(v1.6.0.9016) website update and c() fixes

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.6.0.9015
+Version: 1.6.0.9016
 Date: 2021-05-03
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# `AMR` 1.6.0.9015
+# `AMR` 1.6.0.9016
 ## <small>Last updated:  3 May 2021</small>
 
 ### New

R/aa_helper_functions.R

@@ -458,7 +458,7 @@ stop_ifnot <- function(expr, ..., call = TRUE) {
          ifelse(!is.na(y), y, NA))
 }
 
-class_integrity_check <- function(value, type, check_vector) {
+return_after_integrity_check <- function(value, type, check_vector) {
   if (!all(value[!is.na(value)] %in% check_vector)) {
     warning_(paste0("invalid ", type, ", NA generated"), call = FALSE)
     value[!value %in% check_vector] <- NA

R/ab.R

@@ -551,7 +551,7 @@ as.data.frame.ab <- function(x, ...) {
 "[<-.ab" <- function(i, j, ..., value) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
-  class_integrity_check(y, "antimicrobial code", antibiotics$ab)
+  return_after_integrity_check(y, "antimicrobial code", antibiotics$ab)
 }
 #' @method [[<- ab
 #' @export
@@ -559,15 +559,16 @@ as.data.frame.ab <- function(x, ...) {
 "[[<-.ab" <- function(i, j, ..., value) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
-  class_integrity_check(y, "antimicrobial code", antibiotics$ab)
+  return_after_integrity_check(y, "antimicrobial code", antibiotics$ab)
 }
 #' @method c ab
 #' @export
 #' @noRd
-c.ab <- function(x, ...) {
+c.ab <- function(...) {
+  x <- list(...)[[1L]]
   y <- NextMethod()
   attributes(y) <- attributes(x)
-  class_integrity_check(y, "antimicrobial code", antibiotics$ab)
+  return_after_integrity_check(y, "antimicrobial code", antibiotics$ab)
 }
 
 #' @method unique ab

R/disk.R

@@ -182,11 +182,8 @@ print.disk <- function(x, ...) {
 #' @method c disk
 #' @export
 #' @noRd
-c.disk <- function(x, ...) {
-  y <- NextMethod()
-  y <- as.disk(y)
-  attributes(y) <- attributes(x)
-  y
+c.disk <- function(...) {
+  as.disk(unlist(lapply(list(...), as.character)))
 }
 
 #' @method unique disk

R/italicise_taxonomy.R

@@ -115,5 +115,8 @@ italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
 #' @rdname italicise_taxonomy
 #' @export
 italicize_taxonomy <- function(string, type = c("markdown", "ansi")) {
-  italicise(string = string, type = type)
+  if (missing(type)) {
+    type <- "markdown"
+  }
+  italicise_taxonomy(string = string, type = type)
 }

R/mic.R

@@ -307,10 +307,8 @@ as.matrix.mic <- function(x, ...) {
 #' @method c mic
 #' @export
 #' @noRd
-c.mic <- function(x, ...) {
-  y <- unlist(lapply(list(...), as.character))
-  x <- as.character(x)
-  as.mic(c(x, y))
+c.mic <- function(...) {
+  as.mic(unlist(lapply(list(...), as.character)))
 }
 
 #' @method unique mic

R/mo.R

@@ -1677,7 +1677,7 @@ pillar_shaft.mo <- function(x, ...) {
     } else {
       col <- "The data"
     }
-    warning_(col, " contains old microbial codes (from a previous AMR package version). ",
+    warning_(col, " contains old MO codes (from a previous AMR package version). ",
              "Please update your MO codes with `as.mo()`.",
              call = FALSE)
   }
@@ -1751,6 +1751,11 @@ print.mo <- function(x, print.shortnames = FALSE, ...) {
   }
   x <- as.character(x)
   names(x) <- x_names
+  if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
+    warning_("Some MO codes are from a previous AMR package version. ",
+             "Please update these MO codes with `as.mo()`.",
+             call = FALSE)
+  }
   print.default(x, quote = FALSE)
 }
 
@@ -1777,7 +1782,7 @@ summary.mo <- function(object, ...) {
 #' @noRd
 as.data.frame.mo <- function(x, ...) {
   if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
-    warning_("The data contains old microbial codes (from a previous AMR package version). ",
+    warning_("The data contains old MO codes (from a previous AMR package version). ",
              "Please update your MO codes with `as.mo()`.",
              call = FALSE)
   }
@@ -1812,8 +1817,8 @@ as.data.frame.mo <- function(x, ...) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
   # must only contain valid MOs
-  class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
-                                                   as.character(microorganisms.translation$mo_old)))
+  return_after_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
+                                                          as.character(microorganisms.translation$mo_old)))
 }
 #' @method [[<- mo
 #' @export
@@ -1822,18 +1827,18 @@ as.data.frame.mo <- function(x, ...) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
   # must only contain valid MOs
-  class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
-                                                   as.character(microorganisms.translation$mo_old)))
+  return_after_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
+                                                          as.character(microorganisms.translation$mo_old)))
 }
 #' @method c mo
 #' @export
 #' @noRd
-c.mo <- function(x, ...) {
+c.mo <- function(...) {
+  x <- list(...)[[1L]]
   y <- NextMethod()
   attributes(y) <- attributes(x)
-  # must only contain valid MOs
-  class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
-                                                   as.character(microorganisms.translation$mo_old)))
+  return_after_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
+                                                          as.character(microorganisms.translation$mo_old)))
 }
 
