(v1.1.0.9007) lose dependencies

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.1.0.9006
+Version: 1.1.0.9007
 Date: 2020-05-16
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.1.0.9006
+# AMR 1.1.0.9007
 ## <small>Last updated: 16-May-2020</small>
 
 ### Breaking 

R/availability.R

@@ -32,6 +32,7 @@
 #' @examples
 #' availability(example_isolates)
 #'
+#' \dontrun{
 #' library(dplyr)
 #' example_isolates %>% availability()
 #'
@@ -43,6 +44,7 @@
 #'   filter(mo == as.mo("E. coli")) %>%
 #'   select_if(is.rsi) %>%
 #'   availability()
+#' }
 availability <- function(tbl, width = NULL) {
   x <- base::sapply(tbl, function(x) {
     1 - base::sum(base::is.na(x)) / base::length(x) 

R/count.R

@@ -69,7 +69,7 @@
 #' susceptibility(example_isolates$AMX) * n_rsi(example_isolates$AMX)
 #'
 #' 
-#' if (!require("dplyr")) {
+#' if (require("dplyr")) {
 #'   example_isolates %>%
 #'     group_by(hospital_id) %>%
 #'     summarise(R  = count_R(CIP),

R/disk.R

@@ -33,6 +33,7 @@
 #' @seealso [as.rsi()]
 #' @inheritSection AMR Read more on our website!
 #' @examples
+#' \dontrun{
 #' # transform existing disk zones to the `disk` class
 #' library(dplyr)
 #' df <- data.frame(microorganism = "E. coli",
@@ -50,6 +51,7 @@
 #'        guideline = "EUCAST")
 #'        
 #' as.rsi(df)
+#' }
 as.disk <- function(x, na.rm = FALSE) {
   if (is.disk(x)) {
     x

R/eucast_rules.R

@@ -206,7 +206,8 @@ eucast_rules <- function(x,
                   "\n\nThis may overwrite your existing data if you use e.g.:",
                   "\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?")
     if ("rstudioapi" %in% rownames(utils::installed.packages())) {
-      q_continue <- rstudioapi::showQuestion("Using verbose = TRUE with eucast_rules()", txt)
+      showQuestion <- get("showQuestion", envir = asNamespace("rstudioapi"))
+      q_continue <- showQuestion("Using verbose = TRUE with eucast_rules()", txt)
     } else {
       q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)
     }

R/ggplot_rsi.R

@@ -62,7 +62,7 @@
 #' @export
 #' @inheritSection AMR Read more on our website!
 #' @examples
-#' if (!require("ggplot2") & !require("dplyr")) {
+#' if (require("ggplot2") & require("dplyr")) {
 #'  
 #'   # get antimicrobial results for drugs against a UTI:
 #'   ggplot(example_isolates %>% select(AMX, NIT, FOS, TMP, CIP)) +

R/key_antibiotics.R

@@ -73,6 +73,7 @@
 #' # `example_isolates` is a dataset available in the AMR package.
 #' # See ?example_isolates.
 #'
+#' \dontrun{
 #' library(dplyr)
 #' # set key antibiotics to a new variable
 #' my_patients <- example_isolates %>%
@@ -87,7 +88,7 @@
 #' # Check the difference, in this data set it results in 7% more isolates:
 #' sum(my_patients$first_regular, na.rm = TRUE)
 #' sum(my_patients$first_weighted, na.rm = TRUE)
-#'
+#' }
 #'
 #' # output of the `key_antibiotics` function could be like this:
 #' strainA <- "SSSRR.S.R..S"

R/like.R

@@ -57,10 +57,12 @@
 #' #> TRUE TRUE TRUE
 #'
 #' # get isolates whose name start with 'Ent' or 'ent'
+#' \dontrun{
 #' library(dplyr)
 #' example_isolates %>%
 #'   filter(mo_name(mo) %like% "^ent") %>% 
 #'   freq(mo)
+#' }
 like <- function(x, pattern, ignore.case = TRUE) {
   # set to fixed if no regex found
   fixed <- all(!grepl("[$.^*?+}{|)(]", pattern))

