mirror of https://github.com/msberends/AMR.git
guess_ab()
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Package: AMR
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Version: 0.5.0.9009
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Date: 2019-01-06
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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given = c("Matthijs", "S."),
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family = "Berends",
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email = "m.s.berends@umcg.nl",
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role = c("aut", "cre"),
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comment = c(ORCID = "0000-0001-7620-1800")),
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person(
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given = c("Christian", "F."),
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family = "Luz",
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email = "c.f.luz@umcg.nl",
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role = c("aut", "rev"),
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comment = c(ORCID = "0000-0001-5809-5995")),
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person(
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given = c("Erwin", "E.", "A."),
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family = "Hassing",
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email = "e.hassing@certe.nl",
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role = "ctb"),
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person(
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given = "Corinna",
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family = "Glasner",
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email = "c.glasner@umcg.nl",
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role = c("aut", "ths"),
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comment = c(ORCID = "0000-0003-1241-1328")),
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person(
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given = c("Alex", "W."),
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family = "Friedrich",
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email = "alex.friedrich@umcg.nl",
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role = c("aut", "ths"),
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comment = c(ORCID = "0000-0003-4881-038X")),
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person(
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given = c("Bhanu", "N.", "M."),
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family = "Sinha",
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email = "b.sinha@umcg.nl",
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role = c("aut", "ths"),
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comment = c(ORCID = "0000-0003-1634-0010")))
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Description: Functions to simplify the analysis and prediction of Antimicrobial
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Resistance (AMR) and to work with microbial and antimicrobial properties by
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using evidence-based methods.
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Depends:
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R (>= 3.1.0)
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Imports:
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backports,
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curl,
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crayon (>= 1.3.0),
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data.table (>= 1.9.0),
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dplyr (>= 0.7.0),
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hms,
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knitr (>= 1.0.0),
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rlang (>= 0.2.0),
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rvest (>= 0.3.2),
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tidyr (>= 0.7.0),
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xml2 (>= 1.0.0)
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Suggests:
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covr (>= 3.0.1),
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ggplot2,
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rmarkdown,
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rstudioapi,
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testthat (>= 1.0.2)
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VignetteBuilder: knitr
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URL: https://msberends.gitlab.io/AMR, https://gitlab.com/msberends/AMR
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BugReports: https://gitlab.com/msberends/AMR/issues
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License: GPL-2 | file LICENSE
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 6.1.1
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@ -48,7 +48,7 @@ ratio <- function(x, ratio) {
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}
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#' @rdname AMR-deprecated
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#' @exported
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#' @export
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guess_mo <- function(...) {
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.Deprecated(new = "as.mo", package = "AMR")
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as.mo(...)
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@ -75,8 +75,8 @@ reference:
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desc: >
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Some pages about our package and its external sources.
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contents:
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- 'AMR'
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- itis
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- '`AMR`'
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- '`itis`'
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- title: Cleaning your data
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desc: >
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Functions for cleaning and optimising your data, to be able
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@ -240,6 +240,7 @@
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<h4 class="hasAnchor">
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<a href="#changed" class="anchor"></a>Changed</h4>
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<ul>
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<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>
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<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>
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<li>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:</li>
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<li>Finds better results when input is in other languages</li>
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@ -220,7 +220,9 @@
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</div>
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<pre class="usage"><span class='fu'>ratio</span>(<span class='no'>x</span>, <span class='no'>ratio</span>)</pre>
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<pre class="usage"><span class='fu'>ratio</span>(<span class='no'>x</span>, <span class='no'>ratio</span>)
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<span class='fu'>guess_mo</span>(<span class='no'>...</span>)</pre>
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<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>
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@ -223,10 +223,7 @@
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<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>,
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<span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
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<span class='fu'>is.mo</span>(<span class='no'>x</span>)
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<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>,
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<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>
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<span class='fu'>is.mo</span>(<span class='no'>x</span>)</pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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@ -292,7 +289,6 @@
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<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>
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<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>
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</ul>
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<p><code>guess_mo</code> is an alias of <code>as.mo</code>.</p>
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<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
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@ -341,12 +337,11 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
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<span class='fu'>as.mo</span>(<span class='st'>"GAS"</span>) <span class='co'># Group A Streptococci</span>
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<span class='fu'>as.mo</span>(<span class='st'>"GBS"</span>) <span class='co'># Group B Streptococci</span>
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<span class='co'># guess_mo is an alias of as.mo and works the same</span>
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<span class='fu'>guess_mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPI</span>
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<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>
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<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPI</span>
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<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>
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<span class='fu'>guess_mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPTC_PYO</span>
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<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>
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<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPTC_PYO</span>
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<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>
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<span class='co'># Use mo_* functions to get a specific property based on `mo`</span>
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<span class='no'>Ecoli</span> <span class='kw'><-</span> <span class='fu'>as.mo</span>(<span class='st'>"E. coli"</span>) <span class='co'># returns `B_ESCHR_COL`</span>
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@ -362,16 +357,16 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
