(v1.1.0.9017) as.ab() update, added ab_url()

.gitlab-ci.yml

@@ -56,7 +56,7 @@ before_script:
 
 # ---- TEST
 
-R-release:
+R-release_test:
   stage: test
   when: always
   allow_failure: false
@@ -70,7 +70,7 @@ R-release:
     paths:
       - installed_deps/
       
-R-devel:
+R-devel_test:
   stage: test
   when: always
   image: rocker/r-devel

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.1.0.9016
+Version: 1.1.0.9017
-Date: 2020-05-21
+Date: 2020-05-22
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NAMESPACE

@@ -72,6 +72,7 @@ export(ab_name)
 export(ab_property)
 export(ab_synonyms)
 export(ab_tradenames)
+export(ab_url)
 export(age)
 export(age_groups)
 export(anti_join_microorganisms)

NEWS.md

@@ -1,22 +1,26 @@
-# AMR 1.1.0.9016
+# AMR 1.1.0.9017
-## <small>Last updated: 21-May-2020</small>
+## <small>Last updated: 22-May-2020</small>
 
 ### Breaking 
-* Removed code dependency on all other R packages, making this package fully independent on the development process of others. This is a major code change, but will probably not be noticeable by most users.
+* Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.
+
+  Making this package independent of especially the tidyverse (e.g. packages `dplyr` and `tidyr`) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.
   
-  Making this package independent on especially the tidyverse tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.
   Negative effects of this change are:
   * Function `freq()` that was borrowed from the `cleaner` package was removed. Use `cleaner::freq()`, or run `library("cleaner")` before you use `freq()`.
-  * Printing values of class `mo` or `ab` in a tibble will no longer be in colour and printing `rsi` in a tibble will show the class `<ord>`, not `<rsi>` anymore. This is purely a visual effect.
+  * Printing values of class `mo` or `rsi` in a tibble will no longer be in colour and printing `rsi` in a tibble will show the class `<ord>`, not `<rsi>` anymore. This is purely a visual effect.
   * All functions from the `mo_*` family (like `mo_name()` and `mo_gramstain()`) are noticeably slower when running on hundreds of thousands of rows.
   * For developers: classes `mo` and `ab` now both also inherit class `character`, to support any data transformation. This change invalidates code that checks for class length == 1.
 
 ### Changed
-* The EUCAST rules function (`eucast_rules()`) at default no longer applies "other" rules that are made available by this package (like setting ampicillin = R when ampicillin + enzym inhibitor = R). The default input value for `rules` is now `c("breakpoints", "expert")` instead of `"all"`, but this can be changed by the user. To return to the old behaviour, set `options(AMR.eucast_rules = "all")`.
+* EUCAST rules:
-* Small fix for some text input that could not be coerced as valid MIC values 
+  * The `eucast_rules()` function no longer applies "other" rules at default that are made available by this package (like setting ampicillin = R when ampicillin + enzym inhibitor = R). The default input value for `rules` is now `c("breakpoints", "expert")` instead of `"all"`, but this can be changed by the user. To return to the old behaviour, set `options(AMR.eucast_rules = "all")`.
-* Fix for cases where some functions of newer versions of the `dplyr` package (such as `bind_rows()`) would not preserve the right class for microorganisms (class `mo`) and antibiotics (class `ab`)
-* Fixed interpretation of generic CLSI interpretation rules (thanks to Anthony Underwood)
   * Added official drug names to verbose output of `eucast_rules()`
+* Added function `ab_url()` to return the direct URL of an antimicrobial agent from the official WHO website
+* Improvements for algorithm in `as.ab()`, so that e.g. `as.ab("ampi sul")` and `ab_name("ampi sul")` work
+* Functions `ab_atc()` and `ab_group()` now return `NA` if no antimicrobial agent could be found
+* Small fix for some text input that could not be coerced as valid MIC values 
+* Fixed interpretation of generic CLSI interpretation rules (thanks to Anthony Underwood)
 
 ### Other
 * Removed previously deprecated function `p.symbol()` - it was replaced with `p_symbol()`

R/ab.R

@@ -216,7 +216,7 @@ as.ab <- function(x, ...) {
     # replace multiple same characters to single one with '+', like "ll" -> "l+"
     x_spelling <- gsub("(.)\\1+", "\\1+", x_spelling)
     # replace spaces and slashes with a possibility on both
-    x_spelling <- gsub("[ /]", "( |/)", x_spelling)
+    x_spelling <- gsub("[ /]", "( .*|.*/)", x_spelling)
   
     # try if name starts with it
     found <- antibiotics[which(antibiotics$name %like% paste0("^", x_spelling)), ]$ab

R/ab_property.R

@@ -31,6 +31,8 @@
 #' @param units a logical to indicate whether the units instead of the DDDs itself must be returned, see Examples
 #' @param ... other parameters passed on to [as.ab()]
 #' @details All output will be [translate]d where possible.
+#' 
+#' The function [ab_url()] will return the direct URL to the official WHO website. A warning will be returned if the reauired ATC code is not available.
 #' @inheritSection as.ab Source
 #' @rdname ab_property
 #' @name ab_property
@@ -52,6 +54,7 @@
 #' ab_group("AMX")      # "Beta-lactams/penicillins"
 #' ab_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
 #' ab_atc_group2("AMX") # "Penicillins with extended spectrum"
+#' ab_url("AMX")        # link to the official WHO page
 #'
 #' # smart lowercase tranformation
 #' ab_name(x = c("AMC", "PLB"))  # "Amoxicillin/clavulanic acid" "Polymyxin B"
@@ -183,6 +186,31 @@ ab_info <- function(x, language = get_locale(), ...) {
                                   units = ab_ddd(x, administration = "iv", units = TRUE))))
 }
 
+
+#' @rdname ab_property
+#' @export
+ab_url <- function(x, open = FALSE, ...) {
+  ab <- as.ab(x = x, ... = ...)
+  u <- paste0("https://www.whocc.no/atc_ddd_index/?code=", ab_atc(ab), "&showdescription=no")
+  u[is.na(ab_atc(ab))] <- NA_character_
+  names(u) <- ab_name(ab)
+  
+  NAs <- ab_name(ab, tolower = TRUE, language = NULL)[!is.na(ab) & is.na(ab_atc(ab))]
+  if (length(NAs) > 0) {
+    warning("No ATC code available for ", paste0(NAs, collapse = ", "), ".")
+  }
+  
+  if (open == TRUE) {
+    if (length(u) > 1 & !is.na(u[1L])) {
+      warning("only the first URL will be opened, as `browseURL()` only suports one string.")
+    }
+    if (!is.na(u[1L])) {
+      utils::browseURL(u[1L])
+    }
+  }
+  u
+}
+
 #' @rdname ab_property
 #' @export
 ab_property <- function(x, property = "name", language = get_locale(), ...) {
@@ -217,8 +245,7 @@ ab_validate <- function(x, property, ...) {
   } else if (property %like% "ddd") {
     return(as.double(x))
   } else {
-    # return "(input)" for NAs
+    x[is.na(x) & !is.na(x_bak)] <- NA
-    x[is.na(x) & !is.na(x_bak)] <- paste0("(", x_bak[is.na(x) & !is.na(x_bak)], ")")
     return(x)
   }
 }

R/lifecycle.R

@@ -20,37 +20,31 @@
 # ==================================================================== #
 
 ###############
-# NOTE TO SELF: could also have done this with the 'lifecycle' package, but why add another dependency for such an easy job?
+# NOTE TO SELF: could also have done this with the 'lifecycle' package, but why add a package dependency for such an easy job??
 ###############
 