R/mdro.R

@@ -66,7 +66,7 @@
 #' @source
 #' Please see *Details* for the list of publications used for this function.
 #' @examples
-#' \donttest{
+#' \dontrun{
 #' library(dplyr)
 #' 
 #' example_isolates %>%
@@ -94,7 +94,8 @@ mdro <- function(x,
                   "\n\nThis may overwrite your existing data if you use e.g.:",
                   "\ndata <- mdro(data, verbose = TRUE)\n\nDo you want to continue?")
     if ("rstudioapi" %in% rownames(utils::installed.packages())) {
-      q_continue <- rstudioapi::showQuestion("Using verbose = TRUE with mdro()", txt)
+      showQuestion <- get("showQuestion", envir = asNamespace("rstudioapi"))
+      q_continue <- showQuestion("Using verbose = TRUE with mdro()", txt)
     } else {
       q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)
     }

R/mo_source.R

@@ -126,7 +126,8 @@ set_mo_source <- function(path) {
   } else if (path %like% "[.]xlsx?$") {
     # is Excel file (old or new)
     stopifnot_installed_package("readxl")
-    df <- readxl::read_excel(path)
+    read_excel <- get("read_excel", envir = asNamespace("readxl"))
+    df <- read_excel(path)
 
   } else if (path %like% "[.]tsv$") {
     df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE)

R/proportion.R

@@ -99,8 +99,7 @@
 #' proportion_IR(example_isolates$AMX)
 #' proportion_R(example_isolates$AMX)
 #'
-#' if (!require("dplyr")) {
-#'   library(dplyr)
+#' if (require("dplyr")) {
 #'   example_isolates %>%
 #'     group_by(hospital_id) %>%
 #'     summarise(r = resistance(CIP),
@@ -157,7 +156,9 @@
 #'     select(hospital_id, AMX, CIP) %>%
 #'     group_by(hospital_id) %>%
 #'     proportion_df(translate = FALSE)
-#'  
+#' }
+#' 
+#' \dontrun{  
 #'   # calculate current empiric combination therapy of Helicobacter gastritis:
 #'   my_table %>%
 #'     filter(first_isolate == TRUE,

R/resistance_predict.R

@@ -66,11 +66,12 @@
 #'                         year_min = 2010,
 #'                         model = "binomial")
 #' plot(x)
-#' ggplot_rsi_predict(x)
+#' if (require("ggplot2")) {
+#'   ggplot_rsi_predict(x)
+#' }
 #'
 #' # using dplyr:
-#' if (!require("dplyr")) {
-#'   library(dplyr)
+#' if (require("dplyr")) {
 #'   x <- example_isolates %>%
 #'     filter_first_isolate() %>%
 #'     filter(mo_genus(mo) == "Staphylococcus") %>%
@@ -83,7 +84,7 @@
 #' }
 #'
 #' # create nice plots with ggplot2 yourself
-#' if (!require(ggplot2) & !require("dplyr")) {
+#' if (require(ggplot2) & require("dplyr")) {
 #'
 #'   data <- example_isolates %>%
 #'     filter(mo == as.mo("E. coli")) %>%

R/rsi.R

@@ -70,7 +70,7 @@
 #'                  NIT = as.mic(32))
 #' as.rsi(df)
 #' 
-#' \donttest{
+#' \dontrun{
 #' 
 #' # the dplyr way
 #' library(dplyr)
@@ -117,6 +117,7 @@
 #' plot(rsi_data)    # for percentages
 #' barplot(rsi_data) # for frequencies
 #'
+#' \dontrun{
 #' library(dplyr)
 #' example_isolates %>%
 #'   mutate_at(vars(PEN:RIF), as.rsi)
@@ -132,6 +133,7 @@
 #' # default threshold of `is.rsi.eligible` is 5%.
 #' is.rsi.eligible(WHONET$`First name`) # fails, >80% is invalid
 #' is.rsi.eligible(WHONET$`First name`, threshold = 0.99) # succeeds
+#' }
 as.rsi <- function(x, ...) {
   UseMethod("as.rsi")
 }

appveyor.yml

@@ -23,7 +23,7 @@
 init:
   ps: |
         $ErrorActionPreference = "Stop"
-        Invoke-WebRequest https://gitlab.com/msberends/AMR/raw/master/tests/appveyor/appveyor_tool.ps1 -OutFile "..\appveyor-tool.ps1"
+        Invoke-WebRequest https://gitlab.com/msberends/AMR/raw/premaster/tests/appveyor/appveyor_tool.ps1 -OutFile "..\appveyor-tool.ps1"
         Import-Module '..\appveyor-tool.ps1'
 
 install:

