre {
   font-size: 0.8em !important;
 }

pkgdown/extra.js

@@ -52,7 +52,7 @@ $(document).ready(function() {
   // add doctoral titles to authors
   function doct_tit(x) {
     if (typeof(x) != "undefined") {
-      x = x.replace(/Author, maintainer/g, "Principle maintainer");
+      x = x.replace(/Author, maintainer/g, "Principle developer");
       x = x.replace(/Author, contributor/g, "Contributing maintainer");
       x = x.replace(/Thesis advisor/g, "(former) Doctoral advisor");
       // contributors