(v0.7.1.9056) mo and ab subsetting

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.7.1.9055
-Date: 2019-08-13
+Version: 0.7.1.9056
+Date: 2019-08-14
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 
@@ -11,6 +11,8 @@ Authors@R: c(
            family = "Friedrich", given = c("Alex", "W."), email = "alex.friedrich@umcg.nl", comment = c(ORCID = "0000-0003-4881-038X")),
     person(role = c("aut", "ths"),
            family = "Sinha", given = c("Bhanu", "N.", "M."), email = "b.sinha@umcg.nl", comment = c(ORCID = "0000-0003-1634-0010")),
+    person(role = c("aut", "ths"),
+           family = "Albers", given = c("Casper", "J."), email = "c.j.albers@rug.nl", comment = c(ORCID = "0000-0002-9213-6743")),
     person(role = c("aut", "ths"),
            family = "Glasner", given = "Corinna", email = "c.glasner@umcg.nl", comment = c(ORCID = "0000-0003-1241-1328")),
     person(role = "ctb",

NAMESPACE

@@ -2,6 +2,12 @@
 
 S3method("[",ab)
 S3method("[",mo)
+S3method("[<-",ab)
+S3method("[<-",mo)
+S3method("[[",ab)
+S3method("[[",mo)
+S3method("[[<-",ab)
+S3method("[[<-",mo)
 S3method(as.data.frame,ab)
 S3method(as.data.frame,mo)
 S3method(as.double,mic)
@@ -13,6 +19,8 @@ S3method(as.rsi,disk)
 S3method(as.rsi,mic)
 S3method(barplot,mic)
 S3method(barplot,rsi)
+S3method(c,ab)
+S3method(c,mo)
 S3method(droplevels,mic)
 S3method(droplevels,rsi)
 S3method(freq,mo)
@@ -172,6 +180,12 @@ export(skewness)
 export(theme_rsi)
 exportMethods("[.ab")
 exportMethods("[.mo")
+exportMethods("[<-.ab")
+exportMethods("[<-.mo")
+exportMethods("[[.ab")
+exportMethods("[[.mo")
+exportMethods("[[<-.ab")
+exportMethods("[[<-.mo")
 exportMethods(as.data.frame.ab)
 exportMethods(as.data.frame.mo)
 exportMethods(as.double.mic)
@@ -179,6 +193,8 @@ exportMethods(as.integer.mic)
 exportMethods(as.numeric.mic)
 exportMethods(barplot.mic)
 exportMethods(barplot.rsi)
+exportMethods(c.ab)
+exportMethods(c.mo)
 exportMethods(droplevels.mic)
 exportMethods(droplevels.rsi)
 exportMethods(freq.mo)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.7.1.9055
+# AMR 0.7.1.9056
 
 ### 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.
@@ -73,7 +73,7 @@
 * Classes `ab` and `mo` will now be preserved in any subsetting
 
 #### Other
-* Added Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors
+* Added Prof Dr Casper Albers as doctoral advisor and Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors
 
 # AMR 0.7.1
 

R/ab.R

@@ -282,10 +282,42 @@ as.data.frame.ab <- function (x, ...) {
 #' @exportMethod [.ab
 #' @export
 #' @noRd
-"[.ab" <- function (x, ...) {
-  # this function is needed to preserve the "ab" class for any subsetting, like df %>% filter(...)
+"[.ab" <- function(x, ...) {
   y <- NextMethod()
-  structure(y, class = "ab")
+  attributes(y) <- attributes(x)
+  y
+}
+#' @exportMethod [<-.ab
+#' @export
+#' @noRd
+"[<-.ab" <- function(value) {
+  y <- NextMethod()
+  attributes(y) <- attributes(value)
+  y
+}
+#' @exportMethod [[.ab
+#' @export
+#' @noRd
+"[[.ab" <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+#' @exportMethod [[<-.ab
+#' @export
+#' @noRd
+"[[<-.ab" <- function(i, j, ..., value) {
+  y <- NextMethod()
+  attributes(y) <- attributes(value)
+  y
+}
+#' @exportMethod c.ab
+#' @export
+#' @noRd
+c.ab <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
 }
 
