(v1.6.0.9020) fix for skimr in dplyr 1.0.6

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.6.0.9019
+Version: 1.6.0.9020
-Date: 2021-05-05
+Date: 2021-05-06
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,5 +1,5 @@
-# `AMR` 1.6.0.9019
+# `AMR` 1.6.0.9020
-## <small>Last updated:  5 May 2021</small>
+## <small>Last updated:  6 May 2021</small>
 
 ### New
 * Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
@@ -36,6 +36,7 @@
 * Colour fix for using `barplot()` on an RSI class
 * Added 25 common system codes for bacteria to the `microorganisms.codes` data set
 * Added 16 common system codes for antimicrobial agents to the `antibiotics` data set
+* Fix for using `skimr::skim()` on classes `mo`, `mic` and `disk` when using the just released `dplyr` v1.0.6
 
 
 # `AMR` 1.6.0

R/disk.R

@@ -202,7 +202,7 @@ get_skimmers.disk <- function(column) {
     min = ~min(as.double(.), na.rm = TRUE),
     max = ~max(as.double(.), na.rm = TRUE),
     median = ~stats::median(as.double(.), na.rm = TRUE),
-    n_unique = ~pm_n_distinct(., na.rm = TRUE),
+    n_unique = ~length(unique(stats::na.omit(.))),
     hist = ~skimr::inline_hist(stats::na.omit(as.double(.)))
   )
 }

R/mic.R

@@ -348,7 +348,7 @@ get_skimmers.mic <- function(column) {
     min = ~min(., na.rm = TRUE),
     max = ~max(., na.rm = TRUE),
     median = ~stats::median(., na.rm = TRUE),
-    n_unique = ~pm_n_distinct(., na.rm = TRUE),
+    n_unique = ~length(unique(stats::na.omit(.))),
     hist_log2 = ~skimr::inline_hist(log2(stats::na.omit(.)))
   )
 }

R/mo.R

@@ -1732,9 +1732,9 @@ freq.mo <- function(x, ...) {
 get_skimmers.mo <- function(column) {
   skimr::sfl(
     skim_type = "mo",
-    unique_total = ~pm_n_distinct(., na.rm = TRUE),
+    unique_total = ~length(unique(stats::na.omit(.))),
-    gram_negative = ~sum(mo_is_gram_negative(stats::na.omit(.))),
+    gram_negative = ~sum(mo_is_gram_negative(.), na.rm = TRUE),
-    gram_positive = ~sum(mo_is_gram_positive(stats::na.omit(.))),
+    gram_positive = ~sum(mo_is_gram_positive(.), na.rm = TRUE),
     top_genus = ~names(sort(-table(mo_genus(stats::na.omit(.), language = NULL))))[1L],
     top_species = ~names(sort(-table(mo_name(stats::na.omit(.), language = NULL))))[1L]
   )

R/rsi.R

@@ -934,28 +934,16 @@ get_skimmers.rsi <- function(column) {
   # get the variable name 'skim_variable'
   name_call <- function(.data) {
     calls <- sys.calls()
+    frms <- sys.frames()
     calls_txt <- vapply(calls, function(x) paste(deparse(x), collapse = ""), FUN.VALUE = character(1))
     if (any(calls_txt %like% "skim_variable", na.rm = TRUE)) {
       ind <- which(calls_txt %like% "skim_variable")[1L]
-      vars <- tryCatch(eval(parse(text = ".data$skim_variable"), envir = sys.frame(ind)), 
+      vars <- tryCatch(eval(parse(text = ".data$skim_variable$rsi"), envir = frms[[ind]]), 
                        error = function(e) NULL)
+      tryCatch(ab_name(as.character(calls[[length(calls)]][[2]]), language = NULL),
+               error = function(e) NA_character_)
     } else {
-      vars <- NULL
-    }
-    i <- tryCatch(attributes(calls[[length(calls)]])$position, 
-                  error = function(e) NULL)
-    if (is.null(vars) | is.null(i)) {
       NA_character_
-    } else {
-      lengths <- vapply(FUN.VALUE = double(1), vars, length)
-      when_starts_rsi <- which(names(vapply(FUN.VALUE = double(1), vars, length)) == "rsi")
-      offset <- sum(lengths[c(1:when_starts_rsi - 1)])
-      var <- vars$rsi[i - offset]
-      if (!isFALSE(var == "data")) {
-        NA_character_
-      } else{
-        ab_name(var)
-      }
     }
   }
   

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">1.6.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</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">1.6.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</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">1.6.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</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">1.6.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </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">1.6.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</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">1.6.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</span>
       </span>
     </div>
 
@@ -236,12 +236,12 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1609019" class="section level1">
+    <div id="amr-1609020" class="section level1">
-<h1 class="page-header" data-toc-text="1.6.0.9019">
+<h1 class="page-header" data-toc-text="1.6.0.9020">
-<a href="#amr-1609019" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9019</h1>
+<a href="#amr-1609020" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9020</h1>
-<div id="last-updated-5-may-2021" class="section level2">
+<div id="last-updated-6-may-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-5-may-2021" class="anchor"></a><small>Last updated: 5 May 2021</small>
+<a href="#last-updated-6-may-2021" class="anchor"></a><small>Last updated: 6 May 2021</small>
 </h2>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
@@ -300,6 +300,7 @@
 <li>Colour fix for using <code><a href="https://rdrr.io/r/graphics/barplot.html">barplot()</a></code> on an RSI class</li>
 <li>Added 25 common system codes for bacteria to the <code>microorganisms.codes</code> data set</li>
 <li>Added 16 common system codes for antimicrobial agents to the <code>antibiotics</code> data set</li>
+<li>Fix for using <code><a href="https://docs.ropensci.org/skimr/reference/skim.html">skimr::skim()</a></code> on classes <code>mo</code>, <code>mic</code> and <code>disk</code> when using the just released <code>dplyr</code> v1.0.6</li>
 </ul>
 </div>
 </div>

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: 2021-05-05T13:26Z
+last_built: 2021-05-06T13:16Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles

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">1.6.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</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">1.6.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</span>
       </span>
     </div>