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</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">1.1.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</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">1.1.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</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">1.1.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</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">1.1.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
       </span>
     </div>
 

docs/pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   WHONET: WHONET.html
   benchmarks: benchmarks.html
   resistance_predict: resistance_predict.html
-last_built: 2020-05-16T18:05Z
+last_built: 2020-05-16T19:39Z
 urls:
   reference: https://msberends.gitlab.io/AMR/reference
   article: https://msberends.gitlab.io/AMR/articles

docs/reference/as.disk.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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
       </span>
     </div>
 
@@ -275,7 +275,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
     <div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># transform existing disk zones to the `disk` class</span>
+    <pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
+<span class='co'># transform existing disk zones to the `disk` class</span>
 <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>microorganism</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>,
                  <span class='kw'>AMP</span> <span class='kw'>=</span> <span class='fl'>20</span>,
@@ -291,7 +292,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
        <span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"ampicillin"</span>,  <span class='co'># and `ab` with as.ab()</span>
        <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
 
-<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='no'>df</span>)</pre>
+<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='no'>df</span>)
+}</pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -307,7 +309,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
       </footer>

docs/reference/as.rsi.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">1.1.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
       </span>
     </div>
 
@@ -353,7 +353,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
                  <span class='kw'>NIT</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>32</span>))
 <span class='fu'>as.rsi</span>(<span class='no'>df</span>)
 
-<span class='co'># \donttest{</span>
+<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
 
 <span class='co'># the dplyr way</span>
 <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
@@ -376,7 +376,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
 <span class='no'>df</span> <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>AMP</span>:<span class='no'>NIT</span>), <span class='no'>as.rsi</span>, <span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>, <span class='kw'>uti</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='co'># }</span>
+}
 
 <span class='co'># for single values</span>
 <span class='fu'>as.rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>2</span>),
@@ -400,6 +400,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>rsi_data</span>)    <span class='co'># for percentages</span>
 <span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for frequencies</span>
 
+<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
 <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>PEN</span>:<span class='no'>RIF</span>), <span class='no'>as.rsi</span>)
@@ -414,7 +415,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
 <span class='co'># default threshold of `is.rsi.eligible` is 5%.</span>
 <span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>) <span class='co'># fails, &gt;80% is invalid</span>
-<span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>0.99</span>) <span class='co'># succeeds</span></pre>
+<span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>0.99</span>) <span class='co'># succeeds</span>
+}</pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">

docs/reference/atc_online.html

@@ -83,7 +83,7 @@ This function requires an internet connection." />
       </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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
       </span>
     </div>
 
@@ -315,7 +315,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
 <p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># \donttest{</span>
+    <pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
 <span class='co'># oral DDD (Defined Daily Dose) of amoxicillin</span>
 <span class='fu'>atc_online_property</span>(<span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"O"</span>)
 <span class='co'># parenteral DDD (Defined Daily Dose) of amoxicillin</span>
@@ -326,7 +326,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
 <span class='co'># [2] "ANTIBACTERIALS FOR SYSTEMIC USE"</span>
 <span class='co'># [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"</span>
 <span class='co'># [4] "Penicillins with extended spectrum"</span>
-<span class='co'># }</span></pre>
+}</pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -342,7 +342,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
       </footer>

docs/reference/availability.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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
       </span>
     </div>
 
@@ -272,6 +272,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='fu'>availability</span>(<span class='no'>example_isolates</span>)
 
+<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
 <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>availability</span>()
 
@@ -282,7 +283,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select_all.html'>select_if</a></span>(<span class='no'>is.rsi</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'>availability</span>()</pre>
+  <span class='fu'>availability</span>()
+}</pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -298,7 +300,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
       </footer>

docs/reference/count.html

@@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
       </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">1.1.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
       </span>
     </div>
 
@@ -392,7 +392,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 <span class='fu'><a href='proportion.html'>susceptibility</a></span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) * <span class='fu'>n_rsi</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
 
 
-<span class='kw'>if</span> (!<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
+<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
   <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span>  <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>CIP</span>),

docs/reference/ggplot_rsi.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">1.1.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
       </span>
     </div>
 
