WHONET/EARS-Net support

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.5.0.9014
+Version: 0.5.0.9015
-Date: 2019-01-28
+Date: 2019-01-29
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(

NEWS.md

@@ -3,6 +3,9 @@
 
 #### New
 * **BREAKING**: removed deprecated functions, parameters and references to 'bactid'. Use `as.mo()` to identify an MO code.
+* Support for data from [WHONET](https://whonet.org/) and [EARS-Net](https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net) (European Antimicrobial Resistance Surveillance Network):
+  * Exported files from WHONET can be read and used in this package. For functions like `first_isolate()` and `eucast_rules()`, all parameters will be filled in automatically.
+  * This package now knows all antibiotic abbrevations by EARS-Net (which are also being used by WHONET) - the `antibiotics` data set now contains a column `ears_net`.
 * All `ab_*` functions are deprecated and replaced by `atc_*` functions:
   ```r
   ab_property -> atc_property()
@@ -75,10 +78,11 @@
 * Merged data sets `microorganisms.certe` and `microorganisms.umcg` into `microorganisms.codes`
 * Function `mo_taxonomy()` now contains the kingdom too
 * Reduce false positives for `is.rsi.eligible()`
+* New colours for `scale_rsi_colours()`
 * Summaries of class `mo` will now return the top 3 and the unique count, e.g. using `summary(mo)`
 * Small text updates to summaries of class `rsi` and `mic`
 * Frequency tables (`freq()` function):
-  * Support for tidyverse quasiquotation! So now you can create frequency tables of function outcomes:
+  * Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:
     ```r
     # Determine genus of microorganisms (mo) in `septic_patients` data set:
     # OLD WAY

R/atc.R

@@ -60,10 +60,15 @@ as.atc <- function(x) {
   x[!x %like% "[A-Z][0-9]{2}[A-Z]{2}[0-9]{2}"] <- gsub("[^a-zA-Z]+", "", x[!x %like% "[A-Z][0-9]{2}[A-Z]{2}[0-9]{2}"])
 
   x.bak <- x
-  x <- unique(x[!is.na(x)])
+  x <- unique(x)
   failures <- character(0)
 
   for (i in 1:length(x)) {
+    if (is.na(x[i]) | is.null(x[i]) | identical(x[i], "")) {
+      x.new[i] <- x[i]
+      next
+    }
+
     fail <- TRUE
 
     # first try atc
@@ -80,6 +85,13 @@ as.atc <- function(x) {
       x.new[is.na(x.new) & x.bak == x[i]] <- x[i]
     }
 
+    # try abbreviation of EARS-Net/WHONET
+    found <- AMR::antibiotics[which(tolower(AMR::antibiotics$ears_net) == tolower(x[i])),]$atc
+    if (length(found) > 0) {
+      fail <- FALSE
+      x.new[is.na(x.new) & x.bak == x[i]] <- found[1L]
+    }
+
     # try abbreviation of certe and glims
     found <- AMR::antibiotics[which(tolower(AMR::antibiotics$certe) == tolower(x[i])),]$atc
     if (length(found) > 0) {

R/data.R

@@ -22,9 +22,10 @@
 #' Data set with ~500 antibiotics
 #'
 #' A data set containing all antibiotics with a J0 code and some other antimicrobial agents, with their DDDs. Except for trade names and abbreviations, all properties were downloaded from the WHO, see Source.
