v1.8.2
parent 0205b6178d
commit bc15f660d6
  1. 70
      DESCRIPTION
  2. 2
      R/deprecated.R
  3. 4
      _pkgdown.yml
  4. 1
      docs/news/index.html
  5. 4
      docs/reference/AMR-deprecated.html
  6. 21
      docs/reference/as.mo.html
  7. 29
      docs/reference/index.html
  8. 4
      docs/reference/key_antibiotics.html
  9. 2
      docs/reference/mdro.html
  10. 3
      man/AMR-deprecated.Rd
  11. 15
      man/as.mo.Rd

@ -0,0 +1,70 @@
Package: AMR
Version: 0.5.0.9009
Date: 2019-01-06
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(
given = c("Matthijs", "S."),
family = "Berends",
email = "m.s.berends@umcg.nl",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0001-7620-1800")),
person(
given = c("Christian", "F."),
family = "Luz",
email = "c.f.luz@umcg.nl",
role = c("aut", "rev"),
comment = c(ORCID = "0000-0001-5809-5995")),
person(
given = c("Erwin", "E.", "A."),
family = "Hassing",
email = "e.hassing@certe.nl",
role = "ctb"),
person(
given = "Corinna",
family = "Glasner",
email = "c.glasner@umcg.nl",
role = c("aut", "ths"),
comment = c(ORCID = "0000-0003-1241-1328")),
person(
given = c("Alex", "W."),
family = "Friedrich",
email = "alex.friedrich@umcg.nl",
role = c("aut", "ths"),
comment = c(ORCID = "0000-0003-4881-038X")),
person(
given = c("Bhanu", "N.", "M."),
family = "Sinha",
email = "b.sinha@umcg.nl",
role = c("aut", "ths"),
comment = c(ORCID = "0000-0003-1634-0010")))
Description: Functions to simplify the analysis and prediction of Antimicrobial
Resistance (AMR) and to work with microbial and antimicrobial properties by
using evidence-based methods.
Depends:
R (>= 3.1.0)
Imports:
backports,
curl,
crayon (>= 1.3.0),
data.table (>= 1.9.0),
dplyr (>= 0.7.0),
hms,
knitr (>= 1.0.0),
rlang (>= 0.2.0),
rvest (>= 0.3.2),
tidyr (>= 0.7.0),
xml2 (>= 1.0.0)
Suggests:
covr (>= 3.0.1),
ggplot2,
rmarkdown,
rstudioapi,
testthat (>= 1.0.2)
VignetteBuilder: knitr
URL: https://msberends.gitlab.io/AMR, https://gitlab.com/msberends/AMR
BugReports: https://gitlab.com/msberends/AMR/issues
License: GPL-2 | file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1

@ -48,7 +48,7 @@ ratio <- function(x, ratio) {
}
#' @rdname AMR-deprecated
#' @exported
#' @export
guess_mo <- function(...) {
.Deprecated(new = "as.mo", package = "AMR")
as.mo(...)

@ -75,8 +75,8 @@ reference:
desc: >
Some pages about our package and its external sources.
contents:
- 'AMR'
- itis
- '`AMR`'
- '`itis`'
- title: Cleaning your data
desc: >
Functions for cleaning and optimising your data, to be able

@ -240,6 +240,7 @@
<h4 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h4>
<ul>
<li>Function <code><a href="../reference/AMR-deprecated.html">guess_mo()</a></code> is now deprecated in favour of <code><a href="../reference/as.mo.html">as.mo()</a></code> and will be remover in future versions</li>
<li>Fixed a critical bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where some rules that depend on previous applied rules would not be applied adequately</li>
<li>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:</li>
<li>Finds better results when input is in other languages</li>

@ -220,7 +220,9 @@
</div>
<pre class="usage"><span class='fu'>ratio</span>(<span class='no'>x</span>, <span class='no'>ratio</span>)</pre>
<pre class="usage"><span class='fu'>ratio</span>(<span class='no'>x</span>, <span class='no'>ratio</span>)
<span class='fu'>guess_mo</span>(<span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

@ -223,10 +223,7 @@
<pre class="usage"><span class='fu'>as.mo</span>(<span class='no'>x</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>allow_uncertain</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
<span class='fu'>is.mo</span>(<span class='no'>x</span>)
<span class='fu'>guess_mo</span>(<span class='no'>x</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>allow_uncertain</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
<span class='fu'>is.mo</span>(<span class='no'>x</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -292,7 +289,6 @@
<li><p><code>"S. aureus - please mind: MRSA"</code>. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result <em>Staphylococcus aureus</em> (<code>B_STPHY_AUR</code>) needs review.</p></li>
<li><p><code>"D. spartina"</code>. This is the abbreviation of an old taxonomic name: <em>Didymosphaeria spartinae</em> (the last "e" was missing from the input). This fungus was renamed to <em>Leptosphaeria obiones</em>, so a warning will be thrown that this result (<code>F_LPTSP_OBI</code>) needs review.</p></li>
</ul>
<p><code>guess_mo</code> is an alias of <code>as.mo</code>.</p>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
@ -341,12 +337,11 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
<span class='fu'>as.mo</span>(<span class='st'>"GAS"</span>) <span class='co'># Group A Streptococci</span>
<span class='fu'>as.mo</span>(<span class='st'>"GBS"</span>) <span class='co'># Group B Streptococci</span>
<span class='co'># guess_mo is an alias of as.mo and works the same</span>
<span class='fu'>guess_mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPI</span>
<span class='fu'>guess_mo</span>(<span class='st'>"S. epidermidis"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STPHY_CNS</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPI</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STPHY_CNS</span>
<span class='fu'>guess_mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPTC_PYO</span>
<span class='fu'>guess_mo</span>(<span class='st'>"S. pyogenes"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPTC_GRA</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPTC_PYO</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPTC_GRA</span>
<span class='co'># Use mo_* functions to get a specific property based on `mo`</span>
<span class='no'>Ecoli</span> <span class='kw'>&lt;-</span> <span class='fu'>as.mo</span>(<span class='st'>"E. coli"</span>) <span class='co'># returns `B_ESCHR_COL`</span>
@ -362,16 +357,16 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
<span class='co'># the select function of tidyverse is also supported:</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>microorganism_name</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>microorganism_name</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>as.mo</span>()
<span class='co'># and can even contain 2 columns, which is convenient for genus/species combinations:</span>
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>as.mo</span>()
<span class='co'># although this works easier and does the same:</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'>as.mo</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)))
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'>as.mo</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)))
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

