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(v1.4.0.9016) as.rsi() older R versions

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dr. M.S. (Matthijs) Berends 2020-11-10 19:59:14 +01:00
parent 15c732703d
commit 68ac39aa7f
14 changed files with 28 additions and 17 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.4.0.9015
Version: 1.4.0.9016
Date: 2020-11-10
Title: Antimicrobial Resistance Analysis
Authors@R: c(

3
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.4.0.9015
# AMR 1.4.0.9016
## <small>Last updated: 10 November 2020</small>
### New
@ -16,6 +16,7 @@
* Better determination of disk zones and MIC values when running `as.rsi()` on a data.frame
* Updated coagulase-negative staphylococci determination with Becker *et al.* 2020 (PMID 32056452), meaning that the species *S. argensis*, *S. caeli*, *S. debuckii*, *S. edaphicus* and *S. pseudoxylosus* are now all considered CoNS
* Fix for using parameter `reference_df` in `as.mo()` and `mo_*()` functions that contain old microbial codes (from previous package versions)
* Fix for using `as.rsi()` on a data.frame in older R versions
### Other
* All messages and warnings thrown by this package now break sentences on whole words

2
R/aa_helper_functions.R
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@ -313,6 +313,8 @@ word_wrap <- function(...,
}
msg <- gsub("\n", paste0("\n", strrep(" ", indentation)), msg, fixed = TRUE)
msg <- gsub("*|*", paste0("*|*", strrep(" ", indentation)), msg, fixed = TRUE)
# remove trailing empty characters
msg <- gsub("(\n| )+$", "", msg)
if (length(add_fn) > 0) {
if (!is.list(add_fn)) {

7
R/rsi.R
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@ -469,6 +469,13 @@ as.rsi.data.frame <- function(x,
meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1)
meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
for (i in seq_len(ncol(x))) {
# don't keep factors
if (is.factor(x[, i, drop = TRUE])) {
x[, i] <- as.character(x[, i, drop = TRUE])
}
}
# -- MO
col_mo.bak <- col_mo
if (is.null(col_mo)) {

2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</span>
</span>
</div>

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docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</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">1.4.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</span>
</span>
</div>

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docs/articles/index.html
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@ -81,7 +81,7 @@
</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">1.4.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</span>
</span>
</div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</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">1.4.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</span>
</span>
</div>

2
docs/index.html
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@ -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">1.4.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</span>
</span>
</div>

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docs/news/index.html
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@ -81,7 +81,7 @@
</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">1.4.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1409015" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9015">
<a href="#amr-1409015" class="anchor"></a>AMR 1.4.0.9015<small> Unreleased </small>
<div id="amr-1409016" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9016">
<a href="#amr-1409016" class="anchor"></a>AMR 1.4.0.9016<small> Unreleased </small>
</h1>
<div id="last-updated-10-november-2020" class="section level2">
<h2 class="hasAnchor">
@ -267,6 +267,7 @@
<li>Better determination of disk zones and MIC values when running <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame</li>
<li>Updated coagulase-negative staphylococci determination with Becker <em>et al.</em> 2020 (PMID 32056452), meaning that the species <em>S. argensis</em>, <em>S. caeli</em>, <em>S. debuckii</em>, <em>S. edaphicus</em> and <em>S. pseudoxylosus</em> are now all considered CoNS</li>
<li>Fix for using parameter <code>reference_df</code> in <code><a href="../reference/as.mo.html">as.mo()</a></code> and <code>mo_*()</code> functions that contain old microbial codes (from previous package versions)</li>
<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame in older R versions</li>
</ul>
</div>
<div id="other" class="section level3">

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docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2020-11-10T15:32Z
last_built: 2020-11-10T18:58Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

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docs/reference/index.html
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@ -81,7 +81,7 @@
</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">1.4.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</span>
</span>
</div>

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docs/survey.html
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@ -81,7 +81,7 @@
</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">1.4.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9016</span>
</span>
</div>

4
tests/testthat/test-mdro.R
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@ -46,7 +46,7 @@ test_that("mdro works", {
library(dplyr)
# example_isolates should have these finding using Dutch guidelines
expect_equal(outcome %>% cleaner::freq() %>% pull(count),
expect_equal(as.double(table(outcome)),
c(1969, 25, 6)) # 1969 neg, 25 unconfirmed, 6 pos
expect_equal(brmo(example_isolates, info = FALSE),
@ -104,7 +104,7 @@ test_that("mdro works", {
expect_equal(
# select only rifampicine, mo will be determined automatically (as M. tuberculosis),
# number of mono-resistant strains should be equal to number of rifampicine-resistant strains
cleaner::freq(mdr_tb(example_isolates[, "RIF", drop = FALSE]))$count[2],
as.double(table(mdr_tb(example_isolates[, "RIF", drop = FALSE])))[2],
count_R(example_isolates$RIF))
sample_rsi <- function() {