(v1.3.0.9017) small fix

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.3.0.9016
+Version: 1.3.0.9017
 Date: 2020-09-12
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.3.0.9016
+# AMR 1.3.0.9017
 ## <small>Last updated: 12 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!

R/mo.R

@@ -281,6 +281,43 @@ exec_as.mo <- function(x,
                        reference_data_to_use = MO_lookup) {
   
   check_dataset_integrity()
+  
+  lookup <- function(needle, column = property, haystack = reference_data_to_use, n = 1, debug_mode = debug, input = "") {
+    # `column` can be NULL for all columns, or a selection
+    # returns a character (vector) - if `column` > length 1 then with columns as names
+    if (isTRUE(debug_mode)) {
+      cat(font_silver("looking up: ", substitute(needle), "\n", collapse = ""))
+    }
+    if (length(column) == 1) {
+      res_df <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
+      res <- as.character(res_df[, column, drop = TRUE])
+      if (length(res) == 0) {
+        NA_character_ 
+      } else {
+        if (length(res) > n) {
+          # save the other possible results as well
+          uncertainties <<- rbind(uncertainties,
+                                  format_uncertainty_as_df(uncertainty_level = 1,
+                                                           input = x_backup[i],
+                                                           result_mo = res_df[1, "mo", drop = TRUE],
+                                                           candidates = as.character(res_df[, "fullname", drop = TRUE])))
+        }
+        res[seq_len(min(n, length(res)))]
+      }
+    } else {
+      if (is.null(column)) {
+        column <- names(haystack)
+      }
+      res <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
+      res <- res[seq_len(min(n, nrow(res))), column, drop = TRUE]
+      if (NROW(res) == 0) {
+        res <- rep(NA_character_, length(column))
+      }
+      res <- as.character(res)
+      names(res) <- column
+      res
+    }
+  }
 
   # start off with replaced language-specific non-ASCII characters with ASCII characters
   x <- parse_and_convert(x)
@@ -383,43 +420,6 @@ exec_as.mo <- function(x,
     
   } else if (!all(x %in% microorganisms[, property])) {
     
-    lookup <- function(needle, column = property, haystack = reference_data_to_use, n = 1, debug_mode = debug, input = "") {
-      # `column` can be NULL for all columns, or a selection
-      # returns a character (vector) - if `column` > length 1 then with columns as names
-      if (isTRUE(debug_mode)) {
-        cat(font_silver("looking up: ", substitute(needle), "\n", collapse = ""))
-      }
-      if (length(column) == 1) {
-        res_df <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
-        res <- as.character(res_df[, column, drop = TRUE])
-        if (length(res) == 0) {
-          NA_character_ 
-        } else {
-          if (length(res) > n) {
-            # save the other possible results as well
-            uncertainties <<- rbind(uncertainties,
-                                    format_uncertainty_as_df(uncertainty_level = 1,
-                                                             input = x_backup[i],
-                                                             result_mo = res_df[1, "mo", drop = TRUE],
-                                                             candidates = as.character(res_df[, "fullname", drop = TRUE])))
-          }
-          res[seq_len(min(n, length(res)))]
-        }
-      } else {
-        if (is.null(column)) {
-          column <- names(haystack)
-        }
-        res <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
-        res <- res[seq_len(min(n, nrow(res))), column, drop = TRUE]
-        if (NROW(res) == 0) {
-          res <- rep(NA_character_, length(column))
-        }
-        res <- as.character(res)
-        names(res) <- column
-        res
-      }
-    }
-    
     strip_whitespace <- function(x, dyslexia_mode) {
       # all whitespaces (tab, new lines, etc.) should be one space
       # and spaces before and after should be omitted

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">1.3.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</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">1.3.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</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">1.3.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</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">1.3.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</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">1.3.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</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">1.3.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</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-1309016" class="section level1">
-<h1 class="page-header" data-toc-text="1.3.0.9016">
-<a href="#amr-1309016" class="anchor"></a>AMR 1.3.0.9016<small> Unreleased </small>
+    <div id="amr-1309017" class="section level1">
+<h1 class="page-header" data-toc-text="1.3.0.9017">
+<a href="#amr-1309017" class="anchor"></a>AMR 1.3.0.9017<small> Unreleased </small>
 </h1>
 <div id="last-updated-12-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: 2020-09-12T06:48Z
+last_built: 2020-09-12T11:54Z
 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">1.3.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</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">1.3.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</span>
       </span>
     </div>
 

tests/testthat.R

@@ -23,3 +23,4 @@ library(testthat)
 library(AMR)
 
 test_check("AMR")
+unlink("tests/testthat/Rplots.pdf")