(v1.4.0.9016) as.rsi() older R versions

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.4.0.9015
+Version: 1.4.0.9016
 Date: 2020-11-10
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.4.0.9015
+# AMR 1.4.0.9016
 ## <small>Last updated: 10 November 2020</small>
 
 ### New
@@ -16,6 +16,7 @@
 * Better determination of disk zones and MIC values when running `as.rsi()` on a data.frame
 * Updated coagulase-negative staphylococci determination with Becker *et al.* 2020 (PMID 32056452), meaning that the species *S. argensis*, *S. caeli*, *S. debuckii*, *S. edaphicus* and *S. pseudoxylosus* are now all considered CoNS
 * Fix for using parameter `reference_df` in `as.mo()` and `mo_*()` functions that contain old microbial codes (from previous package versions)
+* Fix for using `as.rsi()` on a data.frame in older R versions
 
 ### Other
 * All messages and warnings thrown by this package now break sentences on whole words

R/aa_helper_functions.R

@@ -313,6 +313,8 @@ word_wrap <- function(...,
   }
   msg <- gsub("\n", paste0("\n", strrep(" ", indentation)), msg, fixed = TRUE)
   msg <- gsub("*|*", paste0("*|*", strrep(" ", indentation)), msg, fixed = TRUE)
+  # remove trailing empty characters
+  msg <- gsub("(\n| )+$", "", msg)
   
   if (length(add_fn) > 0) {
     if (!is.list(add_fn)) {

R/rsi.R

@@ -469,6 +469,13 @@ as.rsi.data.frame <- function(x,
   meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1)
   meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
   
+  for (i in seq_len(ncol(x))) {
+    # don't keep factors
+    if (is.factor(x[, i, drop = TRUE])) {
+      x[, i] <- as.character(x[, i, drop = TRUE])
+    }
+  }
+  
   # -- MO
   col_mo.bak <- col_mo
   if (is.null(col_mo)) {

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">1.4.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</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">1.4.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</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">1.4.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</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">1.4.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</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">1.4.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</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">1.4.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</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-1409015" class="section level1">
+    <div id="amr-1409016" class="section level1">
-<h1 class="page-header" data-toc-text="1.4.0.9015">
+<h1 class="page-header" data-toc-text="1.4.0.9016">
-<a href="#amr-1409015" class="anchor"></a>AMR 1.4.0.9015<small> Unreleased </small>
+<a href="#amr-1409016" class="anchor"></a>AMR 1.4.0.9016<small> Unreleased </small>
 </h1>
 <div id="last-updated-10-november-2020" class="section level2">
 <h2 class="hasAnchor">
@@ -267,6 +267,7 @@
 <li>Better determination of disk zones and MIC values when running <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame</li>
 <li>Updated coagulase-negative staphylococci determination with Becker <em>et al.</em> 2020 (PMID 32056452), meaning that the species <em>S. argensis</em>, <em>S. caeli</em>, <em>S. debuckii</em>, <em>S. edaphicus</em> and <em>S. pseudoxylosus</em> are now all considered CoNS</li>
 <li>Fix for using parameter <code>reference_df</code> in <code><a href="../reference/as.mo.html">as.mo()</a></code> and <code>mo_*()</code> functions that contain old microbial codes (from previous package versions)</li>
+<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame in older R versions</li>
 </ul>
 </div>
 <div id="other" class="section level3">

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: 2020-11-10T15:32Z
+last_built: 2020-11-10T18:58Z
 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">1.4.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</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">1.4.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</span>
       </span>
     </div>
 

tests/testthat/test-mdro.R

@@ -46,7 +46,7 @@ test_that("mdro works", {
 
   library(dplyr)
   # example_isolates should have these finding using Dutch guidelines
-  expect_equal(outcome %>% cleaner::freq() %>% pull(count),
+  expect_equal(as.double(table(outcome)),
                c(1969, 25, 6)) # 1969 neg, 25 unconfirmed, 6 pos
 
   expect_equal(brmo(example_isolates, info = FALSE),
@@ -104,7 +104,7 @@ test_that("mdro works", {
   expect_equal(
     # select only rifampicine, mo will be determined automatically (as M. tuberculosis),
     # number of mono-resistant strains should be equal to number of rifampicine-resistant strains
-    cleaner::freq(mdr_tb(example_isolates[, "RIF", drop = FALSE]))$count[2],
+    as.double(table(mdr_tb(example_isolates[, "RIF", drop = FALSE])))[2],
     count_R(example_isolates$RIF))
 
   sample_rsi <- function() {