(v1.4.0.9059) ab class selector fix

.github/workflows/check.yaml

@@ -123,7 +123,7 @@ jobs:
         run: |
           brew install mariadb-connector-c
 
-      - name: Install dependencies
+      - name: Install package dependencies
         if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
         run: |
           remotes::install_deps(dependencies = TRUE)
@@ -137,22 +137,22 @@ jobs:
           as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
         shell: Rscript {0}
 
-      # - name: Run R CMD check
+      - name: Run R CMD check
-      #   if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
+        if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
-      #   env:
+        env:
-      #     _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_CRAN_INCOMING_: false
-      #   run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-      #   shell: Rscript {0}
+        shell: Rscript {0}
         
       - name: Run R CMD check on older R versions
-        # if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
+        if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
         env:
           _R_CHECK_CRAN_INCOMING_: false
           _R_CHECK_FORCE_SUGGESTS_: false
           _R_CHECK_LENGTH_1_CONDITION_: verbose
           _R_CHECK_LENGTH_1_LOGIC2_: verbose
         run: |
-          R CMD check data-raw/AMR_*.tar.gz --no-manual --as-cran
+          R CMD check data-raw/AMR_*.tar.gz --no-manual --no-build-vignettes
 
       - name: Show testthat output
         if: always()

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.4.0.9058
+Version: 1.4.0.9059
 Date: 2021-01-04
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.4.0.9058
+# AMR 1.4.0.9059
 ## <small>Last updated:  4 January 2021</small>
 ### New
 * Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`):

R/aa_helper_functions.R

@@ -458,7 +458,7 @@ meet_criteria <- function(object,
     stop_if(allow_NULL == FALSE, "argument `", obj_name, "` must not be NULL", call = call_depth)
     return(invisible())
   }
-  if (is.null(dim(object)) && length(object) == 1 && is.na(object)) {
+  if (is.null(dim(object)) && length(object) == 1 && suppressWarnings(is.na(object))) { # suppressWarnings for functions
     stop_if(allow_NA == FALSE, "argument `", obj_name, "` must not be NA", call = call_depth)
     return(invisible())
   }
@@ -527,23 +527,36 @@ meet_criteria <- function(object,
 }
 
 get_current_data <- function(arg_name, call) {
+  if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 100) < 3.2) {
+    if (is.na(arg_name)) {
+      warning_("this function can only be used in R >= 3.2", call = call)
+      return(data.frame())
+    } else {
+      stop_("argument `", arg_name, "` is missing with no default", call = call)
+    }
+  }
+  
   # try a (base R) method, by going over the complete system call stack with sys.frames()
   not_set <- TRUE
   frms <- lapply(sys.frames(), function(el) {
-    if (tryCatch(not_set == TRUE && ".data" %in% names(el) && is.data.frame(el$`.data`), error = function(e) FALSE)) {
+    if (".Generic" %in% names(el)) {
-      # dplyr? - an element `.data` will be in the system call stack
+      if (tryCatch(not_set == TRUE && ".data" %in% names(el) && is.data.frame(el$`.data`), error = function(e) FALSE)) {
-      not_set <<- FALSE
+        # dplyr? - an element `.data` will be in the system call stack
-      el$`.data`
-    } else if (tryCatch(not_set == TRUE && any(c("x", "xx") %in% names(el)), error = function(e) FALSE)) {
-      # otherwise try base R:
-      # an element `x` will be in this environment for only cols, e.g. `example_isolates[, carbapenems()]`
-      # an element `xx` will be in this environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
-      if (is.data.frame(el$xx)) {
         not_set <<- FALSE
-        el$xx
+        el$`.data`
-      } else if (is.data.frame(el$x)) {
+      } else if (tryCatch(not_set == TRUE && any(c("x", "xx") %in% names(el)), error = function(e) FALSE)) {
-        not_set <<- FALSE
+        # otherwise try base R:
-        el$x
+        # an element `x` will be in this environment for only cols, e.g. `example_isolates[, carbapenems()]`
+        # an element `xx` will be in this environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
+        if (tryCatch(is.data.frame(el$xx), error = function(e) FALSE)) {
+          not_set <<- FALSE
+          el$xx
+        } else if (tryCatch(is.data.frame(el$x))) {
+          not_set <<- FALSE
+          el$x
+        } else {
+          NULL
+        }
       } else {
         NULL
       }

R/ab_class_selectors.R

@@ -27,7 +27,9 @@
 #' 
 #' These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
 #' @inheritParams filter_ab_class 
-#' @details All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the [antibiotics] data set. This means that a selector like e.g. [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
+#' @details These functions only work in R 3.2 (2015) and later.
+#' 
+#' All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the [antibiotics] data set. This means that a selector like e.g. [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
 #' @rdname antibiotic_class_selectors
 #' @seealso [filter_ab_class()] for the `filter()` equivalent.
 #' @name antibiotic_class_selectors
@@ -161,7 +163,12 @@ tetracyclines <- function() {
 ab_selector <- function(ab_class, function_name) {
   meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = 1)
   meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
-
+  
+  if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 100) < 3.2) {
+    warning_(function_name, "() can only be used in R >= 3.2", call = FALSE)
+    return(NULL)
+  }
+  
   vars_df <- get_current_data(arg_name = NA, call = -3)
   ab_in_data <- get_column_abx(vars_df, info = FALSE)
   

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
       </span>
     </div>
 

docs/index.html

@@ -43,7 +43,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
       </span>
     </div>
 

docs/news/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
       </span>
     </div>
 
@@ -236,9 +236,9 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1409058" class="section level1">
+    <div id="amr-1409059" class="section level1">
-<h1 class="page-header" data-toc-text="1.4.0.9058">
+<h1 class="page-header" data-toc-text="1.4.0.9059">
-<a href="#amr-1409058" class="anchor"></a>AMR 1.4.0.9058<small> Unreleased </small>
+<a href="#amr-1409059" class="anchor"></a>AMR 1.4.0.9059<small> Unreleased </small>
 </h1>
 <div id="last-updated-4-january-2021" class="section level2">
 <h2 class="hasAnchor">

docs/pkgdown.yml

@@ -12,7 +12,7 @@ articles:
   datasets: datasets.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-01-04T10:27Z
+last_built: 2021-01-04T11:28Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles

docs/reference/antibiotic_class_selectors.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
       </span>
     </div>
 
@@ -281,7 +281,8 @@
 
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
-    <p>All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector like e.g. <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
+    <p>These functions only work in R 3.2 (2015) and later.</p>
+<p>All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector like e.g. <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
     <h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>
 
     

docs/reference/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
       </span>
     </div>
 

docs/survey.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
       </span>
     </div>
 

man/antibiotic_class_selectors.Rd

@@ -53,6 +53,8 @@ tetracyclines()
 These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
 }
 \details{
+These functions only work in R 3.2 (2015) and later.
+
 All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the \link{antibiotics} data set. This means that a selector like e.g. \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
 }
 \section{Reference data publicly available}{