@ -219,6 +219,26 @@
</colgroup>
<tbody>
<tr>
<th colspan="2">
<h2 id="section-backround-information" class="hasAnchor"><a href="#section-backround-information" class="anchor"></a>Backround information</h2>
<p class="section-desc"><p>Some pages about our package and its external sources.</p></p>
</th>
</tr>
<tr>
<td>
<p><code><a href="AMR.html">AMR</a></code> </p>
</td>
<td><p>The <code>AMR</code> Package</p></td>
</tr><tr>
<td>
<p><code><a href="itis.html">itis</a></code> </p>
</td>
<td><p>ITIS: Integrated Taxonomic Information System</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-cleaning-your-data" class="hasAnchor"><a href="#section-cleaning-your-data" class="anchor"></a>Cleaning your data</h2>
@ -240,7 +260,7 @@
</tr><tr>
<td>
<p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">guess_mo()</a></code> </p>
<p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> </p>
</td>
<td><p>Transform to microorganism ID</p></td>
</tr><tr>
@ -257,6 +277,12 @@
<td><p>EUCAST rules</p></td>
</tr><tr>
<td>
<p><code><a href="guess_ab.html">guess_ab()</a></code> </p>
</td>
<td><p>Guess antibiotic column</p></td>
</tr><tr>
<td>
<p><code><a href="read.4D.html">read.4D()</a></code> </p>
</td>
@ -487,6 +513,7 @@
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#section-backround-information">Backround information</a></li>
<li><a href="#section-cleaning-your-data">Cleaning your data</a></li>
<li><a href="#section-adding-variables-to-your-data">Adding variables to your data</a></li>
<li><a href="#section-analysing-your-data">Analysing your data</a></li>

@ -324,8 +324,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># set key antibiotics to a new variable</span>
<span class='no'>my_patients</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>keyab</span> <span class='kw'>=</span> <span class='fu'>key_antibiotics</span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>keyab</span> <span class='kw'>=</span> <span class='fu'>key_antibiotics</span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(
<span class='co'># now calculate first isolates</span>
<span class='kw'>first_regular</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
<span class='co'># and first WEIGHTED isolates</span>

@ -601,7 +601,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>EUCAST</span> <span class='kw'>=</span> <span class='fu'>mdro</span>(<span class='no'>.</span>),
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>EUCAST</span> <span class='kw'>=</span> <span class='fu'>mdro</span>(<span class='no'>.</span>),
<span class='kw'>BRMO</span> <span class='kw'>=</span> <span class='fu'>brmo</span>(<span class='no'>.</span>))
<span class='co'># }</span></pre>
</div>

@ -3,9 +3,12 @@
\name{AMR-deprecated}
\alias{AMR-deprecated}
\alias{ratio}
\alias{guess_mo}
\title{Deprecated functions}
\usage{
ratio(x, ratio)
guess_mo(...)
}
\description{
These functions are \link{Deprecated}. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by.

@ -4,16 +4,12 @@
\alias{as.mo}
\alias{mo}
\alias{is.mo}
\alias{guess_mo}
\title{Transform to microorganism ID}
\usage{
as.mo(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
reference_df = NULL)
is.mo(x)
guess_mo(x, Becker = FALSE, Lancefield = FALSE,
allow_uncertain = TRUE, reference_df = NULL)
}
\arguments{
\item{x}{a character vector or a \code{data.frame} with one or two columns}
@ -77,8 +73,6 @@ When using \code{allow_uncertain = TRUE} (which is the default setting), it will
\item{\code{"S. aureus - please mind: MRSA"}. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result \emph{Staphylococcus aureus} (\code{B_STPHY_AUR}) needs review.}
\item{\code{"D. spartina"}. This is the abbreviation of an old taxonomic name: \emph{Didymosphaeria spartinae} (the last "e" was missing from the input). This fungus was renamed to \emph{Leptosphaeria obiones}, so a warning will be thrown that this result (\code{F_LPTSP_OBI}) needs review.}
}
\code{guess_mo} is an alias of \code{as.mo}.
}
\section{Source}{
@ -124,12 +118,11 @@ as.mo("Streptococcus group A")
as.mo("GAS") # Group A Streptococci
as.mo("GBS") # Group B Streptococci
# guess_mo is an alias of as.mo and works the same
guess_mo("S. epidermidis") # will remain species: B_STPHY_EPI
guess_mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
as.mo("S. epidermidis") # will remain species: B_STPHY_EPI
as.mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
guess_mo("S. pyogenes") # will remain species: B_STRPTC_PYO
guess_mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
as.mo("S. pyogenes") # will remain species: B_STRPTC_PYO
as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
# Use mo_* functions to get a specific property based on `mo`
Ecoli <- as.mo("E. coli") # returns `B_ESCHR_COL`

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