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(v0.7.1.9057) get_column_abx() improvement

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dr. M.S. (Matthijs) Berends 2019-08-15 17:09:27 +02:00
parent 920212e815
commit 04d49a62af
12 changed files with 31 additions and 35 deletions
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DESCRIPTION
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Package: AMR Package: AMR
Version: 0.7.1.9056 Version: 0.7.1.9057
Date: 2019-08-14 Date: 2019-08-15
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

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NEWS.md
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# AMR 0.7.1.9056 # AMR 0.7.1.9057
### Breaking ### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too. * Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
@ -46,6 +46,7 @@
* Printed info now distinguishes between added and changes values * Printed info now distinguishes between added and changes values
* Using Verbose mode (i.e. `eucast_rules(..., verbose = TRUE)`) returns more informative and readable output * Using Verbose mode (i.e. `eucast_rules(..., verbose = TRUE)`) returns more informative and readable output
* Using factors as input now adds missing factors levels when the function changes antibiotic results * Using factors as input now adds missing factors levels when the function changes antibiotic results
* Improved the internal auto-guessing function for determining antibiotics in your data set (`AMR:::get_column_abx()`)
* Added tibble printing support for classes `rsi`, `mic`, `disk`, `ab` `mo`. When using tibbles containing antibiotic columns, values `S` will print in green, values `I` will print in yellow and values `R` will print in red. Microbial IDs (class `mo`) will emphasise on the genus and species, not on the kingdom. * Added tibble printing support for classes `rsi`, `mic`, `disk`, `ab` `mo`. When using tibbles containing antibiotic columns, values `S` will print in green, values `I` will print in yellow and values `R` will print in red. Microbial IDs (class `mo`) will emphasise on the genus and species, not on the kingdom.
```r ```r
# (run this on your own console, as this page does not support colour printing) # (run this on your own console, as this page does not support colour printing)

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R/guess_ab_col.R
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@ -148,27 +148,21 @@ get_column_abx <- function(x,
} }
# sort on name # sort on name
x <- x[sort(names(x))] x <- x[order(names(x), x)]
dupes <- x[base::duplicated(x)] duplicates <- x[base::duplicated(x)]
x <- x[!names(x) %in% names(duplicates)]
if (verbose == TRUE) { if (verbose == TRUE) {
for (i in 1:length(x)) { for (i in 1:length(x)) {
if (x[i] %in% dupes) { message(blue(paste0("NOTE: Using column `", bold(x[i]), "` as input for `", names(x)[i],
message(red(paste0("NOTE: Using column `", bold(x[i]), "` as input for `", names(x)[i], "` (", ab_name(names(x)[i], tolower = TRUE), ").")))
"` (", ab_name(names(x)[i], language = "en", tolower = TRUE), ") [DUPLICATED USE].")))
} else {
message(blue(paste0("NOTE: Using column `", bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], language = "en", tolower = TRUE), ").")))
}
} }
} } else if (length(duplicates) > 0) {
for (i in 1:length(duplicates)) {
if (n_distinct(x) != length(x)) { warning(red(paste0("Using column `", bold(duplicates[i]), "` as input for `", names(x[which(x == duplicates[i])]),
msg_txt <- paste("Column(s)", paste0("`", dupes, "`", collapse = " and "), "used for more than one antibiotic.") "` (", ab_name(names(x[names(which(x == duplicates))[i]]), tolower = TRUE),
if (verbose == FALSE) { "), although it was matched for multiple antibiotics or columns.")), call. = FALSE)
msg_txt <- paste(msg_txt, "Use verbose = TRUE to see which antibiotics are used by which columns.")
} }
stop(msg_txt, call. = FALSE)
} }
if (!is.null(hard_dependencies)) { if (!is.null(hard_dependencies)) {

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docs/LICENSE-text.html
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</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">0.7.1.9056</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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</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">0.7.1.9056</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
</span> </span>
</div> </div>

2
docs/authors.html
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</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">0.7.1.9056</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</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">0.7.1.9056</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
</span> </span>
</div> </div>

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docs/news/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9056</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
</span> </span>
</div> </div>
@ -225,9 +225,9 @@
</div> </div>
<div id="amr-0-7-1-9056" class="section level1"> <div id="amr-0-7-1-9057" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9056" class="anchor"></a>AMR 0.7.1.9056<small> Unreleased </small> <a href="#amr-0-7-1-9057" class="anchor"></a>AMR 0.7.1.9057<small> Unreleased </small>
</h1> </h1>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -288,6 +288,7 @@
<li>Using factors as input now adds missing factors levels when the function changes antibiotic results</li> <li>Using factors as input now adds missing factors levels when the function changes antibiotic results</li>
</ul> </ul>
</li> </li>
<li>Improved the internal auto-guessing function for determining antibiotics in your data set (<code>AMR:::get_column_abx()</code>)</li>
<li> <li>
<p>Added tibble printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using tibbles containing antibiotic columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p> <p>Added tibble printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using tibbles containing antibiotic columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># (run this on your own console, as this page does not support colour printing)</span></a> <div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># (run this on your own console, as this page does not support colour printing)</span></a>
@ -1237,7 +1238,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9056">0.7.1.9056</a></li> <li><a href="#amr-0-7-1-9057">0.7.1.9057</a></li>
<li><a href="#amr-0-7-1">0.7.1</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> <li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li> <li><a href="#amr-0-6-1">0.6.1</a></li>

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docs/reference/first_isolate.html
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</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">0.7.1.9055</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
</span> </span>
</div> </div>
@ -476,7 +476,7 @@ To conduct an analysis of antimicrobial resistance, you should only include the
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

2
docs/reference/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9056</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
</span> </span>
</div> </div>

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docs/reference/key_antibiotics.html
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@ -80,7 +80,7 @@
</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">0.7.1.9055</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
</span> </span>
</div> </div>
@ -388,7 +388,7 @@
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

4
tests/testthat/test-misc.R
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@ -44,6 +44,6 @@ test_that("looking up ab columns works", {
expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE)) expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
expect_warning(get_column_abx(septic_patients, hard_dependencies = "FUS")) expect_warning(get_column_abx(septic_patients, hard_dependencies = "FUS"))
expect_message(get_column_abx(septic_patients, soft_dependencies = "FUS")) expect_message(get_column_abx(septic_patients, soft_dependencies = "FUS"))
expect_error(get_column_abx(dplyr::rename(septic_patients, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE)) expect_message(get_column_abx(dplyr::rename(septic_patients, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
expect_error(get_column_abx(dplyr::rename(septic_patients, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE)) expect_warning(get_column_abx(dplyr::rename(septic_patients, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
}) })