 #' Lifecycles of functions in the `AMR` package
 #' @name lifecycle
 #' @rdname lifecycle
-#' @description Our functions are categorised using [the lifecycle circle of the `tidyverse` as found on www.tidyverse.org/lifecycle](https://www.tidyverse.org/lifecycle).
+#' @description Functions in this `AMR` package are categorised using [the lifecycle circle of the `tidyverse` as found on www.tidyverse.org/lifecycle](https://www.tidyverse.org/lifecycle).
 #' 
 #' \if{html}{\figure{lifecycle_tidyverse.svg}{options: height=200px style=margin-bottom:5px} \cr}
-#' This page contains a section for every lifecycle (with text borrowed from the aforementioned `tidyverse` website), so they can be used in the manual pages of our functions. 
+#' This page contains a section for every lifecycle (with text borrowed from the aforementioned `tidyverse` website), so they can be used in the manual pages of the functions. 
 #' @section Experimental lifecycle:
 #' \if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **experimental**. An experimental function is in the very early stages of development. The unlying code might be changing frequently as we rapidly iterate and explore variations in search of the best fit. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions will not be included in releases we submit to CRAN, since they have not yet matured enough.
+#' The [lifecycle][AMR::lifecycle] of this function is **experimental**. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this `AMR` package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
 #' @section Maturing lifecycle:
 #' \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **maturing**. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
+#' The [lifecycle][AMR::lifecycle] of this function is **maturing**. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
 #' @section Stable lifecycle:
 #' \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **stable**. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+#' The [lifecycle][AMR::lifecycle] of this function is **stable**. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 #' 
-#' If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+#' If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 #' @section Retired lifecycle:
 #' \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **retired**. A retired function is no longer under active development, and (if appropiate) a better alternative is available. We will only make the necessary changes to ensure that retired functions remain available. No new arguments will be added, and only the most critical bugs will be fixed.
+#' The [lifecycle][AMR::lifecycle] of this function is **retired**. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
-#' @section Archived lifecycle:
-#' \if{html}{\figure{lifecycle_archived.svg}{options: style=margin-bottom:5px} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **archived**. The development of an archived function has ended, and it is no longer available in future package versions.
-#' @section Dormant lifecycle:
-#' \if{html}{\figure{lifecycle_dormant.svg}{options: style=margin-bottom:5px} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **dormant**. A dormant function is currently not under active development and has not reached a stable phase. We might return to it in the future. As with experimental functions, you are best off waiting until a function is more mature before you use it in production code.
 #' @section Questioning lifecycle:
 #' \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **questioning**. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our `AMR` package at all.
+#' The [lifecycle][AMR::lifecycle] of this function is **questioning**. This function might be no longer be optimal approach, or is it questionable whether this function should be in this `AMR` package at all.
 NULL

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </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">1.1.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -81,7 +81,7 @@
       </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">1.1.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </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">1.1.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 

docs/index.html

@@ -43,7 +43,7 @@
       </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">1.1.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -191,16 +191,16 @@
 <a href="#amr-for-r" class="anchor"></a><code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px">
 </h1></div>
 <blockquote>
-<p><em>18 October 2019</em><br><strong>METHODS PAPER PREPRINTED</strong><br>
+<p><strong>METHODS PAPER PREPRINTED</strong><br>
-A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/810622). It was <strong>updated on 18 December 2019</strong> and in parallel sent to a journal. Please click <a href="https://doi.org/10.1101/810622">here for the paper on bioRxiv’s publishers page</a>.</p>
+A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/810622). Please click <a href="https://doi.org/10.1101/810622">here for the paper on bioRxiv’s publishers page</a>.</p>
 </blockquote>
 <div id="what-is-amr-for-r" class="section level3">
 <h3 class="hasAnchor">
 <a href="#what-is-amr-for-r" class="anchor"></a>What is <code>AMR</code> (for R)?</h3>
-<p><em>(<help title="Too Long, Didn't Read">TLDR</help> - to find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.</em></p>
+<p><em>(To find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.</em></p>
 <p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org">R package</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
 <p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
-<p>We created this package for both routine data analysis and academic research (as part of our PhD theses) at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>). It is fully independent on any other R package and only requires R version 3.0.0 (April 2013) or higher to run.</p>
+<p>This package was created for both routine data analysis and academic research, at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>). It is fully independent of any other R package and can be used with all versions of R since R-3.0.0 (April 2013) and has a total file size of only 5 MB. It was designed to work in any setting, including those with very limited resources.</p>
 <div class="main-content">
 <p>
 <a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in more than 100 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from more than 100 countries <small>(source: <a href="https://cran-logs.rstudio.com" target="_blank">CRAN logs</a>)</small>. Click the map to enlarge, to see the names of the countries.
@@ -232,26 +232,11 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
 <li>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
 <li>Plotting antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
 <li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
-<li>Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
+<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
-<li>Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
+<li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
 <li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI (<a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt">link</a>)</li>
 <li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li>
 </ul>
-<p>This package is ready-to-use for specialists in many fields:</p>
-<ul>
-<li>Epidemiologists (both clinical microbiological and research)</li>
-<li>(Research) Microbiologists</li>
-<li>Biomedical Researchers</li>
-<li>Research Pharmacologists</li>
-<li>Data Scientists / Data Analysts</li>
-<li>Statisticians</li>
-<li>Bioinformaticians</li>
-<li>Research Veterinarians</li>
-<li>Veterinary Epidemiologists</li>
-<li>Soil Microbiologists</li>
-<li>Extremophile Researchers</li>
-<li>Astrobiologists</li>
-</ul>
 </div>
 <div id="get-this-package" class="section level3">
 <h3 class="hasAnchor">

docs/news/index.html

@@ -81,7 +81,7 @@
       </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">1.1.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -229,24 +229,25 @@
       <small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1-1-0-9016" class="section level1">
+    <div id="amr-1-1-0-9017" class="section level1">
-<h1 class="page-header" data-toc-text="1.1.0.9016">
+<h1 class="page-header" data-toc-text="1.1.0.9017">
-<a href="#amr-1-1-0-9016" class="anchor"></a>AMR 1.1.0.9016<small> Unreleased </small>
+<a href="#amr-1-1-0-9017" class="anchor"></a>AMR 1.1.0.9017<small> Unreleased </small>
 </h1>
-<div id="last-updated-21-may-2020" class="section level2">
+<div id="last-updated-22-may-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-21-may-2020" class="anchor"></a><small>Last updated: 21-May-2020</small>
+<a href="#last-updated-22-may-2020" class="anchor"></a><small>Last updated: 22-May-2020</small>
 </h2>
 <div id="breaking" class="section level3">
 <h3 class="hasAnchor">
 <a href="#breaking" class="anchor"></a>Breaking</h3>
 <ul>
 <li>
-<p>Removed code dependency on all other R packages, making this package fully independent on the development process of others. This is a major code change, but will probably not be noticeable by most users.</p>
+<p>Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.</p>
-Making this package independent on especially the tidyverse tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings. Negative effects of this change are:
+<p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
+Negative effects of this change are:
 <ul>
 <li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://rdrr.io/pkg/cleaner/man">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
-<li>Printing values of class <code>mo</code> or <code>ab</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</code> anymore. This is purely a visual effect.</li>
+<li>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</code> anymore. This is purely a visual effect.</li>
 <li>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</li>
 <li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
 </ul>
@@ -257,13 +258,19 @@ Making this package independent on especially the tidyverse tremendously increas
 <h3 class="hasAnchor">
 <a href="#changed" class="anchor"></a>Changed</h3>
 <ul>
-<li>The EUCAST rules function (<code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>) at default no longer applies “other” rules that are made available by this package (like setting ampicillin = R when ampicillin + enzym inhibitor = R). The default input value for <code>rules</code> is now <code><a href="https://rdrr.io/r/base/c.html">c("breakpoints", "expert")</a></code> instead of <code>"all"</code>, but this can be changed by the user. To return to the old behaviour, set <code><a href="https://rdrr.io/r/base/options.html">options(AMR.eucast_rules = "all")</a></code>.</li>
+<li>EUCAST rules:
-<li>Small fix for some text input that could not be coerced as valid MIC values</li>
+<ul>
-<li>Fix for cases where some functions of newer versions of the <code>dplyr</code> package (such as <code><a href="https://dplyr.tidyverse.org/reference/bind.html">bind_rows()</a></code>) would not preserve the right class for microorganisms (class <code>mo</code>) and antibiotics (class <code>ab</code>)</li>
+<li>The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function no longer applies “other” rules at default that are made available by this package (like setting ampicillin = R when ampicillin + enzym inhibitor = R). The default input value for <code>rules</code> is now <code><a href="https://rdrr.io/r/base/c.html">c("breakpoints", "expert")</a></code> instead of <code>"all"</code>, but this can be changed by the user. To return to the old behaviour, set <code><a href="https://rdrr.io/r/base/options.html">options(AMR.eucast_rules = "all")</a></code>.</li>
-<li>Fixed interpretation of generic CLSI interpretation rules (thanks to Anthony Underwood)</li>
 <li>Added official drug names to verbose output of <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
 </li>
 </ul>
+</li>
+<li>Added function <code><a href="../reference/ab_property.html">ab_url()</a></code> to return the direct URL of an antimicrobial agent from the official WHO website</li>
+<li>Improvements for algorithm in <code><a href="../reference/as.ab.html">as.ab()</a></code>, so that e.g. <code><a href="../reference/as.ab.html">as.ab("ampi sul")</a></code> and <code><a href="../reference/ab_property.html">ab_name("ampi sul")</a></code> work</li>
+<li>Functions <code><a href="../reference/ab_property.html">ab_atc()</a></code> and <code><a href="../reference/ab_property.html">ab_group()</a></code> now return <code>NA</code> if no antimicrobial agent could be found</li>
+<li>Small fix for some text input that could not be coerced as valid MIC values</li>
+<li>Fixed interpretation of generic CLSI interpretation rules (thanks to Anthony Underwood)</li>
+</ul>
 </div>
 <div id="other" class="section level3">
 <h3 class="hasAnchor">

