(v0.8.0.9003) printing fix for AB columns

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 0.8.0.9002
+Version: 0.8.0.9003
 Date: 2019-10-23
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.8.0.9002
+# AMR 0.8.0.9003
 <small>Last updated: 23-Oct-2019</small>
 
 ### Changes

R/guess_ab_col.R

@@ -118,7 +118,7 @@ get_column_abx <- function(x,
                            verbose = FALSE,
                            ...) {
 
-  message(blue("NOTE: Auto-guessing columns suitable for analysis..."))
+  message(blue("NOTE: Auto-guessing columns suitable for analysis..."), appendLF = FALSE)
   
   x <- as.data.frame(x, stringsAsFactors = FALSE)
   x_bak <- x
@@ -169,6 +169,9 @@ get_column_abx <- function(x,
   duplicates <- x[base::duplicated(x)]
   x <- x[!names(x) %in% names(duplicates)]
   
+  # succeeded with aut-guessing
+  message(blue("OK."))
+  
   if (verbose == TRUE) {
     for (i in seq_len(length(x))) {
       message(blue(paste0("NOTE: Using column `", bold(x[i]), "` as input for `", names(x)[i],

R/rsi.R

@@ -504,14 +504,13 @@ type_sum.rsi <- function(x) {
 }
 
 #' @importFrom pillar pillar_shaft
-#' @importFrom crayon bgGreen bgYellow bgRed black make_style
+#' @importFrom crayon bgGreen bgYellow bgRed black white
 #' @export 
 pillar_shaft.rsi <- function(x, ...) {
   out <- trimws(format(x))
   out[is.na(x)] <- pillar::style_subtle(" NA")
-  real_white <- make_style(rgb(1, 1, 1))
+  out[x == "S"] <- bgGreen(white(" S "))
-  out[x == "S"] <- bgGreen(real_white(" S "))
   out[x == "I"] <- bgYellow(black(" I "))
-  out[x == "R"] <- bgRed(real_white(" R "))
+  out[x == "R"] <- bgRed(white(" R "))
   pillar::new_pillar_shaft_simple(out, align = "left", width = 3)
 }

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">0.8.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9003</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">0.8.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9003</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">0.8.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9003</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">0.8.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9003</span>
       </span>
     </div>
 

docs/index.html

@@ -45,7 +45,7 @@
       </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">0.8.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9003</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">0.8.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9003</span>
       </span>
     </div>
 
@@ -231,9 +231,9 @@
       
     </div>
 
-    <div id="amr-0-8-0-9002" class="section level1">
+    <div id="amr-0-8-0-9003" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-8-0-9002" class="anchor"></a>AMR 0.8.0.9002<small> Unreleased </small>
+<a href="#amr-0-8-0-9003" class="anchor"></a>AMR 0.8.0.9003<small> Unreleased </small>
 </h1>
 <p><small>Last updated: 23-Oct-2019</small></p>
 <div id="changes" class="section level3">
@@ -1309,7 +1309,7 @@ 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-0-8-0-9002">0.8.0.9002</a></li>
+        <li><a href="#amr-0-8-0-9003">0.8.0.9003</a></li>
         <li><a href="#amr-0-8-0">0.8.0</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>

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">0.8.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9003</span>
       </span>
     </div>