-#' @format A \code{\link{data.frame}} with 488 observations and 16 variables:
+#' @format A \code{\link{data.frame}} with 488 observations and 17 variables:
 #' \describe{
-#'   \item{\code{atc}}{ATC code, like \code{J01CR02}}
+#'   \item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical), like \code{J01CR02}}
+#'   \item{\code{ears_net}}{EARS-Net code (European Antimicrobial Resistance Surveillance Network), like \code{AMC}}
 #'   \item{\code{certe}}{Certe code, like \code{amcl}}
 #'   \item{\code{umcg}}{UMCG code, like \code{AMCL}}
 #'   \item{\code{abbr}}{Abbreviation as used by many countries, used internally by \code{\link{as.atc}}}
@@ -43,6 +44,8 @@
 #' }
 #' @source - World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
 #'
+#' Table antibiotic coding EARSS (from WHONET 5.3): \url{http://www.madsonline.dk/Tutorials/landskoder_antibiotika_WM.pdf}
+#'
 #' EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016: \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
 #'
 #' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}

R/first_isolate.R

@@ -220,6 +220,14 @@ first_isolate <- function(tbl,
     col_keyantibiotics <- NULL
   }
 
+  # -- specimen
+  if (is.null(col_specimen)) {
+    col_specimen <- search_type_in_df(tbl = tbl, type = "specimen")
+  }
+  if (isFALSE(col_specimen)) {
+    col_specimen <- NULL
+  }
+
   # check if columns exist
   check_columns_existance <- function(column, tblname = tbl) {
     if (NROW(tblname) <= 1 | NCOL(tblname) <= 1) {

R/ggplot_rsi.R

@@ -313,8 +313,8 @@ scale_y_percent <- function(breaks = seq(0, 1, 0.1), limits = NULL) {
 #' @rdname ggplot_rsi
 #' @export
 scale_rsi_colours <- function() {
-  ggplot2::scale_fill_brewer(palette = "RdYlGn")
+  #ggplot2::scale_fill_brewer(palette = "RdYlGn")
-  #ggplot2::scale_fill_gradient2(low = "#d5613e", mid = "#ae5ac0", high = "#7daf44")
+  ggplot2::scale_fill_manual(values = c("#b22222", "#ae9c20", "#7cfc00"))
 }
 
 #' @rdname ggplot_rsi

R/guess_ab_col.R

@@ -21,7 +21,7 @@
 
 #' Guess antibiotic column
 #'
-#' This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. You can look for an antibiotic (trade) name or abbreviation and it will search the \code{data.frame} for any column containing a name or ATC code of that antibiotic.
+#' This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. Also supports WHONET abbreviations. You can look for an antibiotic (trade) name or abbreviation and it will search the \code{data.frame} for any column containing a name or ATC code of that antibiotic.
 #' @param tbl a \code{data.frame}
 #' @param col a character to look for
 #' @param verbose a logical to indicate whether additional info should be printed
@@ -40,6 +40,16 @@
 #' guess_ab_col(df, "J01AA07", verbose = TRUE)
 #' # using column `tetr` for col "J01AA07"
 #' # [1] "tetr"
+#'
+#' # WHONET codes
+#' df <- data.frame(AMP_ND10 = "R",
+#'                  AMC_ED20 = "S")
+#' guess_ab_col(df, "ampicillin")
+#' # [1] "AMP_ND10"
+#' guess_ab_col(df, "J01CR02")
+#' # [1] "AMC_ED20"
+#' guess_ab_col(df, as.atc("augmentin"))
+#' # [1] "AMC_ED20"
 guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
   if (is.null(tbl) & is.null(col)) {
     return(as.name("guess_ab_col"))