docs/pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   WHONET: WHONET.html
   benchmarks: benchmarks.html
   resistance_predict: resistance_predict.html
-last_built: 2020-05-21T10:28Z
+last_built: 2020-05-22T18:14Z
 urls:
   reference: https://msberends.gitlab.io/AMR/reference
   article: https://msberends.gitlab.io/AMR/articles

docs/reference/AMR-deprecated.html

@@ -82,7 +82,7 @@
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -253,7 +253,7 @@
     
 
 <p><img src='figures/lifecycle_retired.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</strong>. A retired function is no longer under active development, and (if appropiate) a better alternative is available. We will only make the necessary changes to ensure that retired functions remain available. No new arguments will be added, and only the most critical bugs will be fixed.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</strong>. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.</p>
     <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>
 
     

docs/reference/AMR-tidyverse.html

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-      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
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-      <a href="../articles/PCA.html">
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-        <span class="fa fa-skull-crossbones"></span>
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-        <span class="fa fa-bug"></span>
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-        <span class="fa fa-capsules"></span>
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-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/tidyverse.R'><code>R/tidyverse.R</code></a></small>
-    <div class="hidden name"><code>AMR-tidyverse.Rd</code></div>
-    </div>
-
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-    <p>These methods are needed to support methods used by the tidyverse, like joining and transforming data, with new classes that come with this package.</p>
-    </div>
-
-    <pre class="usage"><span class='fu'>scale_type.mo</span>(<span class='no'>x</span>)
-
-<span class='fu'>scale_type.ab</span>(<span class='no'>x</span>)
-
-<span class='fu'>vec_ptype2.mo</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='no'>...</span>)
-
-<span class='fu'>vec_cast.mo</span>(<span class='no'>x</span>, <span class='no'>to</span>, <span class='no'>...</span>)
-
-<span class='fu'>vec_ptype2.ab</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='no'>...</span>)
-
-<span class='fu'>vec_cast.ab</span>(<span class='no'>x</span>, <span class='no'>to</span>, <span class='no'>...</span>)</pre>
-
-
-    <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
-
-    
-
-<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
-    <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>
-
-    
-
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9000</span>
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-        <span class="fa fa-dice"></span>
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-        Predict antimicrobial resistance
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-      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
-         
-        Work with WHONET data
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-        <span class="fa fa-file-upload"></span>
-         
-        Import data from SPSS/SAS/Stata
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-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1><code>vctrs</code> methods</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/vctrs.R'><code>R/vctrs.R</code></a></small>
-    <div class="hidden name"><code>AMR-vctrs.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>These methods are needed to support methods used by the tidyverse, like joining and transforming data, with new classes that come with this package.</p>
-    </div>
-
-    <pre class="usage"><span class='fu'>vec_ptype2.mo</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='no'>...</span>)
-
-<span class='fu'>vec_cast.mo</span>(<span class='no'>x</span>, <span class='no'>to</span>, <span class='no'>...</span>)
-
-<span class='fu'>vec_ptype2.ab</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='no'>...</span>)
-
-<span class='fu'>vec_cast.ab</span>(<span class='no'>x</span>, <span class='no'>to</span>, <span class='no'>...</span>)</pre>
-
-
-    <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
-
-    
-
-<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
-    <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>
-
-    
-
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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-  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
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-  <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/'>Alexander 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>
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docs/reference/ab_property.html

@@ -82,7 +82,7 @@
       </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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -257,6 +257,8 @@
 
 <span class='fu'>ab_info</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
 
+<span class='fu'>ab_url</span>(<span class='no'>x</span>, <span class='kw'>open</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
+
 <span class='fu'>ab_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -305,12 +307,13 @@
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     <p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
+<p>The function <code>ab_url()</code> will return the direct URL to the official WHO website. A warning will be returned if the reauired ATC code is not available.</p>
     <h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
 
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
 
     
@@ -337,6 +340,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
 <span class='fu'>ab_group</span>(<span class='st'>"AMX"</span>)      <span class='co'># "Beta-lactams/penicillins"</span>
 <span class='fu'>ab_atc_group1</span>(<span class='st'>"AMX"</span>) <span class='co'># "Beta-lactam antibacterials, penicillins"</span>
 <span class='fu'>ab_atc_group2</span>(<span class='st'>"AMX"</span>) <span class='co'># "Penicillins with extended spectrum"</span>
+<span class='fu'>ab_url</span>(<span class='st'>"AMX"</span>)        <span class='co'># link to the official WHO page</span>
 
 <span class='co'># smart lowercase tranformation</span>
 <span class='fu'>ab_name</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"AMC"</span>, <span class='st'>"PLB"</span>))  <span class='co'># "Amoxicillin/clavulanic acid" "Polymyxin B"</span>
@@ -379,7 +383,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
       </footer>

docs/reference/age.html

@@ -82,7 +82,7 @@
       </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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -266,8 +266,8 @@
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <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>
 
     
@@ -301,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
       </footer>

docs/reference/age_groups.html

@@ -82,7 +82,7 @@
       </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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -275,8 +275,8 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <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>
 
     
@@ -333,7 +333,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
       </footer>

docs/reference/antivirals.html

@@ -1,326 +0,0 @@
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-<meta property="og:title" content="Data set with ~100 antivirals — antivirals" />
-<meta property="og:description" content="A data set containing all antivirals, according to the ATC code group 'J05' (Antivirals for systemic use)." />
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-     
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-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
-         
-        Conduct AMR analysis
-      </a>
-    </li>
-    <li>
-      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
-         
-        Predict antimicrobial resistance
-      </a>
-    </li>
-    <li>
-      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
-         
-        Determine multi-drug resistance (MDR)
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-    </li>
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-      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
-         
-        Work with WHONET data
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-        <span class="fa fa-file-upload"></span>
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-      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
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-    <li>
-      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
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-        Get properties of a microorganism
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-  <a href="https://gitlab.com/msberends/AMR">
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-      
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Data set with ~100 antivirals</h1>
-    
-    <div class="hidden name"><code>antivirals.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>A data set containing all antivirals, according to the ATC code group 'J05' (Antivirals for systemic use).</p>
-    </div>
-
-    <pre class="usage"><span class='no'>antivirals</span></pre>
-
-
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 102 observations and 7 variables:</p><dl class='dl-horizontal'>
-  <dt><code>atc</code></dt><dd><p>ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></dd>
-  <dt><code>name</code></dt><dd><p>Official name as used by WHONET/EARS-Net or the WHO</p></dd>
-  <dt><code>atc_group</code></dt><dd><p>Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></dd>
-  <dt><code>oral_ddd</code></dt><dd><p>Defined Daily Dose (DDD), oral treatment</p></dd>
-  <dt><code>oral_units</code></dt><dd><p>Units of <code>oral_ddd</code></p></dd>
-  <dt><code>iv_ddd</code></dt><dd><p>Defined Daily Dose (DDD), parenteral treatment</p></dd>
-  <dt><code>iv_units</code></dt><dd><p>Units of <code>iv_ddd</code></p></dd>
-
-</dl>
-    <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
-
-    <p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
-    <h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
-
-    
-
-<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
-This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
-<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
-<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</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/'>https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
-    <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>
-
-    
-
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p><code><a href='antibiotics.html'>antibiotics</a></code> <code><a href='microorganisms.html'>microorganisms</a></code></p></div>
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#format">Format</a></li>
-      <li><a href="#source">Source</a></li>
-      <li><a href="#whocc">WHOCC</a></li>
-      <li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
-      <li><a href="#see-also">See also</a></li>
-    </ul>
-
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-      <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.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
-</div>
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-<script>
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docs/reference/as.ab.html

