(v0.7.0.9006) ab algorithm fix for ATC codes

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 0.7.0.9005
+Version: 0.7.0.9006
 Date: 2019-06-11
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.7.0.9005
+# AMR 0.7.0.9006
 
 #### New
 * Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*:

R/ab.R

@@ -203,7 +203,8 @@ as.ab <- function(x) {
     # try by removing all spaces
     if (x[i] %like% " ") {
       found <- suppressWarnings(as.ab(gsub(" +", "", x[i])))
-      if (length(found) > 0) {
+      print(found)
+      if (length(found) > 0 & !is.na(found)) {
         x_new[i] <- found[1L]
         next
       }
@@ -212,7 +213,7 @@ as.ab <- function(x) {
     # try by removing all spaces and numbers
     if (x[i] %like% " " | x[i] %like% "[0-9]") {
       found <- suppressWarnings(as.ab(gsub("[ 0-9]", "", x[i])))
-      if (length(found) > 0) {
+      if (length(found) > 0 & !is.na(found)) {
         x_new[i] <- found[1L]
         next
       }
@@ -222,6 +223,16 @@ as.ab <- function(x) {
     x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
   }
 
+  # take failed ATC codes apart from rest
+  x_unknown_ATCs <- x_unknown[x_unknown %like% "[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]"]
+  x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
+  if (length(x_unknown_ATCs) > 0) {
+    warning("These ATC codes are not (yet) in the antibiotics data set: ",
+            paste('"', sort(unique(x_unknown_ATCs)), '"', sep = "", collapse = ', '),
+            ".",
+            call. = FALSE)
+  }
+
   if (length(x_unknown) > 0) {
     warning("These values could not be coerced to a valid antibiotic ID: ",
             paste('"', sort(unique(x_unknown)), '"', sep = "", collapse = ', '),

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">0.7.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</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">0.7.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</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">0.7.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</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">0.7.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</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">0.7.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</span>
       </span>
     </div>
 
@@ -232,9 +232,9 @@
       
     </div>
 
-    <div id="amr-0709005" class="section level1">
+    <div id="amr-0709006" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0709005" class="anchor"></a>AMR 0.7.0.9005<small> Unreleased </small>
+<a href="#amr-0709006" class="anchor"></a>AMR 0.7.0.9006<small> Unreleased </small>
 </h1>
 <div id="new" class="section level4">
 <h4 class="hasAnchor">
@@ -1106,7 +1106,7 @@ 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-0709005">0.7.0.9005</a></li>
+        <li><a href="#amr-0709006">0.7.0.9006</a></li>
         <li><a href="#amr-070">0.7.0</a></li>
         <li><a href="#amr-061">0.6.1</a></li>
         <li><a href="#amr-060">0.6.0</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">0.7.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</span>
       </span>
     </div>
 

git_premaster.sh

@@ -30,31 +30,25 @@ if [ -z "$new_version" ]; then
   new_version="$current_tag.9000"
   echo
   echo "** COULD NOT CREATE NEW VERSION NUMBER! **"
-  echo "Are there some unpushed changes in a new tag?? Then mind NEWS.md. Assuming sequence number 9000."
+  echo "Are there some unpushed changes in a new tag? Then mind NEWS.md. Assuming sequence number 9000."
   echo
 fi
 sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION
 # update 1st line of NEWS.md
 sed -i -- "1s/.*/# AMR ${new_version}/" NEWS.md
-echo "First 3 lines of DESCRIPTION:"
+echo "• First 3 lines of DESCRIPTION:"
 head -3 DESCRIPTION
 echo
-echo "First line of NEWS.md:"
+echo "• First line of NEWS.md:"
 head -1 NEWS.md
 echo
-read -p "Continue (Y/n)? " choice
-case "$choice" in
-  n|N ) exit 1;;
-  * ) ;;
-esac
-echo
 echo "•••••••••••••••••••••••••••••••••"
 echo "• Reloading/documenting package •"
 echo "•••••••••••••••••••••••••••••••••"
 Rscript -e "devtools::load_all(quiet = TRUE)"
-echo "Documenting..."
+echo "• Documenting..."
 Rscript -e "suppressMessages(devtools::document())"
-echo "Installing..."
+echo "• Installing..."
 Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
 echo
 echo "••••••••••••••••••••••••••"
@@ -73,7 +67,7 @@ echo "••••••••••••••••••••••••
 git status --short
 echo
 
-read -p "Continue (Y/n)? " choice
+read -p "Pushing version ${new_version}. Continue (Y/n)? " choice
 case "$choice" in
   n|N ) exit 1;;
   * ) ;;