@@ -54,6 +64,11 @@ guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
   }
 
   tbl_names <- colnames(tbl)
+  tbl_names_stripped <- colnames(tbl) %>%
+    strsplit("_") %>%
+    lapply(function(x) {x[1]}) %>%
+    unlist()
+
   if (col %in% tbl_names) {
     return(col)
   }
@@ -70,6 +85,15 @@ guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
       filter_all(any_vars(. %in% tbl_names))
   }
 
+  # WHONET
+  if (nrow(ab_result) == 0) {
+    # use like when col >= 5 characters
+    ab_result <- antibiotics %>%
+      select(atc:trade_name) %>%
+      filter_all(any_vars(tolower(.) == tolower(col))) %>%
+      filter_all(any_vars(. %in% tbl_names_stripped))
+  }
+
   if (nrow(ab_result) > 1) {
     # looking more and more for reliable hit
     ab_result_1 <- ab_result %>% filter(tolower(atc) == tolower(col))
@@ -95,6 +119,9 @@ guess_ab_col <- function(tbl = NULL, col = NULL, verbose = FALSE) {
     return(NULL)
   } else {
     result <- tbl_names[tbl_names %in% ab_result]
+    if (length(result) == 0) {
+      result <- tbl_names[tbl_names_stripped %in% ab_result]
+    }
     if (length(result) == 0) {
       if (verbose == TRUE) {
         message('no result found for col "', col, '"')

R/misc.R

@@ -130,11 +130,18 @@ search_type_in_df <- function(tbl, type) {
   # try to find columns based on type
   found <- NULL
 
+  colnames(tbl) <- trimws(colnames(tbl))
+
   # -- mo
   if (type == "mo") {
     if ("mo" %in% lapply(tbl, class)) {
       found <- colnames(tbl)[lapply(tbl, class) == "mo"][1]
+    } else if (any(colnames(tbl) %like% "^(mo|microorganism|organism|bacteria)")) {
+      found <- colnames(tbl)[colnames(tbl) %like% "^(mo|microorganism|organism|bacteria)"][1]
+    } else if (any(colnames(tbl) %like% "species")) {
+      found <- colnames(tbl)[colnames(tbl) %like% "species"][1]
     }
+
   }
   # -- key antibiotics
   if (type == "keyantibiotics") {
@@ -154,15 +161,23 @@ search_type_in_df <- function(tbl, type) {
   }
   # -- patient id
   if (type == "patient_id") {
-    if (any(colnames(tbl) %like% "^(patient|patid)")) {
+    if (any(colnames(tbl) %like% "^(identification |patient|patid)")) {
-      found <- colnames(tbl)[colnames(tbl) %like% "^(patient|patid)"][1]
+      found <- colnames(tbl)[colnames(tbl) %like% "^(identification |patient|patid)"][1]
+    }
+  }
+  # -- specimen
+  if (type == "specimen") {
+    if (any(colnames(tbl) %like% "(specimen type)")) {
+      found <- colnames(tbl)[colnames(tbl) %like% "(specimen type)"][1]
+    } else if (any(colnames(tbl) %like% "^(specimen)")) {
+      found <- colnames(tbl)[colnames(tbl) %like% "^(specimen)"][1]
     }
   }
 
   if (!is.null(found)) {
     msg <- paste0("NOTE: Using column `", bold(found), "` as input for `col_", type, "`.")
-    if (type == "keyantibiotics") {
+    if (type %in% c("keyantibiotics", "specimen")) {
-      msg <- paste(msg, "Use", bold("col_keyantibiotics = FALSE"), "to prevent this.")
+      msg <- paste(msg, "Use", bold(paste0("col_", type), " = FALSE"), "to prevent this.")
     }
     message(blue(msg))
   }

R/mo_source.R

@@ -107,11 +107,7 @@ set_mo_source <- function(path) {
     if (!"readxl" %in% utils::installed.packages()) {
       stop("Install the 'readxl' package first.")