 #' @importFrom pillar type_sum

R/first_isolate.R

@@ -79,8 +79,8 @@
 #' @source Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
 #' @inheritSection AMR Read more on our website!
 #' @examples
-#' # septic_patients is a dataset available in the AMR package. It is true, genuine data.
-#' ?septic_patients
+#' # `septic_patients` is a dataset available in the AMR package. It is true, genuine data.
+#' # See ?septic_patients.
 #'
 #' library(dplyr)
 #' # Filter on first isolates:
@@ -97,7 +97,7 @@
 #' # or for first weighted isolates:
 #' septic_patients %>%
 #'   filter_first_weighted_isolate()
-#'
+#' 
 #' # Now let's see if first isolates matter:
 #' A <- septic_patients %>%
 #'   group_by(hospital_id) %>%

R/key_antibiotics.R

@@ -48,8 +48,8 @@
 #' @seealso \code{\link{first_isolate}}
 #' @inheritSection AMR Read more on our website!
 #' @examples
-#' # septic_patients is a dataset available in the AMR package
-#' ?septic_patients
+#' # `septic_patients` is a dataset available in the AMR package. It is true, genuine data.
+#' # See ?septic_patients.
 #'
 #' library(dplyr)
 #' # set key antibiotics to a new variable

R/mo.R

@@ -1723,10 +1723,42 @@ as.data.frame.mo <- function(x, ...) {
 #' @exportMethod [.mo
 #' @export
 #' @noRd
-"[.mo" <- function (x, ...) {
-  # this function is needed to preserve the "mo" class for any subsetting, like df %>% filter(...)
+"[.mo" <- function(x, ...) {
   y <- NextMethod()
-  to_class_mo(y)
+  attributes(y) <- attributes(x)
+  y
+}
+#' @exportMethod [<-.mo
+#' @export
+#' @noRd
+"[<-.mo" <- function(i, j, ..., value) {
+  y <- NextMethod()
+  attributes(y) <- attributes(value)
+  y
+}
+#' @exportMethod [[.mo
+#' @export
+#' @noRd
+"[[.mo" <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+#' @exportMethod [[<-.mo
+#' @export
+#' @noRd
+"[[<-.mo" <- function(value) {
+  y <- NextMethod()
+  attributes(y) <- attributes(value)
+  y
+}
+#' @exportMethod c.mo
+#' @export
+#' @noRd
+c.mo <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
 }
 
 #' @rdname as.mo

_pkgdown.yml

@@ -172,12 +172,14 @@ authors:
     href: https://www.rug.nl/staff/m.s.berends/
   Christian F. Luz:
     href: https://www.rug.nl/staff/c.f.luz/
-  Corinna Glasner:
-    href: https://www.rug.nl/staff/c.glasner/
   Alex W. Friedrich:
     href: https://www.rug.nl/staff/a.w.friedrich/
   Bhanu N. M. Sinha:
     href: https://www.rug.nl/staff/b.sinha/
+  Casper J. Albers:
+    href: https://www.rug.nl/staff/c.j.albers/
+  Corinna Glasner:
+    href: https://www.rug.nl/staff/c.glasner/
 
 template:
   assets: "pkgdown/logos" # use logos in this folder

docs/LICENSE-text.html

@@ -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">0.7.1.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
       </span>
     </div>
 
@@ -513,7 +513,7 @@ END OF TERMS AND CONDITIONS
 
       <footer>
       <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 class="pkgdown">

docs/articles/index.html

@@ -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">0.7.1.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
       </span>
     </div>
 
@@ -243,7 +243,7 @@
 
       <footer>
       <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 class="pkgdown">

docs/authors.html

@@ -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">0.7.1.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
       </span>
     </div>
 
@@ -241,6 +241,10 @@
         <p><strong><a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1634-0010' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
         </p>
       </li>
+      <li>
+        <p><strong><a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0002-9213-6743' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
+        </p>
+      </li>
       <li>
         <p><strong><a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1241-1328' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
         </p>
@@ -270,7 +274,7 @@
 
       <footer>
       <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 class="pkgdown">

docs/extra.js

@@ -77,16 +77,14 @@ $( document ).ready(function() {
   // doctoral titles of authors
   function doct_tit(x) {
     if (typeof(x) != "undefined") {
-      x = x.replace("Corinna", "Dr Corinna");
       x = x.replace("Alex", "Prof Dr Alex");
       x = x.replace("Bhanu", "Prof Dr Bhanu");
+      x = x.replace("Corinna", "Dr Corinna");
+      x = x.replace("Casper", "Prof Dr Casper");
       x = x.replace("Bart", "Dr Bart");
       x = x.replace("Dennis", "Dr Dennis");
       x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
-      x = x.replace(/Authors/g, "aut_plural");
-      x = x.replace(/Author, maintainer[.]?/g, "");
-      x = x.replace(/Author[.]?/g, "");
-      x = x.replace(/aut_plural/g, "Authors");
+      x = x.replace(/Author(, maintainer)?[.]?[^s]/g, "");
     }
     return(x);
   }

docs/index.html

@@ -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">0.7.1.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
       </span>
     </div>
 
