(v1.6.0.9065) unit tests

.github/workflows/check.yaml

@@ -121,6 +121,7 @@ jobs:
       # - name: Only keep vignettes on release version
       - name: Remove vignettes
         # if: matrix.config.r != 'release'
+        if: always()
         # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite
         run: |
           rm -rf AMR/vignettes

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.6.0.9064
+Version: 1.6.0.9065
 Date: 2021-05-24
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# `AMR` 1.6.0.9064
+# `AMR` 1.6.0.9065
 ## <small>Last updated: 24 May 2021</small>
 
 ### Breaking change

R/aa_helper_functions.R

@@ -864,8 +864,13 @@ unique_call_id <- function(entire_session = FALSE) {
   } else {
     # combination of environment ID (like "0x7fed4ee8c848")
     # and highest system call
+    call <- paste0(deparse(sys.calls()[[1]]), collapse = "")
+    if (call %like% "run_test_dir|test_all|tinytest|test_package|testthat") {
+      # unit tests will keep the same call and environment - give them a unique ID
+      call <- paste0(sample(c(c(0:9), letters[1:6]), size = 64, replace = TRUE), collapse = "")
+    }
     c(envir = gsub("<environment: (.*)>", "\\1", utils::capture.output(sys.frames()[[1]])),
-      call = paste0(deparse(sys.calls()[[1]]), collapse = ""))
+      call = call)
   }
 }
 
@@ -881,14 +886,6 @@ message_not_thrown_before <- function(fn, entire_session = FALSE) {
   is.null(pkg_env[[paste0("thrown_msg.", fn)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn)]], unique_call_id(entire_session))
 }
 
-reset_all_thrown_messages <- function() {
-  # for unit tests, where the environment and highest system call do not change
-  # can be found in tests/testthat/*.R
-  pkg_env_contents <- ls(envir = pkg_env)
-  rm(list = pkg_env_contents[pkg_env_contents %like% "^thrown_msg."],
-     envir = pkg_env)
-}
-
 has_colour <- function() {
   # this is a base R version of crayon::has_color, but disables colours on emacs
   

R/ggplot_rsi.R

@@ -115,35 +115,35 @@
 #'     ggplot() +
 #'     geom_col(aes(x = x, y = y, fill = z)) +
 #'     scale_rsi_colours(Value4 = "S", Value5 = "I", Value6 = "R")
+#'   
+#'   # resistance of ciprofloxacine per age group
+#'   example_isolates %>%
+#'     mutate(first_isolate = first_isolate()) %>%
+#'     filter(first_isolate == TRUE,
+#'            mo == as.mo("E. coli")) %>%
+#'     # age_groups() is also a function in this AMR package:
+#'     group_by(age_group = age_groups(age)) %>%
+#'     select(age_group,
+#'            CIP) %>%
+#'     ggplot_rsi(x = "age_group")
+#'   
+#'   # a shorter version which also adjusts data label colours:
+#'   example_isolates %>%
+#'     select(AMX, NIT, FOS, TMP, CIP) %>%
+#'     ggplot_rsi(colours = FALSE)
+#'
+#'
+#'   # it also supports groups (don't forget to use the group var on `x` or `facet`):
+#'   example_isolates %>%
+#'     select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>%
+#'     group_by(hospital_id) %>%
+#'     ggplot_rsi(x = "hospital_id",
+#'                facet = "antibiotic",
+#'                nrow = 1,
+#'                title = "AMR of Anti-UTI Drugs Per Hospital",
+#'                x.title = "Hospital",
+#'                datalabels = FALSE)
 #' }
-#'   
-#' # resistance of ciprofloxacine per age group
-#' example_isolates %>%
-#'   mutate(first_isolate = first_isolate(.)) %>%
-#'   filter(first_isolate == TRUE,
-#'          mo == as.mo("E. coli")) %>%
-#'   # age_groups() is also a function in this AMR package:
-#'   group_by(age_group = age_groups(age)) %>%
-#'   select(age_group,
-#'          CIP) %>%
-#'   ggplot_rsi(x = "age_group")
-#'   
-#' # a shorter version which also adjusts data label colours:
-#' example_isolates %>%
-#'   select(AMX, NIT, FOS, TMP, CIP) %>%
-#'   ggplot_rsi(colours = FALSE)
-#'
-#'
-#' # it also supports groups (don't forget to use the group var on `x` or `facet`):
-#' example_isolates %>%
-#'   select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>%
-#'   group_by(hospital_id) %>%
-#'   ggplot_rsi(x = "hospital_id",
-#'              facet = "antibiotic",
-#'              nrow = 1,
-#'              title = "AMR of Anti-UTI Drugs Per Hospital",
-#'              x.title = "Hospital",
-#'              datalabels = FALSE)
 #' }
 ggplot_rsi <- function(data,
                        position = NULL,