@@ -82,7 +82,7 @@
       </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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -271,7 +271,7 @@
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
     <h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
 
     
@@ -328,7 +328,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
       </footer>

docs/reference/as.disk.html

@@ -82,7 +82,7 @@
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -263,8 +263,8 @@
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <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>
 
     

docs/reference/as.mic.html

@@ -82,7 +82,7 @@
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -263,8 +263,8 @@
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <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>
 
     

docs/reference/as.mo.html

@@ -82,7 +82,7 @@
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -365,8 +365,8 @@
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
 
     

docs/reference/as.rsi.html

@@ -82,7 +82,7 @@
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -330,8 +330,8 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <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>
 
     

docs/reference/atc_online.html

@@ -83,7 +83,7 @@ This function requires an internet connection." />
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -307,7 +307,7 @@ This function requires an internet connection." />
     
 
 <p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our <code>AMR</code> package at all.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. This function might be no longer be optimal approach, or is it questionable whether this function should be in this <code>AMR</code> package at all.</p>
     <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>
 
     

docs/reference/availability.html

@@ -82,7 +82,7 @@
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -261,8 +261,8 @@
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <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>
 
     

docs/reference/bug_drug_combinations.html

@@ -82,7 +82,7 @@
       </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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -327,8 +327,8 @@
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <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>
 
     
@@ -365,7 +365,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
       </footer>

docs/reference/count.html

@@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -310,8 +310,8 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
 
     

docs/reference/eucast_rules.html

@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
       </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">1.1.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -398,7 +398,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
     <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>
 
     

docs/reference/extended-functions.html

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-    <h1>Extended functions</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/extended.R'><code>R/extended.R</code></a></small>
-    <div class="hidden name"><code>extended-functions.Rd</code></div>
-    </div>
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-    <p>These functions are extensions of functions in other packages.</p>
-    </div>
-
-    <pre class="usage"><span class='fu'>scale_type.mo</span>(<span class='no'>x</span>)
-
-<span class='fu'>scale_type.ab</span>(<span class='no'>x</span>)</pre>
-
-
-    <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
-
-    
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-<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
-    <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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-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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docs/reference/filter_ab_class.html

@@ -82,7 +82,7 @@
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -294,8 +294,8 @@
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {

docs/reference/first_isolate.html

@@ -82,7 +82,7 @@
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -387,8 +387,8 @@ To conduct an analysis of antimicrobial resistance, you should only include the
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <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>
 
     

docs/reference/g.test.html

@@ -82,7 +82,7 @@
       </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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -329,7 +329,7 @@
     
 
 <p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our <code>AMR</code> package at all.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. This function might be no longer be optimal approach, or is it questionable whether this function should be in this <code>AMR</code> package at all.</p>
     <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>
 
     
@@ -393,7 +393,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
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docs/reference/ggplot_pca.html

@@ -82,7 +82,7 @@
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         <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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -376,7 +376,7 @@
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>

docs/reference/ggplot_rsi.html

@@ -82,7 +82,7 @@
       </button>
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         <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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -404,7 +404,7 @@
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
     <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>
 
     

docs/reference/guess_ab_col.html

@@ -82,7 +82,7 @@
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -265,7 +265,7 @@
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
     <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>
 
     
@@ -315,7 +315,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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@@ -81,7 +81,7 @@
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -312,7 +312,7 @@
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         <td>
-          <p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_loinc()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
+          <p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_loinc()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_url()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
         </td>
         <td><p>Property of an antibiotic</p></td>
       </tr><tr>

docs/reference/join.html

@@ -82,7 +82,7 @@
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -277,8 +277,8 @@
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <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>
 
     

docs/reference/key_antibiotics.html

@@ -82,7 +82,7 @@
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -362,8 +362,8 @@
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key antibiotics</h2>
 
     

docs/reference/kurtosis.html

@@ -82,7 +82,7 @@
       </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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -264,7 +264,7 @@
     
 
 <p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our <code>AMR</code> package at all.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. This function might be no longer be optimal approach, or is it questionable whether this function should be in this <code>AMR</code> package at all.</p>
     <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>
 
     
@@ -289,7 +289,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
       </footer>

docs/reference/lifecycle.html

@@ -49,9 +49,9 @@
   <script src="../extra.js"></script>
 
 <meta property="og:title" content="Lifecycles of functions in the <code>AMR</code> package — lifecycle" />
-<meta property="og:description" content="Our functions are categorised using the lifecycle circle of the tidyverse as found on www.tidyverse.org/lifecycle.
+<meta property="og:description" content="Functions in this AMR package are categorised using the lifecycle circle of the tidyverse as found on www.tidyverse.org/lifecycle.
  
-This page contains a section for every lifecycle (with text borrowed from the aforementioned tidyverse website), so they can be used in the manual pages of our functions." />
+This page contains a section for every lifecycle (with text borrowed from the aforementioned tidyverse website), so they can be used in the manual pages of the functions." />
 <meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
 
 
@@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
       </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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -234,9 +234,9 @@ This page contains a section for every lifecycle (with text borrowed from the af
     </div>
 
     <div class="ref-description">
-    <p>Our functions are categorised using <a href='https://www.tidyverse.org/lifecycle'>the lifecycle circle of the <code>tidyverse</code> as found on www.tidyverse.org/lifecycle</a>.</p>
+    <p>Functions in this <code>AMR</code> package are categorised using <a href='https://www.tidyverse.org/lifecycle'>the lifecycle circle of the <code>tidyverse</code> as found on www.tidyverse.org/lifecycle</a>.</p>
 <p><img src='figures/lifecycle_tidyverse.svg' height=200px style=margin-bottom:5px /> <br />
-This page contains a section for every lifecycle (with text borrowed from the aforementioned <code>tidyverse</code> website), so they can be used in the manual pages of our functions.</p>
+This page contains a section for every lifecycle (with text borrowed from the aforementioned <code>tidyverse</code> website), so they can be used in the manual pages of the functions.</p>
     </div>
 
 
@@ -246,44 +246,32 @@ This page contains a section for every lifecycle (with text borrowed from the af
     
 
 <p><img src='figures/lifecycle_experimental.svg' style=margin-bottom:5px /> <br />
-The lifecycle of this function is <strong>experimental</strong>. An experimental function is in the very early stages of development. The unlying code might be changing frequently as we rapidly iterate and explore variations in search of the best fit. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions will not be included in releases we submit to CRAN, since they have not yet matured enough.</p>
+The lifecycle of this function is <strong>experimental</strong>. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this <code>AMR</code> package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.</p>
     <h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
 
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The lifecycle of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
+The lifecycle of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
     <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
 
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The lifecycle of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The lifecycle of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <h2 class="hasAnchor" id="retired-lifecycle"><a class="anchor" href="#retired-lifecycle"></a>Retired lifecycle</h2>
 
     
 
 <p><img src='figures/lifecycle_retired.svg' style=margin-bottom:5px /> <br />
-The lifecycle of this function is <strong>retired</strong>. A retired function is no longer under active development, and (if appropiate) a better alternative is available. We will only make the necessary changes to ensure that retired functions remain available. No new arguments will be added, and only the most critical bugs will be fixed.</p>
+The lifecycle of this function is <strong>retired</strong>. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.</p>
-    <h2 class="hasAnchor" id="archived-lifecycle"><a class="anchor" href="#archived-lifecycle"></a>Archived lifecycle</h2>
-
-    
-
-<p><img src='figures/lifecycle_archived.svg' style=margin-bottom:5px /> <br />
-The lifecycle of this function is <strong>archived</strong>. The development of an archived function has ended, and it is no longer available in future package versions.</p>
-    <h2 class="hasAnchor" id="dormant-lifecycle"><a class="anchor" href="#dormant-lifecycle"></a>Dormant lifecycle</h2>
-
-    
-
-<p><img src='figures/lifecycle_dormant.svg' style=margin-bottom:5px /> <br />
-The lifecycle of this function is <strong>dormant</strong>. A dormant function is currently not under active development and has not reached a stable phase. We might return to it in the future. As with experimental functions, you are best off waiting until a function is more mature before you use it in production code.</p>
     <h2 class="hasAnchor" id="questioning-lifecycle"><a class="anchor" href="#questioning-lifecycle"></a>Questioning lifecycle</h2>
 
