v1.8.1

.Rbuildignore

@@ -33,3 +33,4 @@
 ^vignettes/SPSS.Rmd$
 ^vignettes/WHONET.Rmd$
 ^logo.svg$
+^CRAN-SUBMISSION$

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 1.8.1
+Date: 2022-03-16 18:22:51 UTC
+SHA: 7b0f1596bd65fbb72681a7e3a6a7e4e469a891e8

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
 Version: 1.8.1
-Date: 2022-03-14
+Date: 2022-03-17
 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
@@ -9,7 +9,7 @@ Description: Functions to simplify and standardise antimicrobial resistance (AMR
 Authors@R: c(
   person(given = c("Matthijs", "S."),
          family = "Berends", 
-         email = "m.s.berends@umcg.nl",
+         email = "m.berends@certe.nl",
          role = c("aut", "cre"),
          comment = c(ORCID = "0000-0001-7620-1800")),
   person(given = c("Christian", "F."),

NEWS.md

@@ -14,6 +14,7 @@ All functions in this package are considered to be stable. Updates to the AMR in
 * More informative warning messages
 * Added 192 as valid MIC
 * Updated MIC printing in tibbles
+* Increased speed for loading the package
 
 ### Other
 * Fix for unit testing on R 3.3
@@ -275,7 +276,7 @@ All functions in this package are considered to be stable. Updates to the AMR in
     filter(is_new_episode(date, episode_days = 60))
   ```
 * Functions `mo_is_gram_negative()` and `mo_is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
-* Function `mo_is_intrinsic_resistant()` to test for intrinsic resistance, based on [EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) from 2020.
+* Function `mo_is_intrinsic_resistant()` to test for intrinsic resistance, based on EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2 from 2020.
 * Functions `random_mic()`, `random_disk()` and `random_rsi()` for random value generation. The functions `random_mic()` and `random_disk()` take microorganism names and antibiotic names as input to make generation more realistic.
 
 ### Changed
@@ -1371,7 +1372,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
 * Function `guess_atc` to **determine the ATC** of an antibiotic based on name, trade name, or known abbreviations
 * Function `freq` to create **frequency tables**, with additional info in a header
 * Function `MDRO` to **determine Multi Drug Resistant Organisms (MDRO)** with support for country-specific guidelines.
-  * [Exceptional resistances defined by EUCAST](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) are also supported instead of countries alone
+  * Exceptional resistances defined by EUCAST are also supported instead of countries alone
   * Functions `BRMO` and `MRGN` are wrappers for Dutch and German guidelines, respectively
 * New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate`
 * New print format for `tibble`s and `data.table`s

R/aa_globals.R

@@ -36,15 +36,15 @@ EUCAST_VERSION_BREAKPOINTS <- list("11.0" = list(version_txt = "v11.0",
 EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1",
                                                  year = 2016, 
                                                  title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'",
-                                                 url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"),
+                                                 url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"),
                                     "3.2" = list(version_txt = "v3.2",
                                                  year = 2020, 
                                                  title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
-                                                 url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"),
+                                                 url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"),
                                     "3.3" = list(version_txt = "v3.3",
                                                  year = 2021, 
                                                  title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
-                                                 url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"))
