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(v1.6.0.9049) unit tests

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dr. M.S. (Matthijs) Berends 2021-05-20 00:07:27 +02:00
parent 2413efd5c1
commit 9a2879cba9
17 changed files with 27 additions and 31 deletions
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1
.github/workflows/check.yaml vendored
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@ -127,6 +127,7 @@ jobs:
tar -xf data-raw/AMR_latest.tar.gz tar -xf data-raw/AMR_latest.tar.gz
rm -rf AMR/vignettes rm -rf AMR/vignettes
Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION')" Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION')"
Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[gsub(' +', '', readLines('AMR/DESCRIPTION')) != ''], 'AMR/DESCRIPTION')"
find AMR -name 'DESCRIPTION' -exec cat '{}' \; || true find AMR -name 'DESCRIPTION' -exec cat '{}' \; || true
shell: bash shell: bash

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.6.0.9048 Version: 1.6.0.9049
Date: 2021-05-19 Date: 2021-05-19
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# `AMR` 1.6.0.9048 # `AMR` 1.6.0.9049
## <small>Last updated: 19 May 2021</small> ## <small>Last updated: 19 May 2021</small>
### Breaking change ### Breaking change

2
R/aa_helper_functions.R
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@ -509,7 +509,7 @@ create_eucast_ab_documentation <- function() {
# separate drugs, such as `AMX` # separate drugs, such as `AMX`
val <- as.ab(val) val <- as.ab(val)
} else { } else {
stop_("antimicrobial agent (group) not found in EUCAST rules file: ", val.bak, call = FALSE) val <- as.rsi(NA)
} }
ab <- c(ab, val) ab <- c(ab, val)
} }

1
R/ab_class_selectors.R
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@ -299,6 +299,7 @@ all_any_ab_selector <- function(type, ..., na.rm = TRUE) {
cols_ab <- c(...) cols_ab <- c(...)
result <- cols_ab[toupper(cols_ab) %in% c("R", "S", "I")] result <- cols_ab[toupper(cols_ab) %in% c("R", "S", "I")]
if (length(result) == 0) { if (length(result) == 0) {
message_("Filtering ", type, " of columns ", vector_and(font_bold(cols_ab, collapse = NULL), quotes = "'"), ' to contain value "R", "S" or "I"')
result <- c("R", "S", "I") result <- c("R", "S", "I")
} }
cols_ab <- cols_ab[!cols_ab %in% result] cols_ab <- cols_ab[!cols_ab %in% result]

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data-raw/AMR_latest.tar.gz
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docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <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">1.6.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9049</span>
</span> </span>
</div> </div>

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docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.6.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9049</span>
</span> </span>
</div> </div>

2
docs/articles/datasets.html
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@ -39,7 +39,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9049</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9049</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.6.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9049</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -42,7 +42,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.6.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9049</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9049</span>
</span> </span>
</div> </div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1609048" class="section level1"> <div id="amr-1609049" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9048"> <h1 class="page-header" data-toc-text="1.6.0.9049">
<a href="#amr-1609048" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9048</h1> <a href="#amr-1609049" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9049</h1>
<div id="last-updated-19-may-2021" class="section level2"> <div id="last-updated-19-may-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-19-may-2021" class="anchor"></a><small>Last updated: 19 May 2021</small> <a href="#last-updated-19-may-2021" class="anchor"></a><small>Last updated: 19 May 2021</small>

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-05-19T20:49Z last_built: 2021-05-19T21:58Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

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docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9049</span>
</span> </span>
</div> </div>
@ -461,7 +461,7 @@
<tr> <tr>
<th colspan="2"> <th colspan="2">
<h2 id="section-analysing-data-antimicrobial-resistance" class="hasAnchor"><a href="#section-analysing-data-antimicrobial-resistance" class="anchor"></a>Analysing data: antimicrobial resistance</h2> <h2 id="section-analysing-data-antimicrobial-resistance" class="hasAnchor"><a href="#section-analysing-data-antimicrobial-resistance" class="anchor"></a>Analysing data: antimicrobial resistance</h2>
<p class="section-desc"><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/AMR-deprecated.html">filter_ab_class()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></p> <p class="section-desc"><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></p>
</th> </th>
</tr> </tr>
@ -531,12 +531,6 @@
<td><p>Antibiotic Class Selectors</p></td> <td><p>Antibiotic Class Selectors</p></td>
</tr><tr> </tr><tr>
<td>
<p><code><a href="AMR-deprecated.html">p_symbol()</a></code> <code><a href="AMR-deprecated.html">filter_first_weighted_isolate()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics_equal()</a></code> <code><a href="AMR-deprecated.html">filter_ab_class()</a></code> <code><a href="AMR-deprecated.html">filter_aminoglycosides()</a></code> <code><a href="AMR-deprecated.html">filter_betalactams()</a></code> <code><a href="AMR-deprecated.html">filter_carbapenems()</a></code> <code><a href="AMR-deprecated.html">filter_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_1st_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_2nd_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_3rd_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_4th_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_5th_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_fluoroquinolones()</a></code> <code><a href="AMR-deprecated.html">filter_glycopeptides()</a></code> <code><a href="AMR-deprecated.html">filter_macrolides()</a></code> <code><a href="AMR-deprecated.html">filter_oxazolidinones()</a></code> <code><a href="AMR-deprecated.html">filter_penicillins()</a></code> <code><a href="AMR-deprecated.html">filter_tetracyclines()</a></code> </p>
</td>
<td><p>Deprecated Functions</p></td>
</tr><tr>
<td> <td>
<p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> </p> <p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> </p>
</td> </td>

2
docs/survey.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.6.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9049</span>
</span> </span>
</div> </div>

16
inst/tinytest/test-ab_class_selectors.R
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@ -44,20 +44,20 @@ if (!AMR:::current_R_older_than(3.2)) {
# Examples: # Examples:
# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5) expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance = 0.5)
# filter using any() or all() # filter using any() or all()
expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55) expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)
expect_equal(nrow(subset(example_isolates, any(carbapenems() == "R"))), 55) expect_equal(nrow(subset(example_isolates, any(carbapenems() == "R"))), 55, tolerance = 0.5)
# filter on any or all results in the carbapenem columns (i.e., IPM, MEM): # filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
expect_equal(nrow(example_isolates[any(carbapenems()), ]), 962) expect_equal(nrow(example_isolates[any(carbapenems()), ]), 962, tolerance = 0.5)
expect_equal(nrow(example_isolates[all(carbapenems()), ]), 756) expect_equal(nrow(example_isolates[all(carbapenems()), ]), 756, tolerance = 0.5)
# filter with multiple antibiotic selectors using c() # filter with multiple antibiotic selectors using c()
expect_equal(nrow(example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]), 26) expect_equal(nrow(example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]), 26, tolerance = 0.5)
# filter + select in one go: get penicillins in carbapenems-resistant strains # filter + select in one go: get penicillins in carbapenems-resistant strains
expect_equal(nrow(example_isolates[any(carbapenems() == "R"), penicillins()]), 55) expect_equal(nrow(example_isolates[any(carbapenems() == "R"), penicillins()]), 55, tolerance = 0.5)
expect_equal(ncol(example_isolates[any(carbapenems() == "R"), penicillins()]), 7) expect_equal(ncol(example_isolates[any(carbapenems() == "R"), penicillins()]), 7, tolerance = 0.5)
} }