(v1.3.0.9025) optimalisation

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.3.0.9024
+Version: 1.3.0.9025
 Date: 2020-09-19
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.3.0.9024
+# AMR 1.3.0.9025
 ## <small>Last updated: 19 September 2020</small>
 
 Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!

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">1.3.0.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</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">1.3.0.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</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">1.3.0.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</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">1.3.0.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</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">1.3.0.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</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">1.3.0.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</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-1309024" class="section level1">
+    <div id="amr-1309025" class="section level1">
-<h1 class="page-header" data-toc-text="1.3.0.9024">
+<h1 class="page-header" data-toc-text="1.3.0.9025">
-<a href="#amr-1309024" class="anchor"></a>AMR 1.3.0.9024<small> Unreleased </small>
+<a href="#amr-1309025" class="anchor"></a>AMR 1.3.0.9025<small> Unreleased </small>
 </h1>
 <div id="last-updated-19-september-2020" class="section level2">
 <h2 class="hasAnchor">

docs/pkgdown.yml

@@ -2,7 +2,7 @@ pandoc: 2.7.3
 pkgdown: 1.5.1.9000
 pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
 articles: []
-last_built: 2020-09-19T10:17Z
+last_built: 2020-09-19T13:07Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles

docs/reference/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</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">1.3.0.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
       </span>
     </div>
 

tests/testthat/test-eucast_rules.R

@@ -30,7 +30,8 @@ test_that("EUCAST rules work", {
                c("if_mo_property", "like.is.one_of", "this_value",
                  "and_these_antibiotics", "have_these_values",
                  "then_change_these_antibiotics", "to_value",
-                 "reference.rule", "reference.rule_group"))
+                 "reference.rule", "reference.rule_group",
+                 "reference.version"))
   
   expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))
   expect_error(eucast_rules(x = "text"))

tests/testthat/test-mic.R

@@ -38,10 +38,10 @@ test_that("mic works", {
 
   expect_warning(as.mic("INVALID VALUE"))
 
-  # print plots
+  pdf(NULL) # prevent Rplots.pdf being created
-  expect_success(x <- barplot(as.mic(c(1, 2, 4, 8))))
+  expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
-  expect_success(x <- plot(as.mic(c(1, 2, 4, 8))))
+  expect_silent(plot(as.mic(c(1, 2, 4, 8))))
-  expect_success(x <- print(as.mic(c(1, 2, 4, 8))))
+  expect_output(print(as.mic(c(1, 2, 4, 8))))
   
   expect_equal(summary(as.mic(c(2, 8))), 
                structure(c("Class" = "mic",

tests/testthat/test-resistance_predict.R

@@ -35,8 +35,9 @@ test_that("prediction of rsi works", {
   expect_true(AMX_R[3] < AMX_R[20])
 
   x <- resistance_predict(example_isolates, col_ab = "AMX", year_min = 2010, model = "binomial")
-  expect_success(y <- plot(x))
+  pdf(NULL) # prevent Rplots.pdf being created
-  expect_success(y <- ggplot_rsi_predict(x))
+  expect_silent(plot(x))
+  expect_silent(ggplot_rsi_predict(x))
   expect_error(ggplot_rsi_predict(example_isolates))
 
   library(dplyr)

tests/testthat/test-rsi.R

@@ -28,10 +28,10 @@ test_that("rsi works", {
   expect_true(as.rsi("I") < as.rsi("R"))
   expect_true(is.rsi(as.rsi("S")))
   
-  # print plots, should not raise errors
+  pdf(NULL) # prevent Rplots.pdf being created
-  expect_success(x <- barplot(as.rsi(c("S", "I", "R"))))
+  expect_silent(barplot(as.rsi(c("S", "I", "R"))))
-  expect_success(x <- plot(as.rsi(c("S", "I", "R"))))
+  expect_silent(plot(as.rsi(c("S", "I", "R"))))
-  expect_success(x <- print(as.rsi(c("S", "I", "R"))))
+  expect_output(print(as.rsi(c("S", "I", "R"))))
   
   expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))