+                                                 url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"))
 
 SNOMED_VERSION <- list(title = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)",
                        current_source = "US Edition of SNOMED CT from 1 September 2020",

R/mdro.R

@@ -65,7 +65,7 @@
 #' 
 #' * `guideline = "TB"`
 #'
-#'   The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" ([link](https://www.who.int/tb/publications/pmdt_companionhandbook/en/))
+#'   The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" ([link](https://www.who.int/publications/i/item/9789241548809))
 #' 
 #' * `guideline = "MRGN"`
 #'
@@ -343,7 +343,7 @@ mdro <- function(x = NULL,
     guideline$name <- "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis"
     guideline$author <- "WHO (World Health Organization)"
     guideline$version <- "WHO/HTM/TB/2014.11, 2014"
-    guideline$source_url <- "https://www.who.int/tb/publications/pmdt_companionhandbook/en/"
+    guideline$source_url <- "https://www.who.int/publications/i/item/9789241548809"
     guideline$type <- "MDR-TB's"
     
     # support per country:

R/mic.R

@@ -243,7 +243,7 @@ droplevels.mic <- function(x, exclude = if (any(is.na(levels(x)))) NULL else NA,
 pillar_shaft.mic <- function(x, ...) {
   crude_numbers <- as.double(x)
   operators <- gsub("[^<=>]+", "", as.character(x))
-  operators[operators != ""] <- font_silver(operators[operators != ""], collapse = NULL)
+  operators[!is.na(operators) & operators != ""] <- font_silver(operators[!is.na(operators) & operators != ""], collapse = NULL)
   out <- trimws(paste0(operators, trimws(format(crude_numbers))))
   out[is.na(x)] <- font_na(NA)
   # maketrailing zeroes almost invisible

R/mo.R

@@ -1003,6 +1003,35 @@ exec_as.mo <- function(x,
             }
           }
           
+          # try splitting of characters in the middle and then find ID based on old names ----
+          # only when text length is 6 or lower
+          # like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus
+          if (nchar(g.x_backup_without_spp) <= 6) {
+            x_length <- nchar(g.x_backup_without_spp)
+            x_split <- paste0("^",
+                              g.x_backup_without_spp %pm>% substr(1, x_length / 2),
+                              ".* ",
+                              g.x_backup_without_spp %pm>% substr((x_length / 2) + 1, x_length))
+            found <- lookup(fullname_lower %like_case% x_split,
+                            haystack = MO.old_lookup,
+                            column = NULL)
+            if (!all(is.na(found))) {
+              # it's an old name, so return it
+              if (property == "ref") {
+                x[i] <- found["ref"]
+              } else {
+                x[i] <- lookup(fullname == found["fullname_new"], haystack = MO_lookup)
+              }
+              pkg_env$mo_renamed_last_run <- found["fullname"]
+              was_renamed(name_old = found["fullname"],
+                          name_new = lookup(fullname == found["fullname_new"], "fullname", haystack = MO_lookup),
+                          ref_old = found["ref"],
+                          ref_new = lookup(fullname == found["fullname_new"], "ref", haystack = MO_lookup),
+                          mo = lookup(fullname == found["fullname_new"], "mo", haystack = MO_lookup))
+              return(x[i])
+            }
+          }
+          
           # try fullname without start and without nchar limit of >= 6 ----
           # like "K. pneu rhino" >> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
           found <- lookup(fullname_lower %like_case% e.x_withspaces_start_only,

cran-comments.md

@@ -1 +1,2 @@
-* This package has a data folder size of ~1.7 MB, which might return a NOTE on some R CMD CHECKs. This package size is needed to provide users reference data for the complete taxonomy of microorganisms - one of the most important features of this package, as it has been in the 16 previous releases of this package. All data sets were compressed using `compression = "xz"` to make them as small as possible.
+Extra release for fixing image options, as requested by CRAN team on 17 February 2022 (Kurt Hornik).
