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(v1.6.0.9056) support codecov again
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parent
b210f1327c
commit
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5
.github/workflows/codecovr.yaml
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5
.github/workflows/codecovr.yaml
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@ -63,13 +63,16 @@ jobs:
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- name: Install dependencies
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run: |
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install.packages(c("remotes"))
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install.packages(c("remotes", "tinytest"))
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("covr")
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remotes::install_local("data-raw/AMR_latest.tar.gz")
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shell: Rscript {0}
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- name: Test coverage
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run: |
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library(AMR)
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library(tinytest)
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source_files <- list.files("R", pattern = ".R$", full.names = TRUE)
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test_files <- list.files("inst/tinytest", full.names = TRUE)
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cov <- covr::file_coverage(source_files = source_files, test_files = test_files, line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.6.0.9055
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Version: 1.6.0.9056
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Date: 2021-05-21
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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2
NEWS.md
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NEWS.md
@ -1,4 +1,4 @@
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# `AMR` 1.6.0.9055
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# `AMR` 1.6.0.9056
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## <small>Last updated: 21 May 2021</small>
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### Breaking change
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9056</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9056</span>
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</span>
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</div>
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@ -39,7 +39,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9056</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9056</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9056</span>
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</span>
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</div>
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@ -42,7 +42,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9056</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9056</span>
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</span>
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</div>
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@ -236,9 +236,9 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1609055" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9055">
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<a href="#amr-1609055" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9055</h1>
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<div id="amr-1609056" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9056">
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<a href="#amr-1609056" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9056</h1>
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<div id="last-updated-21-may-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-21-may-2021" class="anchor"></a><small>Last updated: 21 May 2021</small>
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@ -288,7 +288,7 @@
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</ul>
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</li>
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<li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code><a href="../reference/AMR-deprecated.html">filter_betalactams()</a></code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
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<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
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<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
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</li>
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</ul>
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</div>
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@ -384,7 +384,7 @@
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<span class="co">#> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
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</li>
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<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
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<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code><mic></code> and <code><disk></code></p></li>
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<li><p><code>ggplot()</code> generics for classes <code><mic></code> and <code><disk></code></p></li>
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<li>
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<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
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<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
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@ -441,7 +441,7 @@
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<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
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<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
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<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
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<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
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<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
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</ul>
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</li>
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<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
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@ -458,7 +458,7 @@
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<code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now detects if the column name resembles an antibiotic name or code and now returns <code>TRUE</code> immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li>
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<li>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</li>
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<li>Argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only “S”)</li>
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<li>Functions <code><a href="https://docs.ropensci.org/skimr/reference/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
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<li>Functions <code><a href="https://rdrr.io/r/base/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
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</li>
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<li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
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<li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>
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@ -12,7 +12,7 @@ articles:
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2021-05-21T18:20Z
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last_built: 2021-05-21T18:27Z
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urls:
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9056</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9056</span>
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</span>
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</div>
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