@@ -412,44 +412,45 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
 <p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
-<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>ggplot2</span>)
-
-<span class='co'># get antimicrobial results for drugs against a UTI:</span>
-<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>)) +
-  <span class='fu'>geom_rsi</span>()
-
-<span class='co'># prettify the plot using some additional functions:</span>
-<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>)
-<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>df</span>) +
-  <span class='fu'>geom_rsi</span>() +
-  <span class='fu'>scale_y_percent</span>() +
-  <span class='fu'>scale_rsi_colours</span>() +
-  <span class='fu'>labels_rsi_count</span>() +
-  <span class='fu'>theme_rsi</span>()
-
-<span class='co'># or better yet, simplify this using the wrapper function - a single command:</span>
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'>ggplot_rsi</span>()
-
-<span class='co'># get only proportions and no counts:</span>
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'>ggplot_rsi</span>(<span class='kw'>datalabels</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-
-<span class='co'># add other ggplot2 parameters as you like:</span>
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'>ggplot_rsi</span>(<span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
-             <span class='kw'>colour</span> <span class='kw'>=</span> <span class='st'>"black"</span>,
-             <span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>1</span>,
-             <span class='kw'>linetype</span> <span class='kw'>=</span> <span class='fl'>2</span>,
-             <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.25</span>)
-
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'>ggplot_rsi</span>(<span class='kw'>colours</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>SI</span> <span class='kw'>=</span> <span class='st'>"yellow"</span>))
+    <pre class="examples"><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"ggplot2"</span>) <span class='kw'>&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
+
+  <span class='co'># get antimicrobial results for drugs against a UTI:</span>
+  <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>)) +
+    <span class='fu'>geom_rsi</span>()
+
+  <span class='co'># prettify the plot using some additional functions:</span>
+  <span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>)
+  <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>df</span>) +
+    <span class='fu'>geom_rsi</span>() +
+    <span class='fu'>scale_y_percent</span>() +
+    <span class='fu'>scale_rsi_colours</span>() +
+    <span class='fu'>labels_rsi_count</span>() +
+    <span class='fu'>theme_rsi</span>()
+
+  <span class='co'># or better yet, simplify this using the wrapper function - a single command:</span>
+  <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
+    <span class='fu'>ggplot_rsi</span>()
+
+  <span class='co'># get only proportions and no counts:</span>
+  <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
+    <span class='fu'>ggplot_rsi</span>(<span class='kw'>datalabels</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
+
+  <span class='co'># add other ggplot2 parameters as you like:</span>
+  <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
+    <span class='fu'>ggplot_rsi</span>(<span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
+               <span class='kw'>colour</span> <span class='kw'>=</span> <span class='st'>"black"</span>,
+               <span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>1</span>,
+               <span class='kw'>linetype</span> <span class='kw'>=</span> <span class='fl'>2</span>,
+               <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.25</span>)
+
+  <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>) <span class='kw'>%&gt;%</span>
+    <span class='fu'>ggplot_rsi</span>(<span class='kw'>colours</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>SI</span> <span class='kw'>=</span> <span class='st'>"yellow"</span>))
+
+}
 
 <span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
 

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">1.1.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
       </span>
     </div>
 

docs/reference/key_antibiotics.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">1.1.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
       </span>
     </div>
 
@@ -388,6 +388,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
     <pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
 <span class='co'># See ?example_isolates.</span>
 
+<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
 <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='co'># set key antibiotics to a new variable</span>
 <span class='no'>my_patients</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
@@ -402,7 +403,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='co'># Check the difference, in this data set it results in 7% more isolates:</span>
 <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_regular</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_weighted</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-
+}
 
 <span class='co'># output of the `key_antibiotics` function could be like this:</span>
 <span class='no'>strainA</span> <span class='kw'>&lt;-</span> <span class='st'>"SSSRR.S.R..S"</span>

docs/reference/like.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">1.1.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
       </span>
     </div>
 
@@ -306,10 +306,12 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='co'>#&gt; TRUE TRUE TRUE</span>
 
 <span class='co'># get isolates whose name start with 'Ent' or 'ent'</span>
+<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
 <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='no'>mo</span>) <span class='kw'>%like%</span> <span class='st'>"^ent"</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>mo</span>)</pre>
+  <span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>mo</span>)
+}</pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">

docs/reference/mdro.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">1.1.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
       </span>
     </div>
 
@@ -440,7 +440,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 <p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># \donttest{</span>
+    <pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
 <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
 