+

docs/404.html

@@ -43,7 +43,7 @@
       </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="Released version">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9010</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -17,7 +17,7 @@
       </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="Released version">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9010</span>
       </span>
     </div>
 

docs/articles/datasets.html

@@ -44,7 +44,7 @@
       </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="Released version">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9010</span>
       </span>
     </div>
 
@@ -190,7 +190,7 @@
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Data sets for download / own use</h1>
             
-            <h4 data-toc-skip class="date">14 March 2022</h4>
+            <h4 data-toc-skip class="date">15 March 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="hidden name"><code>datasets.Rmd</code></div>

docs/authors.html

@@ -17,7 +17,7 @@
       </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="Released version">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9010</span>
       </span>
     </div>
 

docs/index.html

@@ -47,7 +47,7 @@
       </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="Released version">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9010</span>
       </span>
     </div>
 

docs/news/index.html

@@ -17,7 +17,7 @@
       </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="Released version">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9010</span>
       </span>
     </div>
 
@@ -157,14 +157,16 @@
     </div>
 
     <div class="section level2">
-<h2 class="page-header" data-toc-text="1.8.1" id="amr-181">
-<code>AMR</code> 1.8.1<a class="anchor" aria-label="anchor" href="#amr-181"></a></h2>
+<h2 class="page-header" data-toc-text="1.8.0.9010" id="amr-1809010">
+<code>AMR</code> 1.8.0.9010<a class="anchor" aria-label="anchor" href="#amr-1809010"></a></h2>
+<div class="section level3">
+<h3 id="last-updated-march-1-8-0-9010"><small>Last updated: 15 March 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-march-1-8-0-9010"></a></h3>
 <p>All functions in this package are considered to be stable. Updates to
 the AMR interpretation rules (such as by EUCAST and CLSI), the microbial
 taxonomy, and the antibiotic dosages will all be updated every 6 to 12
 months.</p>
 <div class="section level4">
-<h4 id="changed-1-8-1">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1"></a></h4>
+<h4 id="changed-1-8-0-9010">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-0-9010"></a></h4>
 <ul><li><p>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on values containing capped
 values (such as <code>&gt;=</code>), sometimes leading to
 <code>NA</code></p></li>
@@ -182,12 +184,14 @@ ignoring non-taxonomic text, such as:</p>
 <li><p>More informative warning messages</p></li>
 <li><p>Added 192 as valid MIC</p></li>
 <li><p>Updated MIC printing in tibbles</p></li>
+<li><p>Increased speed for loading the package</p></li>
 </ul></div>
 <div class="section level4">
-<h4 id="other-1-8-1">Other<a class="anchor" aria-label="anchor" href="#other-1-8-1"></a></h4>
+<h4 id="other-1-8-0-9010">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0-9010"></a></h4>
 <ul><li>Fix for unit testing on R 3.3</li>
 <li>Fix for size of some image elements, as requested by CRAN</li>
 </ul></div>
+</div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.8.0" id="amr-180">
@@ -368,7 +372,7 @@ guideline</li>
 <li>Improved plot legends for MICs and disk diffusion values</li>
 <li>Improved speed of <code><a href="../reference/as.ab.html">as.ab()</a></code> and all <code>ab_*()</code>
 functions</li>
-<li>Added <code><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify()</a></code> extensions for plotting methods</li>
+<li>Added <code>fortify()</code> extensions for plotting methods</li>
 <li>
 <code>NA</code> values of the classes <code>&lt;mic&gt;</code>,
 <code>&lt;disk&gt;</code> and <code>&lt;rsi&gt;</code> are now exported
@@ -484,7 +488,7 @@ rewritten.</li>
 selector and function <code>filter_betalactams()</code> as additional
 antbiotic column filter. The group of betalactams consists of all
 carbapenems, cephalosporins and penicillins.</li>
-<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot()</a></code> method for
+<li>A <code>ggplot()</code> method for
 <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
 </li>
 </ul></div>
@@ -628,7 +632,7 @@ function) to select/filter on e.g. linezolid and tedizolid</p>
 <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" class="external-link">ggplot()</a></code> generics for classes
+<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
@@ -697,7 +701,7 @@ printing)</li>
 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" class="external-link">ggplot()</a></code> on any vector of MIC and disk
+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
@@ -740,7 +744,7 @@ per hour)</li>
 <li>Argument <code>ampc_cephalosporin_resistance</code> in
 <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only
 “S”)</li>
-<li>Functions <code><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> on a
+<li>Functions <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> on a
 Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print
 additional group info if the original data was grouped using
 <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">dplyr::group_by()</a></code>
