(v0.7.1.9094) get_column_abx() improvement

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 0.7.1.9093
+Version: 0.7.1.9094
 Date: 2019-10-06
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.7.1.9093
+# AMR 0.7.1.9094
 <small>Last updated: 06-Oct-2019</small>
 
 ### Breaking
@@ -102,7 +102,7 @@
   * Printed info now distinguishes between added and changes values
   * Using Verbose mode (i.e. `eucast_rules(..., verbose = TRUE)`) returns more informative and readable output
   * Using factors as input now adds missing factors levels when the function changes antibiotic results
-* Improved the internal auto-guessing function for determining antibiotics in your data set (`AMR:::get_column_abx()`)
+* Improved the internal auto-guessing function for determining antimicrobials in your data set (`AMR:::get_column_abx()`)
 * Removed class `atc` - using `as.atc()` is now deprecated in favour of `ab_atc()` and this will return a character, not the `atc` class anymore
 * Removed deprecated functions `abname()`, `ab_official()`, `atc_name()`, `atc_official()`, `atc_property()`, `atc_tradenames()`, `atc_trivial_nl()`
 * Fix and speed improvement for `mo_shortname()`

R/eucast_rules.R

@@ -191,7 +191,7 @@ eucast_rules <- function(x,
     txt <- paste0("WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.",
                   "\n\nThis may overwrite your existing data if you use e.g.:",
                   "\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?")
-    if ("rstudioapi" %in% rownames(installed.packages())) {
+    if ("rstudioapi" %in% rownames(utils::installed.packages())) {
       q_continue <- rstudioapi::showQuestion("Using verbose = TRUE with eucast_rules()", txt)
     } else {
       q_continue <- menu(choices = c("OK", "Cancel"), graphics = TRUE, title = txt)

R/guess_ab_col.R

@@ -122,12 +122,22 @@ get_column_abx <- function(x,
                            ...) {
 
   # determine from given data set
+  x_bak <- x
   df_trans <- data.frame(colnames = colnames(x),
                          abcode = suppressWarnings(as.ab(colnames(x))))
   df_trans <- df_trans[!is.na(df_trans$abcode),]
   x <- as.character(df_trans$colnames)
   names(x) <- df_trans$abcode
   
+  # remove the ones that do not already have the rsi class (as.rsi) and that have >50% invalid values
+  x <- sapply(x, function(col = x, df = x_bak) {
+    ifelse(is.rsi(as.data.frame(df)[, col]) | 
+             is.rsi.eligible(as.data.frame(df)[, col], threshold = 0.5),
+           col,
+           NA)
+  })
+  x <- x[!is.na(x)]
+
   # add from self-defined dots (...):
   # get_column_abx(example_isolates %>% rename(thisone = AMX), amox = "thisone")
   dots <- list(...)

docs/404.html

@@ -84,7 +84,7 @@
       </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">0.7.1.9093</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9094</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -84,7 +84,7 @@
       </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">0.7.1.9093</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9094</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -84,7 +84,7 @@
       </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">0.7.1.9093</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9094</span>
       </span>
     </div>
 

docs/authors.html

@@ -84,7 +84,7 @@
       </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">0.7.1.9093</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9094</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">0.7.1.9093</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9094</span>
       </span>
     </div>
 

docs/news/index.html

@@ -84,7 +84,7 @@
       </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">0.7.1.9093</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9094</span>
       </span>
     </div>
 
@@ -231,9 +231,9 @@
       
     </div>
 
-    <div id="amr-0-7-1-9093" class="section level1">
+    <div id="amr-0-7-1-9094" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-7-1-9093" class="anchor"></a>AMR 0.7.1.9093<small> Unreleased </small>
+<a href="#amr-0-7-1-9094" class="anchor"></a>AMR 0.7.1.9094<small> Unreleased </small>
 </h1>
 <p><small>Last updated: 06-Oct-2019</small></p>
 <div id="breaking" class="section level3">
@@ -349,7 +349,7 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
 <li>Using factors as input now adds missing factors levels when the function changes antibiotic results</li>
 </ul>
 </li>
-<li>Improved the internal auto-guessing function for determining antibiotics in your data set (<code>AMR:::get_column_abx()</code>)</li>
+<li>Improved the internal auto-guessing function for determining antimicrobials in your data set (<code>AMR:::get_column_abx()</code>)</li>
 <li>Removed class <code>atc</code> - using <code><a href="../reference/AMR-deprecated.html">as.atc()</a></code> is now deprecated in favour of <code><a href="../reference/ab_property.html">ab_atc()</a></code> and this will return a character, not the <code>atc</code> class anymore</li>
 <li>Removed deprecated functions <code>abname()</code>, <code>ab_official()</code>, <code>atc_name()</code>, <code>atc_official()</code>, <code>atc_property()</code>, <code>atc_tradenames()</code>, <code>atc_trivial_nl()</code>
 </li>
@@ -1289,7 +1289,7 @@ 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-0-7-1-9093">0.7.1.9093</a></li>
+        <li><a href="#amr-0-7-1-9094">0.7.1.9094</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

@@ -84,7 +84,7 @@
       </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">0.7.1.9093</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9094</span>
       </span>
     </div>