 <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
@@ -451,7 +451,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
   <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>EUCAST</span> <span class='kw'>=</span> <span class='fu'>eucast_exceptional_phenotypes</span>(<span class='no'>.</span>),
          <span class='kw'>BRMO</span> <span class='kw'>=</span> <span class='fu'>brmo</span>(<span class='no'>.</span>),
          <span class='kw'>MRGN</span> <span class='kw'>=</span> <span class='fu'>mrgn</span>(<span class='no'>.</span>))
-<span class='co'># }</span></pre>
+}</pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">

docs/reference/proportion.html

@@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
       </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">1.1.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
       </span>
     </div>
 
@@ -398,8 +398,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 <span class='fu'>proportion_IR</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
 <span class='fu'>proportion_R</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
 
-<span class='kw'>if</span> (!<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
-  <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
+<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
   <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>r</span> <span class='kw'>=</span> <span class='fu'>resistance</span>(<span class='no'>CIP</span>),
@@ -456,7 +455,9 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
     <span class='fu'>proportion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
+}
 
+<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
   <span class='co'># calculate current empiric combination therapy of Helicobacter gastritis:</span>
   <span class='no'>my_table</span> <span class='kw'>%&gt;%</span>
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,

docs/reference/resistance_predict.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">1.1.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
       </span>
     </div>
 
@@ -393,11 +393,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
                         <span class='kw'>year_min</span> <span class='kw'>=</span> <span class='fl'>2010</span>,
                         <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>)
 <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>x</span>)
-<span class='fu'>ggplot_rsi_predict</span>(<span class='no'>x</span>)
+<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"ggplot2"</span>)) {
+  <span class='fu'>ggplot_rsi_predict</span>(<span class='no'>x</span>)
+}
 
 <span class='co'># using dplyr:</span>
-<span class='kw'>if</span> (!<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
-  <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
+<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
   <span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
     <span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%&gt;%</span>
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%&gt;%</span>
@@ -410,7 +411,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 }
 
 <span class='co'># create nice plots with ggplot2 yourself</span>
-<span class='kw'>if</span> (!<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>ggplot2</span>) <span class='kw'>&amp;</span> !<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
+<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>ggplot2</span>) <span class='kw'>&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
 
   <span class='no'>data</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>

man/as.disk.Rd

@@ -38,6 +38,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
 }
 
 \examples{
+\dontrun{
 # transform existing disk zones to the `disk` class
 library(dplyr)
 df <- data.frame(microorganism = "E. coli",
@@ -56,6 +57,7 @@ as.rsi(x = as.disk(18),
        
 as.rsi(df)
 }
+}
 \seealso{
 \code{\link[=as.rsi]{as.rsi()}}
 }

man/as.rsi.Rd

@@ -110,7 +110,7 @@ df <- data.frame(microorganism = "E. coli",
                  NIT = as.mic(32))
 as.rsi(df)
 
-\donttest{
+\dontrun{
 
 # the dplyr way
 library(dplyr)
@@ -157,6 +157,7 @@ is.rsi(rsi_data)
 plot(rsi_data)    # for percentages
 barplot(rsi_data) # for frequencies
 
+\dontrun{
 library(dplyr)
 example_isolates \%>\%
   mutate_at(vars(PEN:RIF), as.rsi)
@@ -173,6 +174,7 @@ example_isolates \%>\%
 is.rsi.eligible(WHONET$`First name`) # fails, >80\% is invalid
 is.rsi.eligible(WHONET$`First name`, threshold = 0.99) # succeeds
 }
+}
 \seealso{
 \code{\link[=as.mic]{as.mic()}}
 }

man/atc_online.Rd

@@ -75,7 +75,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
 }
 
 \examples{
-\donttest{
+\dontrun{
 # oral DDD (Defined Daily Dose) of amoxicillin
 atc_online_property("J01CA04", "DDD", "O")
 # parenteral DDD (Defined Daily Dose) of amoxicillin

man/availability.Rd

@@ -36,6 +36,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
 \examples{
 availability(example_isolates)
 
+\dontrun{
 library(dplyr)
 example_isolates \%>\% availability()
 
@@ -48,3 +49,4 @@ example_isolates \%>\%
   select_if(is.rsi) \%>\%
   availability()
 }
+}

man/count.Rd

@@ -158,7 +158,7 @@ count_susceptible(example_isolates$AMX)
 susceptibility(example_isolates$AMX) * n_rsi(example_isolates$AMX)
 