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9064</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9065</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9064</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9065</span>
       </span>
     </div>
 

docs/articles/datasets.html

@@ -39,7 +39,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9064</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9065</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9064</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9065</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9064</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9065</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9064</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9065</span>
       </span>
     </div>
 

docs/news/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9064</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9065</span>
       </span>
     </div>
 
@@ -236,9 +236,9 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1609064" class="section level1">
+    <div id="amr-1609065" class="section level1">
-<h1 class="page-header" data-toc-text="1.6.0.9064">
+<h1 class="page-header" data-toc-text="1.6.0.9065">
-<a href="#amr-1609064" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9064</h1>
+<a href="#amr-1609065" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9065</h1>
 <div id="last-updated-24-may-2021" class="section level2">
 <h2 class="hasAnchor">
 <a href="#last-updated-24-may-2021" class="anchor"></a><small>Last updated: 24 May 2021</small>
@@ -288,7 +288,7 @@
 </ul>
 </li>
 <li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code><a href="../reference/AMR-deprecated.html">filter_betalactams()</a></code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
-<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
+<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
 </li>
 </ul>
 </div>
@@ -387,7 +387,7 @@
 <span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
 </li>
 <li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
-<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
+<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
 <li>
 <p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
@@ -444,7 +444,7 @@
 <li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
 <li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
 <li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
-<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
+<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
 </ul>
 </li>
 <li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>

docs/pkgdown.yml

@@ -12,7 +12,7 @@ articles:
   datasets: datasets.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-05-24T07:33Z
+last_built: 2021-05-24T09:00Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles

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">1.6.0.9063</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9065</span>
       </span>
     </div>
 
@@ -477,35 +477,35 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
     <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
     <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_bar.html'>geom_col</a></span><span class='op'>(</span><span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='va'>x</span>, y <span class='op'>=</span> <span class='va'>y</span>, fill <span class='op'>=</span> <span class='va'>z</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>+</span>
     <span class='fu'>scale_rsi_colours</span><span class='op'>(</span>Value4 <span class='op'>=</span> <span class='st'>"S"</span>, Value5 <span class='op'>=</span> <span class='st'>"I"</span>, Value6 <span class='op'>=</span> <span class='st'>"R"</span><span class='op'>)</span>
+  
+  <span class='co'># resistance of ciprofloxacine per age group</span>
+  <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>first_isolate <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>first_isolate</span> <span class='op'>==</span> <span class='cn'>TRUE</span>,
+           <span class='va'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
+    <span class='co'># age_groups() is also a function in this AMR package:</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span>age_group <span class='op'>=</span> <span class='fu'><a href='age_groups.html'>age_groups</a></span><span class='op'>(</span><span class='va'>age</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>age_group</span>,
+           <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
+    <span class='fu'>ggplot_rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"age_group"</span><span class='op'>)</span>
+  
+  <span class='co'># a shorter version which also adjusts data label colours:</span>
+  <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
+    <span class='fu'>ggplot_rsi</span><span class='op'>(</span>colours <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
+
+
+  <span class='co'># it also supports groups (don't forget to use the group var on `x` or `facet`):</span>
+  <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>hospital_id</span>, <span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
+    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
+    <span class='fu'>ggplot_rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"hospital_id"</span>,
+               facet <span class='op'>=</span> <span class='st'>"antibiotic"</span>,
+               nrow <span class='op'>=</span> <span class='fl'>1</span>,
+               title <span class='op'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
+               x.title <span class='op'>=</span> <span class='st'>"Hospital"</span>,
+               datalabels <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
 <span class='op'>}</span>
-  
-<span class='co'># resistance of ciprofloxacine per age group</span>
-<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>first_isolate <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>first_isolate</span> <span class='op'>==</span> <span class='cn'>TRUE</span>,
-         <span class='va'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
-  <span class='co'># age_groups() is also a function in this AMR package:</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span>age_group <span class='op'>=</span> <span class='fu'><a href='age_groups.html'>age_groups</a></span><span class='op'>(</span><span class='va'>age</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>age_group</span>,
-         <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
-  <span class='fu'>ggplot_rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"age_group"</span><span class='op'>)</span>
-  
-<span class='co'># a shorter version which also adjusts data label colours:</span>
-<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
-  <span class='fu'>ggplot_rsi</span><span class='op'>(</span>colours <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
-
-
-<span class='co'># it also supports groups (don't forget to use the group var on `x` or `facet`):</span>
-<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>hospital_id</span>, <span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
-  <span class='fu'>ggplot_rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"hospital_id"</span>,
-             facet <span class='op'>=</span> <span class='st'>"antibiotic"</span>,
-             nrow <span class='op'>=</span> <span class='fl'>1</span>,
-             title <span class='op'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
-             x.title <span class='op'>=</span> <span class='st'>"Hospital"</span>,
-             datalabels <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
 <span class='co'># }</span>
 </pre>
   </div>