     
 
 <p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
-The lifecycle of this function is <strong>questioning</strong>. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our <code>AMR</code> package at all.</p>
+The lifecycle of this function is <strong>questioning</strong>. This function might be no longer be optimal approach, or is it questionable whether this function should be in this <code>AMR</code> package at all.</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -300,7 +288,7 @@ The lifecycle of this function is <strong>questioning</strong>. We are no longer
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
       </footer>

docs/reference/like.html

@@ -82,7 +82,7 @@
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -279,8 +279,8 @@
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <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>
 
     

docs/reference/mdro.html

@@ -82,7 +82,7 @@
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -333,7 +333,7 @@ The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WI
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
     <h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
 
     

docs/reference/mo_source.html

@@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
       </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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -307,8 +307,8 @@ mo_genus("lab_Staph_aureus")
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <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>
 
     
@@ -330,7 +330,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
       </footer>

docs/reference/p_symbol.html

@@ -82,7 +82,7 @@
       </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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -258,7 +258,7 @@
     
 
 <p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our <code>AMR</code> package at all.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. This function might be no longer be optimal approach, or is it questionable whether this function should be in this <code>AMR</code> package at all.</p>
     <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>
 
     
@@ -280,7 +280,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
       </footer>

docs/reference/pca.html

@@ -82,7 +82,7 @@
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -309,7 +309,7 @@
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>

docs/reference/portion.html

@@ -1,518 +0,0 @@
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<title>Calculate resistance of isolates — portion • AMR (for R)</title>
-
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-portion_R and portion_IR can be used to calculate resistance, portion_S and portion_SI can be used to calculate susceptibility." />
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-    <h1>Calculate resistance of isolates</h1>
-    
-    <div class="hidden name"><code>portion.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>These functions can be used to calculate the (co-)resistance of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p>
-<p><code>portion_R</code> and <code>portion_IR</code> can be used to calculate resistance, <code>portion_S</code> and <code>portion_SI</code> can be used to calculate susceptibility.<br /></p>
-    </div>
-
-    <pre class="usage"><span class='fu'>portion_R</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-
-<span class='fu'>portion_IR</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-
-<span class='fu'>portion_I</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-
-<span class='fu'>portion_SI</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-
-<span class='fu'>portion_S</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-
-<span class='fu'>portion_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
-  <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-
-<span class='fu'>rsi_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
-  <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>...</th>
-      <td><p>one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with <code><a href='as.rsi.html'>as.rsi</a></code> if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See Examples.</p></td>
-    </tr>
-    <tr>
-      <th>minimum</th>
-      <td><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.</p></td>
-    </tr>
-    <tr>
-      <th>as_percent</th>
-      <td><p>a logical to indicate whether the output must be returned as a hundred fold with % sign (a character). A value of <code>0.123456</code> will then be returned as <code>"12.3%"</code>.</p></td>
-    </tr>
-    <tr>
-      <th>only_all_tested</th>
-      <td><p>(for combination therapies, i.e. using more than one variable for <code>...</code>) a logical to indicate that isolates must be tested for all antibiotics, see section <em>Combination therapy</em> below</p></td>
-    </tr>
-    <tr>
-      <th>data</th>
-      <td><p>a <code>data.frame</code> containing columns with class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi</a></code>)</p></td>
-    </tr>
-    <tr>
-      <th>translate_ab</th>
-      <td><p>a column name of the <code><a href='antibiotics.html'>antibiotics</a></code> data set to translate the antibiotic abbreviations to, using <code><a href='ab_property.html'>ab_property</a></code></p></td>
-    </tr>
-    <tr>
-      <th>language</th>
-      <td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale</a></code>) and can also be set with <code><a href='https://rdrr.io/r/base/options.html'>getOption</a>("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
-    </tr>
-    <tr>
-      <th>combine_SI</th>
-      <td><p>a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is <code>TRUE</code>.</p></td>
-    </tr>
-    <tr>
-      <th>combine_IR</th>
-      <td><p>a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter <code>combine_SI</code>.</p></td>
-    </tr>
-    </table>
-
-    <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
-
-    <p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition</strong>, 2014, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href='https://clsi.org/standards/products/microbiology/documents/m39/'>https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p>
-<p>Wickham H. <strong>Tidy Data.</strong> The Journal of Statistical Software, vol. 59, 2014. <a href='http://vita.had.co.nz/papers/tidy-data.html'>http://vita.had.co.nz/papers/tidy-data.html</a></p>
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Double or, when <code>as_percent = TRUE</code>, a character.</p>
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p><strong>Remember that you should filter your table to let it contain only first isolates!</strong> This is needed to exclude duplicates and to reduce selection bias. Use <code><a href='first_isolate.html'>first_isolate</a></code> to determine them in your data set.</p>
-<p>These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the <code><a href='count.html'>count</a></code> functions to count isolates. The function <code>portion_SI()</code> is essentially equal to <code>count_SI() / count_all()</code>. <em>Low counts can infuence the outcome - the <code>portion</code> functions may camouflage this, since they only return the portion (albeit being dependent on the <code>minimum</code> parameter).</em></p>
-<p>The function <code>portion_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and calculates the portions R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each group and each variable with class <code>"rsi"</code>.</p>
-<p>The function <code>rsi_df</code> works exactly like <code>portion_df</code>, but adds the number of isolates.</p>
-    <h2 class="hasAnchor" id="combination-therapy"><a class="anchor" href="#combination-therapy"></a>Combination therapy</h2>
-
-    
-
-<p>When using more than one variable for <code>...</code> (= combination therapy)), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Antibiotic A and Antibiotic B, about how <code>portion_SI</code> works to calculate the %SI:</p>
-<pre>
---------------------------------------------------------------------
-                    only_all_tested = FALSE  only_all_tested = TRUE
-                    -----------------------  -----------------------
- Drug A    Drug B   include as  include as   include as  include as
-                    numerator   denominator  numerator   denominator
---------  --------  ----------  -----------  ----------  -----------
- S or I    S or I       X            X            X            X
-   R       S or I       X            X            X            X
-  &lt;NA&gt;     S or I       X            X            -            -
- S or I      R          X            X            X            X
-   R         R          -            X            -            X
-  &lt;NA&gt;       R          -            -            -            -
- S or I     &lt;NA&gt;        X            X            -            -
-   R        &lt;NA&gt;        -            -            -            -
-  &lt;NA&gt;      &lt;NA&gt;        -            -            -            -
---------------------------------------------------------------------
-</pre>
-
-<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre>
-   count_S()  +  count_I()  +  count_R()  == count_all()
-  portion_S() + portion_I() + portion_R() == 1
-</pre><p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre>
-   count_S()  +  count_I()  +  count_R()  &gt;= count_all()
-  portion_S() + portion_I() + portion_R() &gt;= 1
-</pre>
-
-<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
-    <h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>
-
-    
-
-<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p>
-<ul>
-<li><p><strong>S</strong> - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
-<li><p><strong>I</strong> - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
-<li><p><strong>R</strong> - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.</p></li>
-</ul>
-
-<p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
-<p>This AMR package honours this new insight. Use <code>portion_SI</code> to determine antimicrobial susceptibility and <code><a href='count.html'>count_SI</a></code> to count susceptible isolates.</p>
-    <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>
-
-    
-
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p><code><a href='count.html'>count</a>_*</code> to count resistant and susceptible isolates.</p></div>
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># example_isolates is a data set available in the AMR package.</span>
-?<span class='no'>example_isolates</span>
-
-<span class='co'># Calculate resistance</span>
-<span class='fu'>portion_R</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
-<span class='fu'>portion_IR</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
-
-<span class='co'># Or susceptibility</span>
-<span class='fu'>portion_S</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
-<span class='fu'>portion_SI</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
-
-<span class='co'># Do the above with pipes:</span>
-<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_R</span>(<span class='no'>AMX</span>)
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_IR</span>(<span class='no'>AMX</span>)
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_S</span>(<span class='no'>AMX</span>)
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_SI</span>(<span class='no'>AMX</span>)
-
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_SI</span>(<span class='no'>CIP</span>),
-            <span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>CIP</span>)) <span class='co'># n_rsi works like n_distinct in dplyr</span>
-
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>portion_R</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
-            <span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>portion_I</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
-            <span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
-            <span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>),  <span class='co'># the actual total; sum of all three</span>
-            <span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>CIP</span>),      <span class='co'># same - analogous to n_distinct</span>
-            <span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>())          <span class='co'># NOT the number of tested isolates!</span>
-
-<span class='co'># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span>
-<span class='co'># so we can see that combination therapy does a lot more than mono therapy:</span>
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_SI</span>(<span class='no'>AMC</span>)      <span class='co'># %SI = 76.3%</span>
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>)       <span class='co'>#   n = 1879</span>
-
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_SI</span>(<span class='no'>GEN</span>)      <span class='co'># %SI = 75.4%</span>
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>GEN</span>)       <span class='co'>#   n = 1855</span>
-
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_SI</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># %SI = 94.1%</span>
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>)  <span class='co'>#   n = 1939</span>
-
-
-<span class='co'># See Details on how `only_all_tested` works. Example:</span>
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>numerator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_SI</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>),
-            <span class='kw'>denominator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>),
-            <span class='kw'>portion</span> <span class='kw'>=</span> <span class='fu'>portion_SI</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>))
-<span class='co'>#   numerator denominator portion</span>
-<span class='co'>#        1764        1936  0.9408</span>
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>numerator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_SI</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
-            <span class='kw'>denominator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
-            <span class='kw'>portion</span> <span class='kw'>=</span> <span class='fu'>portion_SI</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
-<span class='co'>#   numerator denominator portion</span>
-<span class='co'>#       1687        1798   0.9383</span>
-
-
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>cipro_p</span> <span class='kw'>=</span> <span class='fu'>portion_SI</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
-            <span class='kw'>cipro_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>),
-            <span class='kw'>genta_p</span> <span class='kw'>=</span> <span class='fu'>portion_SI</span>(<span class='no'>GEN</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
-            <span class='kw'>genta_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>GEN</span>),
-            <span class='kw'>combination_p</span> <span class='kw'>=</span> <span class='fu'>portion_SI</span>(<span class='no'>CIP</span>, <span class='no'>GEN</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
-            <span class='kw'>combination_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>, <span class='no'>GEN</span>))
-
-<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-
-<span class='co'># It also supports grouping variables</span>
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-
-
-<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
-
-<span class='co'># calculate current empiric combination therapy of Helicobacter gastritis:</span>
-<span class='no'>my_table</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
-         <span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Helicobacter"</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>AMX</span>, <span class='no'>MTR</span>),  <span class='co'># amoxicillin with metronidazole</span>
-            <span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMX</span>, <span class='no'>MTR</span>))
-}</pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      <li><a href="#source">Source</a></li>
-      <li><a href="#value">Value</a></li>
-      <li><a href="#details">Details</a></li>
-      <li><a href="#combination-therapy">Combination therapy</a></li>
-      <li><a href="#interpretation-of-s-i-and-r">Interpretation of S, I and R</a></li>
-      <li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
-      <li><a href="#see-also">See also</a></li>
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docs/reference/proportion.html

