(v0.7.1.9061) mo_property improvement

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.7.1.9060
+Version: 0.7.1.9061
-Date: 2019-08-25
+Date: 2019-08-26
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.7.1.9060
+# AMR 0.7.1.9061
 
 ### Breaking
 * Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). The `freq()` function still works, since it is re-exported from the `clean` package to this `AMR` package. Creating frequency tables is actually not the scope of this package (never was) and this function has matured  a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.

R/mo_property.R

@@ -144,7 +144,6 @@ mo_name <- function(x, language = get_locale(), ...) {
 mo_fullname <- mo_name
 
 #' @rdname mo_property
-#' @importFrom dplyr %>% mutate pull
 #' @export
 mo_shortname <- function(x, language = get_locale(), ...) {
   x.mo <- AMR::as.mo(x, ...)
@@ -417,9 +416,15 @@ mo_validate <- function(x, property, ...) {
   tryCatch(x[1L] %in% AMR::microorganisms[1, property],
            error = function(e) stop(e$message, call. = FALSE))
   
-  if (!all(x %in% pull(AMR::microorganisms, property))
+  if (is.mo(x) 
-      | Becker %in% c(TRUE, "all")
+      & !Becker %in% c(TRUE, "all") 
-      | Lancefield %in% c(TRUE, "all")) {
+      & !Lancefield %in% c(TRUE, "all")) {
+    # this will not reset mo_uncertainties and mo_failures
+    # because it's already a valid MO
+    x <- exec_as.mo(x, property = property, initial_search = FALSE, ...)
+  } else if (!all(x %in% pull(AMR::microorganisms, property))
+             | Becker %in% c(TRUE, "all")
+             | Lancefield %in% c(TRUE, "all")) {
     x <- exec_as.mo(x, property = property, ...)
   }
   

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">0.7.1.9059</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</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">0.7.1.9059</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</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">0.7.1.9059</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</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">0.7.1.9059</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</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">0.7.1.9059</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</span>
       </span>
     </div>
 
@@ -225,9 +225,9 @@
       
     </div>
 
-    <div id="amr-0-7-1-9059" class="section level1">
+    <div id="amr-0-7-1-9061" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-7-1-9059" class="anchor"></a>AMR 0.7.1.9059<small> Unreleased </small>
+<a href="#amr-0-7-1-9061" class="anchor"></a>AMR 0.7.1.9061<small> Unreleased </small>
 </h1>
 <div id="breaking" class="section level3">
 <h3 class="hasAnchor">
@@ -1252,7 +1252,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
     <div id="tocnav">
       <h2>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
-        <li><a href="#amr-0-7-1-9059">0.7.1.9059</a></li>
+        <li><a href="#amr-0-7-1-9061">0.7.1.9061</a></li>
         <li><a href="#amr-0-7-1">0.7.1</a></li>
         <li><a href="#amr-0-7-0">0.7.0</a></li>
         <li><a href="#amr-0-6-1">0.6.1</a></li>

docs/reference/availability.html

@@ -80,7 +80,7 @@
       </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">0.7.1.9059</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</span>
       </span>
     </div>
 

docs/reference/bug_drug_combinations.html

@@ -80,7 +80,7 @@
       </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">0.7.1.9059</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</span>
       </span>
     </div>
 

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">0.7.1.9059</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</span>
       </span>
     </div>
 

docs/reference/reexports.html

@@ -84,7 +84,7 @@ below to see their documentation.
       </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">0.7.1.9059</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</span>
       </span>
     </div>