@@ -1266,10 +1270,10 @@ versions of R since R-3.0.0 (April 2013). Our package is being used in
 settings where the resources are very limited. Fewer dependencies on
 newer software is helpful for such settings.</p>
 <p>Negative effects of this change are:</p>
-<ul><li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> that was borrowed from the
+<ul><li>Function <code>freq()</code> that was borrowed from the
 <code>cleaner</code> package was removed. Use
 <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner" class="external-link">library("cleaner")</a></code>
-before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code>.</li>
+before you use <code>freq()</code>.</li>
 <li><del>Printing values of class <code>mo</code> or <code>rsi</code> in
 a tibble will no longer be in colour and printing <code>rsi</code> in a
 tibble will show the class <code>&lt;ord&gt;</code>, not
@@ -1698,9 +1702,9 @@ data integrity, this means that invalid assignments will now result in
 could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the
 class would suggest a valid microbial code.</p>
 </li>
-<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean" class="external-link"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean" class="external-link">CRAN link</a>), since
+<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean" class="external-link"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean" class="external-link">CRAN link</a>), since
 creating frequency tables actually does not fit the scope of this
-package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> function still works, since it is
+package. The <code>freq()</code> function still works, since it is
 re-exported from the <code>clean</code> package (which will be installed
 automatically upon updating this <code>AMR</code> package).</p></li>
 <li><p>Renamed data set <code>septic_patients</code> to
@@ -2072,7 +2076,7 @@ since it uses <code><a href="../reference/count.html">count_df()</a></code> inte
 <code>guess_atc()</code>, <code>EUCAST_rules()</code>,
 <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
 </li>
-<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code>):
+<li>Frequency tables (<code>freq()</code>):
 <ul><li><p>speed improvement for microbial IDs</p></li>
 <li><p>fixed factor level names for R Markdown</p></li>
 <li><p>when all values are unique it now shows a message instead of a
@@ -2082,12 +2086,12 @@ warning</p></li>
 <div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
+  <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html" class="external-link">boxplot</a></span><span class="op">(</span><span class="op">)</span>
 <span class="co"># grouped boxplots:</span>
 <span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
+  <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
   <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html" class="external-link">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
 </li>
 </ul></li>
@@ -2099,7 +2103,7 @@ be viewed here</a>
 </li>
 <li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let
 groups of fives and tens end with 100+ instead of 120+</li>
-<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> for when all values are
+<li>Fix for <code>freq()</code> for when all values are
 <code>NA</code>
 </li>
 <li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
@@ -2435,7 +2439,7 @@ unique count, e.g. using <code>summary(mo)</code>
 return <code>S</code>
 </li>
 </ul></li>
-<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> function):
+<li>Frequency tables (<code>freq()</code> function):
 <ul><li>
 <p>Support for tidyverse quasiquotation! Now you can create
 frequency tables of function outcomes:</p>
@@ -2445,15 +2449,15 @@ frequency tables of function outcomes:</p>
 <span class="co"># OLD WAY</span>
 <span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
+  <span class="fu">freq</span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
 <span class="co"># NEW WAY</span>
 <span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
+  <span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
 
 <span class="co"># Even supports grouping variables:</span>
 <span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+  <span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
 </li>
 <li><p>Header info is now available as a list, with the
 <code>header</code> function</p></li>
@@ -2580,21 +2584,21 @@ total available isolate is below argument <code>minimum</code></p></li>
 <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not
 set package name as attribute anymore</p></li>
 <li>
-<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code>:</p>
+<p>Frequency tables - <code>freq()</code>:</p>
 <ul><li>
 <p>Support for grouping variables, test with:</p>
 <div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
+  <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
 </li>
 <li>
 <p>Support for (un)selecting columns:</p>
 <div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
+  <span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
 </li>
 <li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html" class="external-link">hms::is.hms</a></code></p></li>
@@ -2623,7 +2627,7 @@ to comply with CRAN policy to only allow ASCII characters</p></li>
 <li><p>Fix for <code>eucast_rules</code> where some Streptococci would
 become ceftazidime R in EUCAST rule 4.5</p></li>
 <li><p>Support for named vectors of class <code>mo</code>, useful for
-<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">top_freq()</a></code></p></li>