docs/reference/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9064</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9065</span>
       </span>
     </div>
 

docs/survey.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9064</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9065</span>
       </span>
     </div>
 

inst/tinytest/test-_misc.R

@@ -22,34 +22,32 @@
 # Visit our website for the full manual and a complete tutorial about  #
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
-   
+
 expect_equal(AMR:::percentage(0.25), "25%")
 expect_equal(AMR:::percentage(0.5), "50%")
 expect_equal(AMR:::percentage(0.500, digits = 1), "50.0%")
 expect_equal(AMR:::percentage(0.1234), "12.3%")
-  # round up 0.5
+# round up 0.5
 expect_equal(AMR:::percentage(0.0054), "0.5%")
 expect_equal(AMR:::percentage(0.0055), "0.6%")
-   
+
 expect_equal(AMR:::strrep("A", 5), "AAAAA")
 expect_equal(AMR:::strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
 expect_equal(AMR:::trimws(" test "), "test")
 expect_equal(AMR:::trimws(" test ", "l"), "test ")
 expect_equal(AMR:::trimws(" test ", "r"), " test")
-   
+
 expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX")))
 expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
 expect_warning(AMR:::get_column_abx(example_isolates, hard_dependencies = "FUS"))
 expect_message(AMR:::get_column_abx(example_isolates, soft_dependencies = "FUS"))
-  if (AMR:::pkg_is_available("dplyr")) {
+
+if (AMR:::pkg_is_available("dplyr")) {
   expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
   expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
-  }
+}
-   
-  
-  # we rely on "grouped_tbl" being a class of grouped tibbles, so implement a test that checks for this:
-  if (AMR:::pkg_is_available("dplyr")) {
-  expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(hospital_id)))
-  }
 
-  
+# we rely on "grouped_tbl" being a class of grouped tibbles, so implement a test that checks for this:
+if (AMR:::pkg_is_available("dplyr")) {
+  expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(hospital_id)))
+}

inst/tinytest/test-count.R

@@ -36,11 +36,9 @@ expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
 expect_equal(suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX),
              count_SI(example_isolates$AMX))
 
-
 # warning for speed loss
-AMR:::reset_all_thrown_messages()
 expect_warning(count_resistant(as.character(example_isolates$AMC)))
-AMR:::reset_all_thrown_messages()
+
 expect_warning(count_resistant(example_isolates$AMC,
                                as.character(example_isolates$GEN)))
 

inst/tinytest/test-eucast_rules.R

@@ -45,6 +45,7 @@ expect_warning(eucast_rules(data.frame(mo = "Escherichia coli", vancomycin = "S"
 
 expect_identical(colnames(example_isolates),
                  colnames(suppressWarnings(eucast_rules(example_isolates, info = FALSE))))
+
 expect_stdout(suppressMessages(eucast_rules(example_isolates, info = TRUE)))
 
 a <- data.frame(mo = c("Klebsiella pneumoniae",
@@ -84,7 +85,7 @@ if (AMR:::pkg_is_available("dplyr")) {
     "R")
 }
 
-# Azithromycin and Clarythromycin must be equal to Erythromycin
+# azithromycin and clarythromycin must be equal to Erythromycin
 a <- suppressWarnings(as.rsi(eucast_rules(data.frame(mo = example_isolates$mo,
                                                      ERY = example_isolates$ERY,
                                                      AZM = as.rsi("R"),
@@ -117,18 +118,21 @@ if (AMR:::pkg_is_available("dplyr")) {
 expect_stdout(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, rules = "all", info = TRUE)))
 