@@ -283,16 +283,12 @@
 <div id="microbial-taxonomic-reference-data" class="section level4">
 <h4 class="hasAnchor">
 <a href="#microbial-taxonomic-reference-data" class="anchor"></a>Microbial (taxonomic) reference data</h4>
-<p><img src="reference/figures/logo_col.png"></p>
 <p>This package contains the complete taxonomic tree of almost all 70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org">www.catalogueoflife.org</a>). With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p>
 <p>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
 </div>
 <div id="antimicrobial-reference-data" class="section level4">
 <h4 class="hasAnchor">
 <a href="#antimicrobial-reference-data" class="anchor"></a>Antimicrobial reference data</h4>
-<div>
-<img src="reference/figures/logo_who.png" height="75px" class="logo_img"><p class="logo_txt">WHO Collaborating Centre for Drug Statistics Methodology</p>
-</div>
 <p>This package contains <strong>all ~450 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="uri">https://www.whocc.no</a>) and the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register of the European Commission</a>.</p>
 <p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
 <p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
@@ -300,7 +296,6 @@
 <div id="whonet-ears-net" class="section level4">
 <h4 class="hasAnchor">
 <a href="#whonet-ears-net" class="anchor"></a>WHONET / EARS-Net</h4>
-<p><img src="./whonet.png"></p>
 <p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure as a WHONET export file. Furthermore, this package also contains a <a href="./reference/antibiotics.html">data set <code>antibiotics</code></a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p>
 <p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
 </div>
@@ -394,6 +389,8 @@
 <li>
 <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
 <li>
+<a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0002-9213-6743" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
+<li>
 <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
 <li><a href="authors.html">All authors...</a></li>
 </ul>
@@ -403,7 +400,7 @@
 </div>
 
       <footer><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 class="pkgdown">

docs/news/index.html

@@ -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">0.7.1.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
       </span>
     </div>
 
@@ -225,9 +225,9 @@
       
     </div>
 
-    <div id="amr-0-7-1-9055" class="section level1">
+    <div id="amr-0-7-1-9056" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-7-1-9055" class="anchor"></a>AMR 0.7.1.9055<small> Unreleased </small>
+<a href="#amr-0-7-1-9056" class="anchor"></a>AMR 0.7.1.9056<small> Unreleased </small>
 </h1>
 <div id="breaking" class="section level3">
 <h3 class="hasAnchor">
@@ -323,7 +323,7 @@
 <h4 class="hasAnchor">
 <a href="#other" class="anchor"></a>Other</h4>
 <ul>
-<li>Added Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors</li>
+<li>Added Prof Dr Casper Albers as doctoral advisor and Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors</li>
 </ul>
 </div>
 </div>
@@ -1237,7 +1237,7 @@ 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-0-7-1-9055">0.7.1.9055</a></li>
+        <li><a href="#amr-0-7-1-9056">0.7.1.9056</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-0-6-1">0.6.1</a></li>
@@ -1256,7 +1256,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 
       <footer>
       <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 class="pkgdown">

docs/reference/as.mo.html

@@ -442,7 +442,7 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
 
       <footer>
       <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 class="pkgdown">

docs/reference/catalogue_of_life.html

@@ -319,7 +319,7 @@ Function <code><a href='as.mo.html'>as.mo</a>()</code> to use the data for intel
 
       <footer>
       <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 class="pkgdown">

docs/reference/catalogue_of_life_version.html

@@ -291,7 +291,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
       <footer>
       <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 class="pkgdown">

docs/reference/first_isolate.html

@@ -373,8 +373,8 @@ To conduct an analysis of antimicrobial resistance, you should only include the
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># NOT RUN {</span>
-<span class='co'># septic_patients is a dataset available in the AMR package. It is true, genuine data.</span>
-?<span class='no'>septic_patients</span>
+<span class='co'># `septic_patients` is a dataset available in the AMR package. It is true, genuine data.</span>
+<span class='co'># See ?septic_patients.</span>
 