 
-if (!require("dplyr")) {
+if (require("dplyr")) {
   example_isolates \%>\%
     group_by(hospital_id) \%>\%
     summarise(R  = count_R(CIP),

man/ggplot_rsi.Rd

@@ -147,44 +147,45 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
 }
 
 \examples{
-library(dplyr)
-library(ggplot2)
-
-# get antimicrobial results for drugs against a UTI:
-ggplot(example_isolates \%>\% select(AMX, NIT, FOS, TMP, CIP)) +
-  geom_rsi()
-
-# prettify the plot using some additional functions:
-df <- example_isolates \%>\% select(AMX, NIT, FOS, TMP, CIP)
-ggplot(df) +
-  geom_rsi() +
-  scale_y_percent() +
-  scale_rsi_colours() +
-  labels_rsi_count() +
-  theme_rsi()
-
-# or better yet, simplify this using the wrapper function - a single command:
-example_isolates \%>\%
-  select(AMX, NIT, FOS, TMP, CIP) \%>\%
-  ggplot_rsi()
-
-# get only proportions and no counts:
-example_isolates \%>\%
-  select(AMX, NIT, FOS, TMP, CIP) \%>\%
-  ggplot_rsi(datalabels = FALSE)
-
-# add other ggplot2 parameters as you like:
-example_isolates \%>\%
-  select(AMX, NIT, FOS, TMP, CIP) \%>\%
-  ggplot_rsi(width = 0.5,
-             colour = "black",
-             size = 1,
-             linetype = 2,
-             alpha = 0.25)
-
-example_isolates \%>\%
-  select(AMX) \%>\%
-  ggplot_rsi(colours = c(SI = "yellow"))
+if (require("ggplot2") & require("dplyr")) {
+ 
+  # get antimicrobial results for drugs against a UTI:
+  ggplot(example_isolates \%>\% select(AMX, NIT, FOS, TMP, CIP)) +
+    geom_rsi()
+ 
+  # prettify the plot using some additional functions:
+  df <- example_isolates \%>\% select(AMX, NIT, FOS, TMP, CIP)
+  ggplot(df) +
+    geom_rsi() +
+    scale_y_percent() +
+    scale_rsi_colours() +
+    labels_rsi_count() +
+    theme_rsi()
+ 
+  # or better yet, simplify this using the wrapper function - a single command:
+  example_isolates \%>\%
+    select(AMX, NIT, FOS, TMP, CIP) \%>\%
+    ggplot_rsi()
+ 
+  # get only proportions and no counts:
+  example_isolates \%>\%
+    select(AMX, NIT, FOS, TMP, CIP) \%>\%
+    ggplot_rsi(datalabels = FALSE)
+ 
+  # add other ggplot2 parameters as you like:
+  example_isolates \%>\%
+    select(AMX, NIT, FOS, TMP, CIP) \%>\%
+    ggplot_rsi(width = 0.5,
+               colour = "black",
+               size = 1,
+               linetype = 2,
+               alpha = 0.25)
+ 
+  example_isolates \%>\%
+    select(AMX) \%>\%
+    ggplot_rsi(colours = c(SI = "yellow"))
+  
+}
   
 \dontrun{
 

man/key_antibiotics.Rd

@@ -136,6 +136,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
 # `example_isolates` is a dataset available in the AMR package.
 # See ?example_isolates.
 
+\dontrun{
 library(dplyr)
 # set key antibiotics to a new variable
 my_patients <- example_isolates \%>\%
@@ -150,7 +151,7 @@ my_patients <- example_isolates \%>\%
 # Check the difference, in this data set it results in 7\% more isolates:
 sum(my_patients$first_regular, na.rm = TRUE)
 sum(my_patients$first_weighted, na.rm = TRUE)
-
+}
 
 # output of the `key_antibiotics` function could be like this:
 strainA <- "SSSRR.S.R..S"

man/like.Rd

@@ -68,11 +68,13 @@ a \%like\% b
 #> TRUE TRUE TRUE
 
 # get isolates whose name start with 'Ent' or 'ent'
+\dontrun{
 library(dplyr)
 example_isolates \%>\%
   filter(mo_name(mo) \%like\% "^ent") \%>\% 
   freq(mo)
 }
+}
 \seealso{
 \code{\link[base:grep]{base::grep()}}
 }

man/mdro.Rd

@@ -206,7 +206,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
 }
 
 \examples{
-\donttest{
+\dontrun{
 library(dplyr)