@@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -359,8 +359,8 @@ resistance() should be used to calculate resistance, susceptibility() should be
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
 
     

docs/reference/read.4D.html

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-    <h1>Read data from 4D database</h1>
-    <small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/read.4d.R'><code>R/read.4d.R</code></a></small>
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-
-    <div class="ref-description">
-    <p>This function is only useful for the MMB department of the UMCG. Use this function to <strong>import data by just defining the <code>file</code> parameter</strong>. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the MO codes with <code><a href='as.mo.html'>as.mo()</a></code> and transform all antimicrobial columns with <code><a href='as.rsi.html'>as.rsi()</a></code>.</p>
-    </div>
-
-    <pre class="usage"><span class='fu'>read.4D</span>(
-  <span class='no'>file</span>,
-  <span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
-  <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
-  <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>,
-  <span class='kw'>quote</span> <span class='kw'>=</span> <span class='st'>"\"'"</span>,
-  <span class='kw'>dec</span> <span class='kw'>=</span> <span class='st'>","</span>,
-  <span class='kw'>na.strings</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"NA"</span>, <span class='st'>""</span>, <span class='st'>"."</span>),
-  <span class='kw'>skip</span> <span class='kw'>=</span> <span class='fl'>2</span>,
-  <span class='kw'>check.names</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>strip.white</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>fill</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>blank.lines.skip</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>fileEncoding</span> <span class='kw'>=</span> <span class='st'>"UTF-8"</span>,
-  <span class='kw'>encoding</span> <span class='kw'>=</span> <span class='st'>"UTF-8"</span>
-)</pre>
-
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>file</th>
-      <td><p>the name of the file which the data are to be read from.
-    Each row of the table appears as one line of the file.  If it does
-    not contain an <em>absolute</em> path, the file name is
-    <em>relative</em> to the current working directory,
-    <code><a href='https://rdrr.io/r/base/getwd.html'>getwd</a>()</code>. Tilde-expansion is performed where supported.
-    This can be a compressed file (see <code><a href='https://rdrr.io/r/base/connections.html'>file</a></code>).</p>
-<p>Alternatively, <code>file</code> can be a readable text-mode
-    <a href='https://rdrr.io/r/base/connections.html'>connection</a> (which will be opened for reading if
-    necessary, and if so <code><a href='https://rdrr.io/r/base/connections.html'>close</a></code>d (and hence destroyed) at
-    the end of the function call).  (If <code><a href='https://rdrr.io/r/base/showConnections.html'>stdin</a>()</code> is used,
-    the prompts for lines may be somewhat confusing.  Terminate input
-    with a blank line or an EOF signal, <code>Ctrl-D</code> on Unix and
-    <code>Ctrl-Z</code> on Windows.  Any pushback on <code><a href='https://rdrr.io/r/base/showConnections.html'>stdin()</a></code> will be
-    cleared before return.)</p>
-<p><code>file</code> can also be a complete URL.  (For the supported URL
-    schemes, see the &#8216;URLs&#8217; section of the help for
-    <code><a href='https://rdrr.io/r/base/connections.html'>url</a></code>.)</p></td>
-    </tr>
-    <tr>
-      <th>info</th>
-      <td><p>a logical to indicate whether info about the import should be printed, defaults to <code>TRUE</code> in interactive sessions</p></td>
-    </tr>
-    <tr>
-      <th>header</th>
-      <td><p>a logical value indicating whether the file contains the
-    names of the variables as its first line.  If missing, the value is
-    determined from the file format: <code>header</code> is set to <code>TRUE</code>
-    if and only if the first row contains one fewer field than the
-    number of columns.</p></td>
-    </tr>
-    <tr>
-      <th>row.names</th>
-      <td><p>a vector of row names.  This can be a vector giving
-    the actual row names, or a single number giving the column of the
-    table which contains the row names, or character string giving the
-    name of the table column containing the row names.</p>
-<p>If there is a header and the first row contains one fewer field than
-    the number of columns, the first column in the input is used for the
-    row names.  Otherwise if <code>row.names</code> is missing, the rows are
-    numbered.</p>
-<p>Using <code>row.names = NULL</code> forces row numbering. Missing or
-    <code>NULL</code> <code>row.names</code> generate row names that are considered
-    to be &#8216;automatic&#8217; (and not preserved by <code><a href='https://rdrr.io/r/base/matrix.html'>as.matrix</a></code>).</p></td>
-    </tr>
-    <tr>
-      <th>sep</th>
-      <td><p>the field separator character.  Values on each line of the
-    file are separated by this character.  If <code>sep = ""</code> (the
-    default for <code>read.table</code>) the separator is &#8216;white space&#8217;,
-    that is one or more spaces, tabs, newlines or carriage returns.</p></td>
-    </tr>
-    <tr>
-      <th>quote</th>
-      <td><p>the set of quoting characters. To disable quoting
-    altogether, use <code>quote = ""</code>.  See <code><a href='https://rdrr.io/r/base/scan.html'>scan</a></code> for the
-    behaviour on quotes embedded in quotes.  Quoting is only considered
-    for columns read as character, which is all of them unless
-    <code>colClasses</code> is specified.</p></td>
-    </tr>
-    <tr>
-      <th>dec</th>
-      <td><p>the character used in the file for decimal points.</p></td>
-    </tr>
-    <tr>
-      <th>na.strings</th>
-      <td><p>a character vector of strings which are to be
-    interpreted as <code><a href='https://rdrr.io/r/base/NA.html'>NA</a></code> values.  Blank fields are also
-    considered to be missing values in logical, integer, numeric and
-    complex fields.  Note that the test happens <em>after</em> 
-    white space is stripped from the input, so <code>na.strings</code> 
-    values may need their own white space stripped in advance.</p></td>
-    </tr>
-    <tr>
-      <th>skip</th>
-      <td><p>integer: the number of lines of the data file to skip before
-    beginning to read data.</p></td>
-    </tr>
-    <tr>
-      <th>check.names</th>
-      <td><p>logical.  If <code>TRUE</code> then the names of the
-    variables in the data frame are checked to ensure that they are
-    syntactically valid variable names.  If necessary they are adjusted
-    (by <code><a href='https://rdrr.io/r/base/make.names.html'>make.names</a></code>) so that they are, and also to ensure
-    that there are no duplicates.</p></td>
-    </tr>
-    <tr>
-      <th>strip.white</th>
-      <td><p>logical. Used only when <code>sep</code> has
-    been specified, and allows the stripping of leading and trailing
-    white space from unquoted <code>character</code> fields (<code>numeric</code> fields
-    are always stripped).  See <code><a href='https://rdrr.io/r/base/scan.html'>scan</a></code> for further details
-    (including the exact meaning of &#8216;white space&#8217;),
-    remembering that the columns may include the row names.</p></td>
-    </tr>
-    <tr>
-      <th>fill</th>
-      <td><p>logical. If <code>TRUE</code> then in case the rows have unequal
-    length, blank fields are implicitly added.  See &#8216;Details&#8217;.</p></td>
-    </tr>
-    <tr>
-      <th>blank.lines.skip</th>
-      <td><p>logical: if <code>TRUE</code> blank lines in the
-    input are ignored.</p></td>
-    </tr>
-    <tr>
-      <th>stringsAsFactors</th>
-      <td><p>logical: should character vectors be converted
-    to factors?  Note that this is overridden by <code>as.is</code> and
-    <code>colClasses</code>, both of which allow finer control.</p></td>
-    </tr>
-    <tr>
-      <th>fileEncoding</th>
-      <td><p>character string: if non-empty declares the
-    encoding used on a file (not a connection) so the character data can
-    be re-encoded.  See the &#8216;Encoding&#8217; section of the help for
-    <code><a href='https://rdrr.io/r/base/connections.html'>file</a></code>, the &#8216;R Data Import/Export Manual&#8217; and
-    &#8216;Note&#8217;.</p></td>
-    </tr>
-    <tr>
-      <th>encoding</th>
-      <td><p>encoding to be assumed for input strings.  It is
-    used to mark character strings as known to be in
-    Latin-1 or UTF-8 (see <code><a href='https://rdrr.io/r/base/Encoding.html'>Encoding</a></code>): it is not used to
-    re-encode the input, but allows <span style="R">R</span> to handle encoded strings in
-    their native encoding (if one of those two).  See &#8216;Value&#8217;
-    and &#8216;Note&#8217;.</p></td>
-    </tr>
-    </table>
-
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Column names will be transformed, but the original column names are set as a "label" attribute and can be seen in e.g. RStudio Viewer.</p>
-    <h2 class="hasAnchor" id="dormant-lifecycle"><a class="anchor" href="#dormant-lifecycle"></a>Dormant lifecycle</h2>
-
-    
-
-<p><img src='figures/lifecycle_dormant.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>dormant</strong>. A dormant function is currently not under active development and has not reached a stable phase. We might return to it in the future. As with experimental functions, you are best off waiting until a function is more mature before you use it in production code.</p>
-    <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>
-
-    
-
-<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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-    <p>These objects are imported from other packages. Follow the links
-below to see their documentation.</p>
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         <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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -362,7 +362,7 @@
     
