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(v0.7.1.9008) ab update

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dr. M.S. (Matthijs) Berends 2019-07-04 19:08:18 +02:00
parent c57ad26c5b
commit d9e257f8db
10 changed files with 19 additions and 12 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 0.7.1.9007
Version: 0.7.1.9008
Date: 2019-07-04
Title: Antimicrobial Resistance Analysis
Authors@R: c(

4
NEWS.md
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# AMR 0.7.1.9007
# AMR 0.7.1.9008
### New
* Additional way to calculate co-resistance, i.e. when using multiple antibiotics as input for `portion_*` functions or `count_*` functions. This can be used to determine the empiric susceptibily of a combination therapy. A new parameter `only_all_tested` (**which defaults to `FALSE`**) replaces the old `also_single_tested` and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the `portion` and `count` help pages), where the %SI is being determined:
@ -39,6 +39,8 @@
* Fix for using `mo_*` functions where the coercion uncertainties and failures would not be available through `mo_uncertainties()` and `mo_failures()` anymore
* Deprecated the `country` parameter of `mdro()` in favour of the already existing `guideline` parameter to support multiple guidelines within one country
* Fix for frequency tables when creating one directly on a group (using `group_by()`)
* The name of `RIF` is now Rifampicin instead of Rifampin
* The `antibiotics` data set is now sorted by name
# AMR 0.7.1

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data-raw/reproduction_of_antibiotics.R
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@ -289,6 +289,8 @@ antibiotics <- filter(antibiotics, ab != "MOX")
antibiotics <- filter(antibiotics, ab != "RFP")
antibiotics[which(antibiotics$ab == "RFP1"), "ab"] <- "RFP"
antibiotics[which(antibiotics$ab == "RFP"), "abbreviations"][[1]] <- list(c("rifp"))
# Rifampicin is better known as a drug than Rifampin (Rifampin is still listed as a brand name), so:
antibiotics[which(antibiotics$ab == "RIF"), "name"] <- "Rifampicin"
# PME and PVM1 (the J0 one) both mean 'Pivmecillinam', so:
antibiotics <- filter(antibiotics, ab != "PME")
antibiotics[which(antibiotics$ab == "PVM1"), "ab"] <- "PME"
@ -300,8 +302,9 @@ antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]] <- list(c(anti
antibiotics[which(antibiotics$ab == "CTC"), "abbreviations"][[1]] <- list(c("xctl"))
antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]], "xct"))
antibiotics <- antibiotics %>% arrange(name)
class(antibiotics$ab) <- "ab"
class(antibiotics$atc) <- "atc"
dim(antibiotics) # for R/data.R
usethis::use_data(antibiotics, overwrite = TRUE)

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data/antibiotics.rda
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docs/LICENSE-text.html
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</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">0.7.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9008</span>
</span>
</div>

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docs/articles/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9008</span>
</span>
</div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</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">0.7.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9008</span>
</span>
</div>

2
docs/index.html
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@ -42,7 +42,7 @@
</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">0.7.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9008</span>
</span>
</div>

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docs/news/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9008</span>
</span>
</div>
@ -232,9 +232,9 @@
</div>
<div id="amr-0719007" class="section level1">
<div id="amr-0719008" class="section level1">
<h1 class="page-header">
<a href="#amr-0719007" class="anchor"></a>AMR 0.7.1.9007<small> Unreleased </small>
<a href="#amr-0719008" class="anchor"></a>AMR 0.7.1.9008<small> Unreleased </small>
</h1>
<div id="new" class="section level3">
<h3 class="hasAnchor">
@ -282,6 +282,8 @@
<li>Fix for using <code>mo_*</code> functions where the coercion uncertainties and failures would not be available through <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code> and <code><a href="../reference/as.mo.html">mo_failures()</a></code> anymore</li>
<li>Deprecated the <code>country</code> parameter of <code><a href="../reference/mdro.html">mdro()</a></code> in favour of the already existing <code>guideline</code> parameter to support multiple guidelines within one country</li>
<li>Fix for frequency tables when creating one directly on a group (using <code>group_by()</code>)</li>
<li>The name of <code>RIF</code> is now Rifampicin instead of Rifampin</li>
<li>The <code>antibiotics</code> data set is now sorted by name</li>
</ul>
</div>
</div>
@ -1194,7 +1196,7 @@ 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-0719007">0.7.1.9007</a></li>
<li><a href="#amr-0719008">0.7.1.9008</a></li>
<li><a href="#amr-071">0.7.1</a></li>
<li><a href="#amr-070">0.7.0</a></li>
<li><a href="#amr-061">0.6.1</a></li>

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docs/reference/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9008</span>
</span>
</div>