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='co'># Filter on first isolates:</span>

docs/reference/index.html

@@ -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">0.7.1.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
       </span>
     </div>
 
@@ -575,7 +575,7 @@
 
       <footer>
       <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 class="pkgdown">

docs/reference/key_antibiotics.html

@@ -337,8 +337,8 @@
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># NOT RUN {</span>
-<span class='co'># septic_patients is a dataset available in the AMR package</span>
-?<span class='no'>septic_patients</span>
+<span class='co'># `septic_patients` is a dataset available in the AMR package. It is true, genuine data.</span>
+<span class='co'># See ?septic_patients.</span>
 
 <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>

docs/reference/microorganisms.codes.html

@@ -279,7 +279,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
       <footer>
       <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 class="pkgdown">

docs/reference/microorganisms.html

@@ -313,7 +313,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
       <footer>
       <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 class="pkgdown">

docs/reference/microorganisms.old.html

@@ -287,7 +287,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
       <footer>
       <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 class="pkgdown">

docs/reference/mo_property.html

@@ -460,7 +460,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
       <footer>
       <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 class="pkgdown">

index.md

@@ -100,16 +100,12 @@ To find out how to conduct AMR analysis, please [continue reading here to get st
 
 #### Microbial (taxonomic) reference data
 
-<img src="man/figures/logo_col.png">
-
 This package contains the complete taxonomic tree of almost all 70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, [www.catalogueoflife.org](http://www.catalogueoflife.org)). With `catalogue_of_life_version()` can be checked which version of the CoL is included in this package.
 
 Read more about which data from the Catalogue of Life [in our manual](./reference/catalogue_of_life.html).
 
 #### Antimicrobial reference data
 
-<div><img src="reference/figures/logo_who.png" height="75px" class="logo_img"><p class="logo_txt">WHO Collaborating Centre for Drug Statistics Methodology</p></div>
-
 This package contains **all ~450 antimicrobial drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, https://www.whocc.no) and the [Pharmaceuticals Community Register of the European Commission](http://ec.europa.eu/health/documents/community-register/html/atc.htm).
 
 **NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See https://www.whocc.no/copyright_disclaimer/.**
@@ -118,8 +114,6 @@ Read more about the data from WHOCC [in our manual](./reference/WHOCC.html).
 
 #### WHONET / EARS-Net
 
-<img src="./whonet.png">
-
 We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an [example data set `WHONET`](./reference/WHONET.html) with the exact same structure as a WHONET export file. Furthermore, this package also contains a [data set `antibiotics`](./reference/antibiotics.html) with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.
 
 Read our tutorial about [how to work with WHONET data here](./articles/WHONET.html).

man/first_isolate.Rd

@@ -106,8 +106,8 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
 }
 
 \examples{
-# septic_patients is a dataset available in the AMR package. It is true, genuine data.
-?septic_patients
+# `septic_patients` is a dataset available in the AMR package. It is true, genuine data.
+# See ?septic_patients.
 
 library(dplyr)
 # Filter on first isolates:

man/key_antibiotics.Rd

@@ -82,8 +82,8 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
 }
 
 \examples{
-# septic_patients is a dataset available in the AMR package
-?septic_patients
+# `septic_patients` is a dataset available in the AMR package. It is true, genuine data.
+# See ?septic_patients.
 
 library(dplyr)
 # set key antibiotics to a new variable

pkgdown/extra.js

@@ -77,16 +77,14 @@ $( document ).ready(function() {
   // doctoral titles of authors
   function doct_tit(x) {
     if (typeof(x) != "undefined") {
-      x = x.replace("Corinna", "Dr Corinna");
       x = x.replace("Alex", "Prof Dr Alex");
       x = x.replace("Bhanu", "Prof Dr Bhanu");
+      x = x.replace("Corinna", "Dr Corinna");
+      x = x.replace("Casper", "Prof Dr Casper");
       x = x.replace("Bart", "Dr Bart");
       x = x.replace("Dennis", "Dr Dennis");
       x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
-      x = x.replace(/Authors/g, "aut_plural");
-      x = x.replace(/Author, maintainer[.]?/g, "");
-      x = x.replace(/Author[.]?/g, "");
-      x = x.replace(/aut_plural/g, "Authors");
+      x = x.replace(/Author(, maintainer)?[.]?[^s]/g, "");
     }
     return(x);
   }