(v1.0.0.9003) prepare for short update

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.0.0.9002
+Version: 1.0.0.9003
-Date: 2020-02-20
+Date: 2020-02-21
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,8 +1,7 @@
-# AMR 1.0.0.9002
+# AMR 1.0.0.9003
-## <small>Last updated: 20-Feb-2020</small>
+## <small>Last updated: 21-Feb-2020</small>
 
 ### Changed
-* Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole
 * Fixed floating point error for some MIC compa in EUCAST 2020 guideline
 * Interpretation from MIC values to R/SI can now be used with `mutate_at()` of the dplyr package:
   ```r
@@ -12,6 +11,7 @@
   yourdata %>% 
     mutate_at(vars(antibiotic1:antibiotic25), as.rsi, mo = .$mybacteria)
   ```
+* Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole
 * Added `uti` (as abbreviation of urinary tract infections) as parameter to `as.rsi()`, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs
 
 # AMR 1.0.0

R/rsi.R

@@ -67,6 +67,8 @@
 #'                  NIT = as.mic(32))
 #' as.rsi(df)
 #' 
+#' \donttest{
+#' 
 #' # the dplyr way
 #' library(dplyr)
 #' df %>%
@@ -88,7 +90,8 @@
 #' 
 #' df %>%
 #'   mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)  
-#'  
+#' }
+#' 
 #' # for single values
 #' as.rsi(x = as.mic(2),
 #'        mo = as.mo("S. pneumoniae"),
@@ -199,20 +202,6 @@ as.rsi.default <- function(x, ...) {
   }
 }
 
-#' @importFrom dplyr %>%
-input_resembles_mic <- function(x) {
-  mic <- x %>%
-    gsub("[^0-9.,]+", "", .) %>%
-    unique()
-  mic_valid <- suppressWarnings(as.mic(mic))
-  result <- sum(!is.na(mic_valid)) / length(mic)
-  if (is.na(result)) {
-    0
-  } else {
-    result
-  }
-}
-
 #' @rdname as.rsi
 #' @export
 as.rsi.mic <- function(x, mo, ab = deparse(substitute(x)), guideline = "EUCAST", uti = FALSE, ...) {
@@ -402,10 +391,14 @@ get_guideline <- function(guideline) {
       rev() %>%
       .[1]
   }
+  if (!guideline_param %like% " ") {
+    # like 'EUCAST2020', should be 'EUCAST 2020'
+    guideline_param <- gsub("([a-z]+)([0-9]+)", "\\1 \\2", guideline_param, ignore.case = TRUE)
+  }
   
   if (!guideline_param %in% rsi_translation$guideline) {
     stop(paste0("invalid guideline: '", guideline,
-                "'.\nValid guidelines are: ", paste0("'", rev(sort(unique(rsi_translation$guideline))), "'", collapse = ", ")),
+                "'.\nValid guidelines are: ", paste0("'", unique(rsi_translation$guideline), "'", collapse = ", "), "."),
          call. = FALSE)
   }
   

docs/404.html

@@ -78,7 +78,7 @@
       </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">1.0.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -78,7 +78,7 @@
       </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">1.0.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -78,7 +78,7 @@
       </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">1.0.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</span>
       </span>
     </div>
 

docs/authors.html

@@ -78,7 +78,7 @@
       </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">1.0.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</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">1.0.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</span>
       </span>
     </div>
 

docs/news/index.html

@@ -78,7 +78,7 @@
       </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">1.0.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</span>
       </span>
     </div>
 
@@ -219,19 +219,18 @@
       
     </div>
 
-    <div id="amr-1009002" class="section level1">
+    <div id="amr-1009003" class="section level1">
 <h1 class="page-header">
-<a href="#amr-1009002" class="anchor"></a>AMR 1.0.0.9002<small> Unreleased </small>
+<a href="#amr-1009003" class="anchor"></a>AMR 1.0.0.9003<small> Unreleased </small>
 </h1>
-<div id="last-updated-20-feb-2020" class="section level2">
+<div id="last-updated-21-feb-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-20-feb-2020" class="anchor"></a><small>Last updated: 20-Feb-2020</small>
+<a href="#last-updated-21-feb-2020" class="anchor"></a><small>Last updated: 21-Feb-2020</small>
 </h2>
 <div id="changed" class="section level3">
 <h3 class="hasAnchor">
 <a href="#changed" class="anchor"></a>Changed</h3>
 <ul>
-<li><p>Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole</p></li>
 <li><p>Fixed floating point error for some MIC compa in EUCAST 2020 guideline</p></li>
 <li>
 <p>Interpretation from MIC values to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the dplyr package:</p>
@@ -241,6 +240,7 @@
 <span id="cb1-4"><a href="#cb1-4"></a>yourdata <span class="op">%&gt;%</span><span class="st"> </span></span>
 <span id="cb1-5"><a href="#cb1-5"></a><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(antibiotic1<span class="op">:</span>antibiotic25), as.rsi, <span class="dt">mo =</span> .<span class="op">$</span>mybacteria)</span></code></pre></div>
 </li>
+<li><p>Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole</p></li>
 <li><p>Added <code>uti</code> (as abbreviation of urinary tract infections) as parameter to <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs</p></li>
 </ul>
 </div>
@@ -1473,7 +1473,7 @@
     <div id="tocnav">
       <h2>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
-        <li><a href="#amr-1009002">1.0.0.9002</a></li>
+        <li><a href="#amr-1009003">1.0.0.9003</a></li>
         <li><a href="#amr-100">1.0.0</a></li>
         <li><a href="#amr-090">0.9.0</a></li>
         <li><a href="#amr-080">0.8.0</a></li>

docs/reference/as.rsi.html

@@ -79,7 +79,7 @@
       </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">1.0.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</span>
       </span>
     </div>
 
@@ -342,6 +342,8 @@ 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='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>)
 <span class='no'>df</span> <span class='kw'>%&gt;%</span>
@@ -363,6 +365,7 @@ 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>),

docs/reference/index.html

@@ -78,7 +78,7 @@
       </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">1.0.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</span>
       </span>
     </div>
 

man/as.rsi.Rd

@@ -108,6 +108,8 @@ df <- data.frame(microorganism = "E. coli",
                  NIT = as.mic(32))
 as.rsi(df)
 
+\donttest{
+
 # the dplyr way
 library(dplyr)
 df \%>\%
@@ -129,7 +131,8 @@ data.frame(mo = "E. coli",
 
 df \%>\%
   mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)  
- 
+}
+
 # for single values
 as.rsi(x = as.mic(2),
        mo = as.mo("S. pneumoniae"),

tests/testthat/test-rsi.R

@@ -34,6 +34,8 @@ test_that("rsi works", {
   barplot(as.rsi(c("S", "I", "R")))
   plot(as.rsi(c("S", "I", "R")))
   print(as.rsi(c("S", "I", "R")))
+  
+  expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))
 
   expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
 
@@ -55,9 +57,17 @@ test_that("rsi works", {
                  as.logical() %>%
                  sum(),
                40)
+  
+  expect_output(tibble(ab = as.rsi("S")))
+  
+  expect_error(as.rsi.mic(as.mic(16)))
+  expect_error(as.rsi.disk(as.disk(16)))
+  
+  expect_error(get_guideline("this one does not exist"))
 
 })
 
+
 test_that("mic2rsi works", {
   
   skip_on_cran()