(v0.7.1.9078) unit tests

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 0.7.1.9077
+Version: 0.7.1.9078
 Date: 2019-09-20
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.7.1.9077
+# AMR 0.7.1.9078
 <small>Last updated: 20-Sep-2019</small>
 
 ### Breaking

R/mo.R

@@ -1539,7 +1539,8 @@ exec_as.mo <- function(x,
       
       # THEN TRY PREVALENT IN HUMAN INFECTIONS ----
       x[i] <- check_per_prevalence(data_to_check = reference_data_to_use[prevalence == 2],
-                                   data.old_to_check = microorganisms.oldDT[prevalence == 2],
+                                   data.old_to_check = microorganisms.oldDT[prevalence %in% c(2, 3)], # run all other old MOs the second time,
+                                                                                                      # otherwise e.g. mo_ref("Chlamydia psittaci") doesn't work correctly
                                    a.x_backup = x_backup[i],
                                    b.x_trimmed = x_trimmed[i],
                                    c.x_trimmed_without_group = x_trimmed_without_group[i],
@@ -1558,7 +1559,7 @@ exec_as.mo <- function(x,
       
       # THEN UNPREVALENT IN HUMAN INFECTIONS ----
       x[i] <- check_per_prevalence(data_to_check = reference_data_to_use[prevalence == 3],
-                                   data.old_to_check = microorganisms.oldDT[prevalence == 3],
+                                   data.old_to_check = microorganisms.oldDT[prevalence == 999],
                                    a.x_backup = x_backup[i],
                                    b.x_trimmed = x_trimmed[i],
                                    c.x_trimmed_without_group = x_trimmed_without_group[i],

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">0.7.1.9077</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9078</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">0.7.1.9077</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9078</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">0.7.1.9077</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9078</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">0.7.1.9077</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9078</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">0.7.1.9077</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9078</span>
       </span>
     </div>
 
@@ -225,9 +225,9 @@
       
     </div>
 
-    <div id="amr-0-7-1-9077" class="section level1">
+    <div id="amr-0-7-1-9078" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-7-1-9077" class="anchor"></a>AMR 0.7.1.9077<small> Unreleased </small>
+<a href="#amr-0-7-1-9078" class="anchor"></a>AMR 0.7.1.9078<small> Unreleased </small>
 </h1>
 <p><small>Last updated: 20-Sep-2019</small></p>
 <div id="breaking" class="section level3">
@@ -1267,7 +1267,7 @@ 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-0-7-1-9077">0.7.1.9077</a></li>
+        <li><a href="#amr-0-7-1-9078">0.7.1.9078</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/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">0.7.1.9077</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9078</span>
       </span>
     </div>
 

inst/mo_history/mo_history.csv

@@ -1,8 +1 @@
 "x","mo","uncertainty_level","package_version"
-"M. SEMESIAE","B_MTHNSR_SEMS",0,"0.7.1.9077"
-"METSEM","B_MTHNSR_SEMS",0,"0.7.1.9077"
-"METHANOSARCINA SEMESIAE","B_MTHNSR_SEMS",0,"0.7.1.9077"
-"PREVOTELLA BREVIS","B_PRVTL_BRVS",0,"0.7.1.9077"
-"P. BREVIS","B_PRVTL_BRVS",0,"0.7.1.9077"
-"E. COLI","B_ESCHR_COLI",0,"0.7.1.9077"
-"ESCHERICHIA COLI","B_ESCHR_COLI",0,"0.7.1.9077"