 
 <p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
     <h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
 
     

docs/reference/skewness.html

@@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
       </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">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -266,7 +266,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
     
 
 <p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our <code>AMR</code> package at all.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. This function might be no longer be optimal approach, or is it questionable whether this function should be in this <code>AMR</code> package at all.</p>
     <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>
 
     
@@ -291,7 +291,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
       </footer>

docs/reference/translate.html

@@ -82,7 +82,7 @@
       </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">1.1.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9017</span>
       </span>
     </div>
 
@@ -250,8 +250,8 @@
     
 
 <p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
-<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
     <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>
 
     

index.md

@@ -1,18 +1,17 @@
 # `AMR` (for R) <img src="./logo.png" align="right" height="120px" />
 
-> *18 October 2019*  
 > **METHODS PAPER PREPRINTED**  
-> A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/810622). It was **updated on 18 December 2019** and in parallel sent to a journal. Please click [here for the paper on bioRxiv's publishers page](https://doi.org/10.1101/810622).
+> A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/810622). Please click [here for the paper on bioRxiv's publishers page](https://doi.org/10.1101/810622).
 
 ### What is `AMR` (for R)?
 
-*(<help title="Too Long, Didn't Read">TLDR</help> - to find out how to conduct AMR analysis, please [continue reading here to get started](./articles/AMR.html).*
+*(To find out how to conduct AMR analysis, please [continue reading here to get started](./articles/AMR.html).*
 
 `AMR` is a free, open-source and independent [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
 
 After installing this package, R knows [**~70,000 distinct microbial species**](./reference/microorganisms.html) and all [**~550 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
 
-We created this package for both routine data analysis and academic research (as part of our PhD theses) at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is [actively maintained](./news) and is free software (see [Copyright](#copyright)). It is fully independent on any other R package and only requires R version 3.0.0 (April 2013) or higher to run.
+This package was created for both routine data analysis and academic research, at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is [actively maintained](./news) and is free software (see [Copyright](#copyright)). It is fully independent of any other R package and can be used with all versions of R since R-3.0.0 (April 2013) and has a total file size of only 5 MB. It was designed to work in any setting, including those with very limited resources.
 
 <div class="main-content"> 
   <p>
@@ -48,26 +47,11 @@ This package can be used for:
   * Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) ([manual](./reference/ab_property.html))
   * Plotting antimicrobial resistance ([tutorial](./articles/AMR.html))
   * Applying EUCAST expert rules ([manual](./reference/eucast_rules.html))
-  * Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code ([manual](./reference/mo_property.html))
+  * Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code ([manual](./reference/mo_property.html))
-  * Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code ([manual](./reference/ab_property.html))
+  * Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code ([manual](./reference/ab_property.html))
   * Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI ([link](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt))
   * Principal component analysis for AMR ([tutorial](./articles/PCA.html))
 
-This package is ready-to-use for specialists in many fields:
-
-  * Epidemiologists (both clinical microbiological and research)
-  * (Research) Microbiologists
-  * Biomedical Researchers
-  * Research Pharmacologists
-  * Data Scientists / Data Analysts
-  * Statisticians
-  * Bioinformaticians
-  * Research Veterinarians
-  * Veterinary Epidemiologists
-  * Soil Microbiologists
-  * Extremophile Researchers
-  * Astrobiologists
-
 ### Get this package
 
 #### Latest released version

man/AMR-deprecated.Rd

@@ -28,7 +28,7 @@ These functions are so-called '\link{Deprecated}'. They will be removed in a fut
 \section{Retired lifecycle}{
 
 \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{retired}. A retired function is no longer under active development, and (if appropiate) a better alternative is available. We will only make the necessary changes to ensure that retired functions remain available. No new arguments will be added, and only the most critical bugs will be fixed.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{retired}. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
 }
 
 \section{Read more on our website!}{

man/ab_property.Rd

@@ -14,6 +14,7 @@
 \alias{ab_loinc}
 \alias{ab_ddd}
 \alias{ab_info}
+\alias{ab_url}
 \title{Property of an antibiotic}
 \usage{
 ab_name(x, language = get_locale(), tolower = FALSE, ...)
@@ -38,6 +39,8 @@ ab_ddd(x, administration = "oral", units = FALSE, ...)
 
 ab_info(x, language = get_locale(), ...)
 