+<code>top_freq()</code></p></li>
 <li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have
 <code>breaks</code> argument</p></li>
 <li>
@@ -2848,13 +2852,13 @@ tables</p></li>
 <div class="sourceCode" id="cb52"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html" class="external-link">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
-<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
+<span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
 <p>For lists, subsetting is possible:</p>
 <div class="sourceCode" id="cb53"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
-<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
-<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
+<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
+<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
 </li>
 </ul></div>
 <div class="section level5">

docs/survey.html

@@ -17,7 +17,7 @@
       </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="Released version">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9010</span>
       </span>
     </div>
 

inst/tinytest/test-mo.R

@@ -201,6 +201,7 @@ expect_equal(as.character(as.mo("g aponina")), "B_GMPHS_APNN")
 expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT")
 print(mo_renamed())
 expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT"))
+expect_equal(suppressMessages(mo_name("eubcom")), "Clostridium combesii")
 
 # check uncertain names
 expect_equal(suppressMessages(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AURS")

man/antibiotic_class_selectors.Rd

@@ -131,7 +131,7 @@ The \code{\link[=ab_selector]{ab_selector()}} function can be used to internally
 
 The \code{\link[=administrable_per_os]{administrable_per_os()}} and \code{\link[=administrable_iv]{administrable_iv()}} functions also rely on the \link{antibiotics} data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the \link{antibiotics} data set.
 
-The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function can be used to only select antibiotic columns that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of \emph{E. coli} and \emph{K. pneumoniae} and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021) to determine intrinsic resistance, using the \code{\link[=eucast_rules]{eucast_rules()}} function internally. Because of this determination, this function is quite slow in terms of performance.
+The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function can be used to only select antibiotic columns that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of \emph{E. coli} and \emph{K. pneumoniae} and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies \href{https://www.eucast.org/expert_rules_and_expected_phenotypes/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021) to determine intrinsic resistance, using the \code{\link[=eucast_rules]{eucast_rules()}} function internally. Because of this determination, this function is quite slow in terms of performance.
 }
 \section{Full list of supported (antibiotic) classes}{
 

man/as.rsi.Rd

@@ -74,7 +74,7 @@ is.rsi.eligible(x, threshold = 0.05)
 
 \item{conserve_capped_values}{a \link{logical} to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"}
 
-\item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a \link{logical} to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).}
+\item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a \link{logical} to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).}
 
 \item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{rsi_translation} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{rsi_translation} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.}
 

man/intrinsic_resistant.Rd

@@ -20,7 +20,7 @@ Data set containing defined intrinsic resistance by EUCAST of all bug-drug combi
 \details{
 The repository of this \code{AMR} package contains a file comprising this data set with full taxonomic and antibiotic names: \url{https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt}. This file \strong{allows for machine reading EUCAST guidelines about intrinsic resistance}, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
 
-This data set is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).
+This data set is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).
 }
 \section{Reference Data Publicly Available}{
 

man/mdro.Rd

@@ -105,7 +105,7 @@ The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsi
 The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})
 \item \code{guideline = "TB"}
 
-The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/tb/publications/pmdt_companionhandbook/en/}{link})
+The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/publications/i/item/9789241548809}{link})
 \item \code{guideline = "MRGN"}
 
 The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; \doi{10.1186/s13756-015-0047-6}

man/mo_property.Rd

@@ -131,7 +131,7 @@ The Gram stain - \code{\link[=mo_gramstain]{mo_gramstain()}} - will be determine
 
 Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). \emph{True yeasts} are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (except when the input is \code{NA} or the MO code is \code{UNKNOWN}).
 
-Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} functions can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics).
+Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} functions can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics).
 
 All output \link[=translate]{will be translated} where possible.