guess_ab()

2025-10-31 02:08:20 +01:00 · 2019-01-06 20:23:49 +01:00
parent 0205b6178d
commit bc15f660d6
11 changed files with 123 additions and 32 deletions
--- a/70
+++ b/70
@@ -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
--- a/R/deprecated.R
+++ b/R/deprecated.R
@@ -48,7 +48,7 @@ ratio <- function(x, ratio) {
 }

 #' @rdname AMR-deprecated
-#' @exported
+#' @export
 guess_mo <- function(...) {
  .Deprecated(new = "as.mo", package = "AMR")
  as.mo(...)
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -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
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -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>
--- a/docs/reference/AMR-deprecated.html
+++ b/docs/reference/AMR-deprecated.html
@@ -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>

--- a/docs/reference/as.mo.html
+++ b/docs/reference/as.mo.html
@@ -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">
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -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>
--- a/docs/reference/key_antibiotics.html
+++ b/docs/reference/key_antibiotics.html
@@ -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>
--- a/docs/reference/mdro.html
+++ b/docs/reference/mdro.html
@@ -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>
--- a/man/AMR-deprecated.Rd
+++ b/man/AMR-deprecated.Rd
@@ -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.
--- a/man/as.mo.Rd
+++ b/man/as.mo.Rd
@@ -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`