(v1.0.0.9001) add uti to as.rsi()

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.0.0.9000
+Version: 1.0.0.9001
 Date: 2020-02-20
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 1.0.0.9000
+# AMR 1.0.0.9001
-## <small>Last updated: 20-Feb-2020</small>
+
 
 ### Changed
 * Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole

R/rsi.R

@@ -87,9 +87,7 @@
 #'   as.rsi() # automatically determines urine isolates
 #' 
 #' df %>%
-#'   mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli", uti = TRUE)  
+#'   mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)  
-#'  
-#'   
 #'  
 #' # for single values
 #' as.rsi(x = as.mic(2),
@@ -139,12 +137,7 @@ as.rsi.default <- function(x, ...) {
     x
   } else if (identical(levels(x), c("S", "I", "R"))) {
     structure(x, class = c("rsi", "ordered", "factor"))
-  } else if (all_valid_mics(x) & !all(is.na(x))) {
+  } else if (inherits(x, "integer") & all(x %in% c(1:3, NA))) {
-    as.rsi(as.mic(x), ab = deparse(substitute(x)), ...)
-  } else if (all_valid_disks(x) & !all(is.na(x))) {
-    #message("These values seem to be disk diffusion diameters and were treated as such.")
-    as.rsi(as.disk(x), ab = deparse(substitute(x)), ...)
-  } else if (identical(class(x), "integer") & all(x %in% c(1:3, NA))) {
     x[x == 1] <- "S"
     x[x == 2] <- "I"
     x[x == 3] <- "R"
@@ -152,6 +145,18 @@ as.rsi.default <- function(x, ...) {
               class =  c("rsi", "ordered", "factor"))
   } else {
 
+    ab <- deparse(substitute(x))
+    if (!any(x %like% "(R|S|I)", na.rm = TRUE)) {
+      if (!is.na(suppressWarnings(as.ab(ab)))) {
+        # check if they are actually MICs or disks now that the antibiotic name is valid
+        if (all_valid_mics(x)) {
+          as.rsi(as.mic(x), ab = ab, ...)
+        } else if (all_valid_disks(x)) {
+          as.rsi(as.disk(x), ab = ab, ...)
+        }
+      }
+    }
+    
     x <- x %>% unlist()
     x.bak <- x
     
@@ -632,9 +637,9 @@ plot.rsi <- function(x,
 #' @importFrom graphics barplot axis par
 #' @noRd
 barplot.rsi <- function(height,
-                        col = c("green3", "orange2", "red3"),
+                        col = c("chartreuse4", "chartreuse3", "brown3"),
                         xlab = ifelse(beside, "Antimicrobial Interpretation", ""),
-                        main = paste("Susceptibility Analysis of", deparse(substitute(height))),
+                        main = paste("Antimicrobial resistance of", deparse(substitute(height))),
                         ylab = "Frequency",
                         beside = TRUE,
                         axes = beside,

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">1.0.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</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">1.0.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</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">1.0.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</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">1.0.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</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">1.0.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</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">1.0.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</span>
       </span>
     </div>
 
@@ -219,14 +219,10 @@
       
     </div>
 
-    <div id="amr-1009000" class="section level1">
+    <div id="amr-1009001" class="section level1">
 <h1 class="page-header">
-<a href="#amr-1009000" class="anchor"></a>AMR 1.0.0.9000<small> Unreleased </small>
+<a href="#amr-1009001" class="anchor"></a>AMR 1.0.0.9001<small> Unreleased </small>
 </h1>
-<div id="last-updated-20-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>
-</h2>
 <div id="changed" class="section level3">
 <h3 class="hasAnchor">
 <a href="#changed" class="anchor"></a>Changed</h3>
@@ -244,7 +240,6 @@
 <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>
-</div>
 </div>
     <div id="amr-100" class="section level1">
 <h1 class="page-header">
@@ -1473,7 +1468,7 @@
     <div id="tocnav">
       <h2>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
-        <li><a href="#amr-1009000">1.0.0.9000</a></li>
+        <li><a href="#amr-1009001">1.0.0.9001</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">0.9.0.9029</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</span>
       </span>
     </div>
 
@@ -362,9 +362,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
   <span class='fu'>as.rsi</span>() <span class='co'># automatically determines urine isolates</span>
 
 <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'>TOB</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='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'># 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">1.0.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</span>
       </span>
     </div>
 

man/as.rsi.Rd

@@ -128,9 +128,7 @@ data.frame(mo = "E. coli",
   as.rsi() # automatically determines urine isolates
 
 df \%>\%
-  mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli", uti = TRUE)  
+  mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)  
- 
-  
  
 # for single values
 as.rsi(x = as.mic(2),