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AMR
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(v0.8.0.9003) printing fix for AB columns

This commit is contained in:
dr. M.S. (Matthijs) Berends 2019-10-23 15:44:11 +02:00
parent 3e5ab53209
commit c01dc8a5b7
11 changed files with 19 additions and 17 deletions
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2
DESCRIPTION
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@ -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(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.8.0.9002
# AMR 0.8.0.9003
<small>Last updated: 23-Oct-2019</small>
### Changes

5
R/guess_ab_col.R
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@ -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],

7
R/rsi.R
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@ -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(real_white(" S "))
out[x == "S"] <- bgGreen(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)
}

2
docs/404.html
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@ -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>

2
docs/LICENSE-text.html
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@ -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>

2
docs/articles/index.html
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@ -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>

2
docs/authors.html
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@ -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>

2
docs/index.html
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@ -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>

8
docs/news/index.html
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@ -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>

2
docs/reference/index.html
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@ -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>