+ab_url(x, open = FALSE, ...)
+
 ab_property(x, property = "name", language = get_locale(), ...)
 }
 \arguments{
@@ -68,11 +71,13 @@ Use these functions to return a specific property of an antibiotic from the \lin
 }
 \details{
 All output will be \link{translate}d where possible.
+
+The function \code{\link[=ab_url]{ab_url()}} will return the direct URL to the official WHO website. A warning will be returned if the reauired ATC code is not available.
 }
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
 }
 
 \section{Source}{
@@ -99,6 +104,7 @@ ab_tradenames("AMX") # same
 ab_group("AMX")      # "Beta-lactams/penicillins"
 ab_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
 ab_atc_group2("AMX") # "Penicillins with extended spectrum"
+ab_url("AMX")        # link to the official WHO page
 
 # smart lowercase tranformation
 ab_name(x = c("AMC", "PLB"))  # "Amoxicillin/clavulanic acid" "Polymyxin B"

man/age.Rd

@@ -24,9 +24,9 @@ Calculates age in years based on a reference date, which is the sytem date at de
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{

man/age_groups.Rd

@@ -36,9 +36,9 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{

man/as.ab.Rd

@@ -38,7 +38,7 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
 }
 
 \section{WHOCC}{

man/as.disk.Rd

@@ -27,9 +27,9 @@ Interpret disk values as RSI values with \code{\link[=as.rsi]{as.rsi()}}. It sup
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{

man/as.mic.Rd

@@ -27,9 +27,9 @@ To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MI
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{

man/as.mo.Rd

@@ -133,9 +133,9 @@ Group 3 (least prevalent microorganisms) consists of all other microorganisms.
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Catalogue of Life}{

man/as.rsi.Rd

@@ -88,9 +88,9 @@ This AMR package honours this new insight. Use \code{\link[=susceptibility]{susc
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{

man/atc_online.Rd

@@ -66,7 +66,7 @@ Abbreviations of return values when using \code{property = "U"} (unit):
 \section{Questioning lifecycle}{
 
 \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our \code{AMR} package at all.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
 }
 
 \section{Read more on our website!}{

man/availability.Rd

@@ -23,9 +23,9 @@ The function returns a \code{\link{data.frame}} with columns \code{"resistant"}
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{

man/bug_drug_combinations.Rd

@@ -68,9 +68,9 @@ The language of the output can be overwritten with \code{options(AMR_locale)}, p
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{

man/count.Rd

@@ -75,9 +75,9 @@ The function \code{\link[=count_df]{count_df()}} takes any variable from \code{d
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Interpretation of R and S/I}{

man/eucast_rules.Rd

@@ -156,7 +156,7 @@ The following antibiotics are used for the functions \code{\link[=eucast_rules]{
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
 }
 
 \section{Read more on our website!}{

man/filter_ab_class.Rd

@@ -62,9 +62,9 @@ The \code{group} column in \link{antibiotics} data set will be searched for \cod
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \examples{

man/first_isolate.Rd

@@ -125,9 +125,9 @@ A difference from I to S|R (or vice versa) means 0.5 points, a difference from S
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{

man/g.test.Rd

@@ -100,7 +100,7 @@ If there are more than two categories and you want to find out which ones are si
 \section{Questioning lifecycle}{
 
 \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our \code{AMR} package at all.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
 }
 
 \section{Read more on our website!}{

man/ggplot_pca.Rd

@@ -107,7 +107,7 @@ The colours for labels and points can be changed by adding another scale layer f
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
 }
 
 \examples{

man/ggplot_rsi.Rd

@@ -138,7 +138,7 @@ At default, the names of antibiotics will be shown on the plots using \code{\lin
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
 }
 
 \section{Read more on our website!}{

man/guess_ab_col.Rd

@@ -25,7 +25,7 @@ You can look for an antibiotic (trade) name or abbreviation and it will search \
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
 }
 
 \section{Read more on our website!}{

man/join.Rd

@@ -43,9 +43,9 @@ These functions rely on \code{\link[=merge]{merge()}}, a base R function to do j
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{

man/key_antibiotics.Rd

@@ -109,9 +109,9 @@ The function \code{\link[=key_antibiotics_equal]{key_antibiotics_equal()}} check
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Key antibiotics}{

man/kurtosis.Rd

@@ -26,7 +26,7 @@ Kurtosis is a measure of the "tailedness" of the probability distribution of a r
 \section{Questioning lifecycle}{
 
 \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our \code{AMR} package at all.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
 }
 
 \section{Read more on our website!}{

man/lifecycle.Rd

@@ -4,52 +4,40 @@
 \alias{lifecycle}
 \title{Lifecycles of functions in the \code{AMR} package}
 \description{
-Our functions are categorised using \href{https://www.tidyverse.org/lifecycle}{the lifecycle circle of the \code{tidyverse} as found on www.tidyverse.org/lifecycle}.
+Functions in this \code{AMR} package are categorised using \href{https://www.tidyverse.org/lifecycle}{the lifecycle circle of the \code{tidyverse} as found on www.tidyverse.org/lifecycle}.
 
 \if{html}{\figure{lifecycle_tidyverse.svg}{options: height=200px style=margin-bottom:5px} \cr}
-This page contains a section for every lifecycle (with text borrowed from the aforementioned \code{tidyverse} website), so they can be used in the manual pages of our functions.
+This page contains a section for every lifecycle (with text borrowed from the aforementioned \code{tidyverse} website), so they can be used in the manual pages of the functions.
 }
 \section{Experimental lifecycle}{
 
 \if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{experimental}. An experimental function is in the very early stages of development. The unlying code might be changing frequently as we rapidly iterate and explore variations in search of the best fit. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions will not be included in releases we submit to CRAN, since they have not yet matured enough.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{experimental}. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this \code{AMR} package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
 }
 
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
 }
 
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Retired lifecycle}{
 
 \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{retired}. A retired function is no longer under active development, and (if appropiate) a better alternative is available. We will only make the necessary changes to ensure that retired functions remain available. No new arguments will be added, and only the most critical bugs will be fixed.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{retired}. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
-}
-
-\section{Archived lifecycle}{
-
-\if{html}{\figure{lifecycle_archived.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{archived}. The development of an archived function has ended, and it is no longer available in future package versions.
-}
-
-\section{Dormant lifecycle}{
-
-\if{html}{\figure{lifecycle_dormant.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{dormant}. A dormant function is currently not under active development and has not reached a stable phase. We might return to it in the future. As with experimental functions, you are best off waiting until a function is more mature before you use it in production code.
 }
 
 \section{Questioning lifecycle}{
 
 \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our \code{AMR} package at all.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
 }
 

man/like.Rd

@@ -42,9 +42,9 @@ Using RStudio? This function can also be inserted from the Addins menu and can h
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{

man/mdro.Rd

@@ -95,7 +95,7 @@ Please suggest your own (country-specific) guidelines by letting us know: \url{h
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
 }
 
 \section{Antibiotics}{

man/mo_source.Rd

@@ -78,9 +78,9 @@ To remove the reference data file completely, just use \code{""} or \code{NULL}
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{

man/p_symbol.Rd

@@ -20,7 +20,7 @@ Return the symbol related to the p-value: 0 '\verb{***}' 0.001 '\verb{**}' 0.01
 \section{Questioning lifecycle}{
 
 \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our \code{AMR} package at all.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
 }
 
 \section{Read more on our website!}{

man/pca.Rd

@@ -62,7 +62,7 @@ The result of the \code{\link[=pca]{pca()}} function is a \link{prcomp} object,
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
 }
 
 \examples{

man/proportion.Rd

@@ -121,9 +121,9 @@ Using \code{only_all_tested} has no impact when only using one antibiotic as inp
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Interpretation of R and S/I}{

man/resistance_predict.Rd

@@ -103,7 +103,7 @@ Valid options for the statistical model (parameter \code{model}) are:
 \section{Maturing lifecycle}{
 
 \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
 }
 
 \section{Interpretation of R and S/I}{

man/skewness.Rd

@@ -28,7 +28,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
 \section{Questioning lifecycle}{
 
 \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our \code{AMR} package at all.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
 }
 
 \section{Read more on our website!}{

man/translate.Rd

@@ -24,9 +24,9 @@ The system language will be used at default, if that language is supported. The
 \section{Stable lifecycle}{
 
 \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
-The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 
-If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 }
 
 \section{Read more on our website!}{

tests/testthat/test-ab_property.R

@@ -58,4 +58,7 @@ test_that("ab_property works", {
   expect_equal(ab_name("21066-6", language = NULL), "Ampicillin")
   expect_equal(ab_loinc("ampicillin"),
                c("21066-6", "3355-5", "33562-0", "33919-2", "43883-8", "43884-6", "87604-5"))
+  
+  expect_true(ab_url("AMX") %like% "whocc.no")
+  expect_warning(ab_url("ASP"))
 })