 # AmpC de-repressed cephalo mutants
+
 expect_identical(
   eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
                           cefotax = as.rsi(c("S", "S"))),
                ampc_cephalosporin_resistance = TRUE,
                info = FALSE)$cefotax,
   as.rsi(c("S", "R")))
+
 expect_identical(
   eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
                           cefotax = as.rsi(c("S", "S"))),
                ampc_cephalosporin_resistance = NA,
                info = FALSE)$cefotax,
   as.rsi(c("S", NA)))
+
 expect_identical(
   eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
                           cefotax = as.rsi(c("S", "S"))),

inst/tinytest/test-proportion.R

@@ -88,14 +88,12 @@ if (AMR:::pkg_is_available("dplyr")) {
       example_isolates$AMX %>% proportion_R())
   )
 }
-AMR:::reset_all_thrown_messages()
+
 expect_warning(proportion_R(as.character(example_isolates$AMC)))
-AMR:::reset_all_thrown_messages()
 expect_warning(proportion_S(as.character(example_isolates$AMC)))
-AMR:::reset_all_thrown_messages()
 expect_warning(proportion_S(as.character(example_isolates$AMC,
                                          example_isolates$GEN)))
-AMR:::reset_all_thrown_messages()
+
 expect_warning(n_rsi(as.character(example_isolates$AMC,
                                   example_isolates$GEN)))
 expect_equal(suppressWarnings(n_rsi(as.character(example_isolates$AMC,
@@ -120,11 +118,8 @@ expect_identical(suppressWarnings(proportion_S(example_isolates$AMX, minimum = n
                  NA_real_)
 
 # warning for speed loss
-AMR:::reset_all_thrown_messages()
 expect_warning(proportion_R(as.character(example_isolates$GEN)))
-AMR:::reset_all_thrown_messages()
 expect_warning(proportion_I(as.character(example_isolates$GEN)))
-AMR:::reset_all_thrown_messages()
 expect_warning(proportion_S(example_isolates$AMC, as.character(example_isolates$GEN)))
 expect_error(proportion_df(c("A", "B", "C")))
 expect_error(proportion_df(example_isolates[, "date"]))

man/ggplot_rsi.Rd

@@ -202,34 +202,34 @@ if (require("ggplot2") & require("dplyr")) {
     ggplot() +
     geom_col(aes(x = x, y = y, fill = z)) +
     scale_rsi_colours(Value4 = "S", Value5 = "I", Value6 = "R")
-}
   
-# resistance of ciprofloxacine per age group
+  # resistance of ciprofloxacine per age group
-example_isolates \%>\%
+  example_isolates \%>\%
-  mutate(first_isolate = first_isolate(.)) \%>\%
+    mutate(first_isolate = first_isolate()) \%>\%
-  filter(first_isolate == TRUE,
+    filter(first_isolate == TRUE,
-         mo == as.mo("E. coli")) \%>\%
+           mo == as.mo("E. coli")) \%>\%
-  # age_groups() is also a function in this AMR package:
+    # age_groups() is also a function in this AMR package:
-  group_by(age_group = age_groups(age)) \%>\%
+    group_by(age_group = age_groups(age)) \%>\%
-  select(age_group,
+    select(age_group,
-         CIP) \%>\%
+           CIP) \%>\%
-  ggplot_rsi(x = "age_group")
+    ggplot_rsi(x = "age_group")
   
-# a shorter version which also adjusts data label colours:
+  # a shorter version which also adjusts data label colours:
-example_isolates \%>\%
+  example_isolates \%>\%
-  select(AMX, NIT, FOS, TMP, CIP) \%>\%
+    select(AMX, NIT, FOS, TMP, CIP) \%>\%
-  ggplot_rsi(colours = FALSE)
+    ggplot_rsi(colours = FALSE)
 
 
-# it also supports groups (don't forget to use the group var on `x` or `facet`):
+  # it also supports groups (don't forget to use the group var on `x` or `facet`):
-example_isolates \%>\%
+  example_isolates \%>\%
-  select(hospital_id, AMX, NIT, FOS, TMP, CIP) \%>\%
+    select(hospital_id, AMX, NIT, FOS, TMP, CIP) \%>\%
-  group_by(hospital_id) \%>\%
+    group_by(hospital_id) \%>\%
-  ggplot_rsi(x = "hospital_id",
+    ggplot_rsi(x = "hospital_id",
-             facet = "antibiotic",
+               facet = "antibiotic",
-             nrow = 1,
+               nrow = 1,
-             title = "AMR of Anti-UTI Drugs Per Hospital",
+               title = "AMR of Anti-UTI Drugs Per Hospital",
-             x.title = "Hospital",
+               x.title = "Hospital",
-             datalabels = FALSE)
+               datalabels = FALSE)
+}
 }
 }