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<span class='co'># the select function of tidyverse is also supported:</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'><-</span> <span class='no'>df</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>microorganism_name</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>microorganism_name</span>) <span class='kw'>%>%</span>
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<span class='fu'>as.mo</span>()
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<span class='co'># and can even contain 2 columns, which is convenient for genus/species combinations:</span>
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<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'><-</span> <span class='no'>df</span> <span class='kw'>%>%</span>
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<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'>%>%</span>
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<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'>%>%</span>
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<span class='fu'>as.mo</span>()
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<span class='co'># although this works easier and does the same:</span>
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<span class='no'>df</span> <span class='kw'><-</span> <span class='no'>df</span> <span class='kw'>%>%</span>
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<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>)))
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<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>)))
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<span class='co'># }</span></pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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@ -219,6 +219,26 @@
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</colgroup>
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<tbody>
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<tr>
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<th colspan="2">
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<h2 id="section-backround-information" class="hasAnchor"><a href="#section-backround-information" class="anchor"></a>Backround information</h2>
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<p class="section-desc"><p>Some pages about our package and its external sources.</p></p>
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</th>
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</tr>
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<tr>
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<td>
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<p><code><a href="AMR.html">AMR</a></code> </p>
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</td>
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<td><p>The <code>AMR</code> Package</p></td>
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</tr><tr>
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<td>
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<p><code><a href="itis.html">itis</a></code> </p>
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</td>
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<td><p>ITIS: Integrated Taxonomic Information System</p></td>
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</tr>
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</tbody><tbody>
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<tr>
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<th colspan="2">
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<h2 id="section-cleaning-your-data" class="hasAnchor"><a href="#section-cleaning-your-data" class="anchor"></a>Cleaning your data</h2>
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@ -240,7 +260,7 @@
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</tr><tr>
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<td>
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<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>
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<p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> </p>
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</td>
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<td><p>Transform to microorganism ID</p></td>
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</tr><tr>
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@ -257,6 +277,12 @@
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<td><p>EUCAST rules</p></td>
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</tr><tr>
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<td>
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<p><code><a href="guess_ab.html">guess_ab()</a></code> </p>
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</td>
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<td><p>Guess antibiotic column</p></td>
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</tr><tr>
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<td>
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<p><code><a href="read.4D.html">read.4D()</a></code> </p>
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</td>
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@ -487,6 +513,7 @@
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#section-backround-information">Backround information</a></li>
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<li><a href="#section-cleaning-your-data">Cleaning your data</a></li>
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<li><a href="#section-adding-variables-to-your-data">Adding variables to your data</a></li>
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<li><a href="#section-analysing-your-data">Analysing your data</a></li>
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@ -324,8 +324,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='co'># set key antibiotics to a new variable</span>
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<span class='no'>my_patients</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<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'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(
|
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<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'>%>%</span>
|
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(
|
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<span class='co'># now calculate first isolates</span>
|
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<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>),
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<span class='co'># and first WEIGHTED isolates</span>
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@ -601,7 +601,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
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||||
|
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
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<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>))
|
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<span class='co'># }</span></pre>
|
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</div>
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@ -3,9 +3,12 @@
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\name{AMR-deprecated}
|
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\alias{AMR-deprecated}
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\alias{ratio}
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\alias{guess_mo}
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\title{Deprecated functions}
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\usage{
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ratio(x, ratio)
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guess_mo(...)
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}
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\description{
|
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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.
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15
man/as.mo.Rd
15
man/as.mo.Rd
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@ -4,16 +4,12 @@
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\alias{as.mo}
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\alias{mo}
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\alias{is.mo}
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\alias{guess_mo}
|
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\title{Transform to microorganism ID}
|
||||
\usage{
|
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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)
|
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}
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\arguments{
|
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\item{x}{a character vector or a \code{data.frame} with one or two columns}
|
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@ -77,8 +73,6 @@ When using \code{allow_uncertain = TRUE} (which is the default setting), it will
|
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\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.}
|
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\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.}
|
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}
|
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|
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\code{guess_mo} is an alias of \code{as.mo}.
|
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}
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\section{Source}{
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@ -124,12 +118,11 @@ as.mo("Streptococcus group A")
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as.mo("GAS") # Group A Streptococci
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as.mo("GBS") # Group B Streptococci
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# guess_mo is an alias of as.mo and works the same
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guess_mo("S. epidermidis") # will remain species: B_STPHY_EPI
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guess_mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
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as.mo("S. epidermidis") # will remain species: B_STPHY_EPI
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as.mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
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guess_mo("S. pyogenes") # will remain species: B_STRPTC_PYO
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guess_mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
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as.mo("S. pyogenes") # will remain species: B_STRPTC_PYO
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as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
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# Use mo_* functions to get a specific property based on `mo`
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Ecoli <- as.mo("E. coli") # returns `B_ESCHR_COL`
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|
|
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Loading…
Reference in New Issue