 #' @method unique mo
@@ -2058,10 +2063,10 @@ replace_old_mo_codes <- function(x, property) {
     n_matched <- length(matched[!is.na(matched)])
     if (property != "mo") {
       message_(font_blue(paste0("The input contained ", n_matched,
-                                " old microbial code", ifelse(n_matched == 1, "", "s"),
+                                " old MO code", ifelse(n_matched == 1, "", "s"),
                                 " (from a previous AMR package version). Please update your MO codes with `as.mo()`.")))
     } else {
-      message_(font_blue(paste0(n_matched, " old microbial code", ifelse(n_matched == 1, "", "s"), 
+      message_(font_blue(paste0(n_matched, " old MO code", ifelse(n_matched == 1, "", "s"), 
                                 " (from a previous AMR package version) ", 
                                 ifelse(n_matched == 1, "was", "were"), 
                                 " updated to ", ifelse(n_matched == 1, "a ", ""), 
@@ -2100,7 +2105,7 @@ repair_reference_df <- function(reference_df) {
   reference_df[, "x"] <- as.character(reference_df[, "x", drop = TRUE])
   reference_df[, "mo"] <- as.character(reference_df[, "mo", drop = TRUE])
   
-  # some microbial codes might be old
+  # some MO codes might be old
   reference_df[, "mo"] <- as.mo(reference_df[, "mo", drop = TRUE])
   reference_df
 }

_pkgdown.yml

@@ -177,6 +177,7 @@ reference:
     - "`availability`"
     - "`get_locale`"
     - "`ggplot_pca`"
+    - "`italicise_taxonomy`"
     - "`join`"
     - "`like`"
     - "`mo_matching_score`"

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">1.6.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</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">1.6.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</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">1.6.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</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">1.6.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</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">1.6.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</span>
       </span>
     </div>
 
@@ -206,7 +206,7 @@
 <p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>. This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
 <div class="main-content" style="display: inline-block;">
 <p>
-<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 155 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from 155 countries. Click the map to enlarge and to see the country names.
+<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 162 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from 162 countries. Click the map to enlarge and to see the country names.
 </p>
 </div>
 <div id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="section level5">

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">1.6.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</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-1609015" class="section level1">
-<h1 class="page-header" data-toc-text="1.6.0.9015">
-<a href="#amr-1609015" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9015</h1>
+    <div id="amr-1609016" class="section level1">
+<h1 class="page-header" data-toc-text="1.6.0.9016">
+<a href="#amr-1609016" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9016</h1>
 <div id="last-updated-3-may-2021" class="section level2">
 <h2 class="hasAnchor">
 <a href="#last-updated-3-may-2021" class="anchor"></a><small>Last updated: 3 May 2021</small>
@@ -340,7 +340,7 @@
 <span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
 </li>
 <li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
-<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
+<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
 <li>
 <p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
@@ -397,7 +397,7 @@
 <li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
 <li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
 <li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
-<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
+<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
 </ul>
 </li>
 <li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>

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: 2021-05-03T08:19Z
+last_built: 2021-05-03T11:04Z
 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">1.6.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</span>
       </span>
     </div>
 
@@ -592,6 +592,12 @@
         <td><p>PCA Biplot with <code>ggplot2</code></p></td>
       </tr><tr>
         
+        <td>
+          <p><code><a href="italicise_taxonomy.html">italicise_taxonomy()</a></code> <code><a href="italicise_taxonomy.html">italicize_taxonomy()</a></code> </p>
+        </td>
+        <td><p>Italicise Taxonomic Families, Genera, Species, Subspecies</p></td>
+      </tr><tr>
+        
         <td>
           <p><code><a href="join.html">inner_join_microorganisms()</a></code> <code><a href="join.html">left_join_microorganisms()</a></code> <code><a href="join.html">right_join_microorganisms()</a></code> <code><a href="join.html">full_join_microorganisms()</a></code> <code><a href="join.html">semi_join_microorganisms()</a></code> <code><a href="join.html">anti_join_microorganisms()</a></code> </p>
         </td>

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">1.6.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9016</span>
       </span>
     </div>
 

index.md

@@ -15,8 +15,8 @@ This package is [fully independent of any other R package](https://en.wikipedia.
 <div class="main-content" style="display: inline-block;">
   <p>
     <a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a>
-    <strong>Used in 155 countries</strong><br>
-    Since its first public release in early 2018, this package has been downloaded from 155 countries. Click the map to enlarge and to see the country names.</p>
+    <strong>Used in 162 countries</strong><br>
+    Since its first public release in early 2018, this package has been downloaded from 162 countries. Click the map to enlarge and to see the country names.</p>
 </div>
 
 ##### With `AMR` (for R), there's always a knowledgeable microbiologist by your side!

tests/testthat/test-italicise_taxonomy.R

@@ -0,0 +1,39 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Data Analysis for R                   #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# Developed at the University of Groningen, the Netherlands, in        #
+# collaboration with non-profit organisations Certe Medical            #
+# Diagnostics & Advice, and University Medical Center Groningen.       # 
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
+# ==================================================================== #
+
+context("italicise_taxonomy.R")
+
+test_that("italic taxonomy works", {
+  skip_on_cran()
+  
+  expect_identical(italicise_taxonomy("test for E. coli"),
+                   "test for *E. coli*")
+  expect_identical(italicise_taxonomy("test for E. coli"),
+                   italicize_taxonomy("test for E. coli"))
+  if (has_colour()) {
+    expect_identical(italicise_taxonomy("test for E. coli", type = "ansi"),
+                     "test for \033[3mE. coli\033[23m")
+  }
+})