     }
-    if (path %like% '[.]xlsx$') {
+    df <- readxl::read_excel(path)
-      df <- readxl::read_xlsx(path)
-    } else {
-      df <- readxl::read_xls(path)
-    }
 
   } else {
     # try comma first

_pkgdown.yml

@@ -38,6 +38,9 @@ navbar:
       - text: 'Predict antimicrobial resistance'
         icon: 'fa-dice'
         href: 'articles/Predict.html'
+      - text: 'Work with WHONET data'
+        icon: 'fa-globe-americas'
+        href: 'articles/WHONET.html'
       - text: 'Apply EUCAST rules'
         icon: 'fa-exchange-alt'
         href: 'articles/EUCAST.html'

docs/LICENSE-text.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -114,6 +114,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/articles/EUCAST.html

@@ -40,7 +40,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -76,6 +76,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -178,7 +185,7 @@
       <h1>How to apply EUCAST rules</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">26 January 2019</h4>
+            <h4 class="date">28 January 2019</h4>
       
       
       <div class="hidden name"><code>EUCAST.Rmd</code></div>

docs/articles/G_test.html

@@ -40,7 +40,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -76,6 +76,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -178,7 +185,7 @@
       <h1>How to use the <em>G</em>-test</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">26 January 2019</h4>
+            <h4 class="date">28 January 2019</h4>
       
       
       <div class="hidden name"><code>G_test.Rmd</code></div>

docs/articles/Predict.html

@@ -40,7 +40,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -76,6 +76,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -178,7 +185,7 @@
       <h1>How to predict antimicrobial resistance</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">26 January 2019</h4>
+            <h4 class="date">28 January 2019</h4>
       
       
       <div class="hidden name"><code>Predict.Rmd</code></div>

docs/articles/WHONET.html

@@ -0,0 +1,233 @@
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+    <li>
+      <a href="../articles/Predict.html">
+        <span class="fa fa-dice"></span>
+         
+        Predict antimicrobial resistance
+      </a>
+    </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
+    <li>
+      <a href="../articles/EUCAST.html">
+        <span class="fa fa-exchange-alt"></span>
+         
+        Apply EUCAST rules
+      </a>
+    </li>
+    <li>
+      <a href="../articles/mo_property.html">
+        <span class="fa fa-bug"></span>
+         
+        Get properties of a microorganism
+      </a>
+    </li>
+    <li>
+      <a href="../articles/ab_property.html">
+        <span class="fa fa-capsules"></span>
+         
+        Get properties of an antibiotic
+      </a>
+    </li>
+    <li>
+      <a href="../articles/freq.html">
+        <span class="fa fa-sort-amount-down"></span>
+         
+        Create frequency tables
+      </a>
+    </li>
+    <li>
+      <a href="../articles/G_test.html">
+        <span class="fa fa-clipboard-check"></span>
+         
+        Use the G-test
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+      <a href="../articles/benchmarks.html">
+        <span class="fa fa-shipping-fast"></span>
+         
+        Other: benchmarks
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+    <div class="page-header toc-ignore">
+      <h1>How to work with WHONET data</h1>
+                        <h4 class="author">Matthijs S. Berends</h4>
+            
+            <h4 class="date">28 January 2019</h4>
+      
+      
+      <div class="hidden name"><code>WHONET.Rmd</code></div>
+
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docs/articles/ab_property.html

@@ -40,7 +40,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -76,6 +76,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -178,7 +185,7 @@
       <h1>How to get properties of an antibiotic</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">26 January 2019</h4>
+            <h4 class="date">28 January 2019</h4>
       
       
       <div class="hidden name"><code>ab_property.Rmd</code></div>

docs/articles/benchmarks.html

@@ -40,7 +40,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -76,6 +76,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -178,7 +185,7 @@
       <h1>Benchmarks</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">26 January 2019</h4>
+            <h4 class="date">28 January 2019</h4>
       
       
       <div class="hidden name"><code>benchmarks.Rmd</code></div>
@@ -240,15 +247,15 @@
 <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a>
 <a class="sourceLine" id="cb4-2" data-line-number="2"><span class="co"># take 500,000 random MO codes from the septic_patients data set</span></a>
 <a class="sourceLine" id="cb4-3" data-line-number="3">x =<span class="st"> </span>septic_patients <span class="op">%&gt;%</span></a>
-<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample_n</a></span>(<span class="dv">500000</span>, <span class="dt">replace =</span> <span class="ot">TRUE</span>) <span class="op">%&gt;%</span></a>
+<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="st">  </span><span class="kw"><a href="https://www.rdocumentation.org/packages/dplyr/topics/sample">sample_n</a></span>(<span class="dv">500000</span>, <span class="dt">replace =</span> <span class="ot">TRUE</span>) <span class="op">%&gt;%</span></a>
-<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span>(mo)</a>
+<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="st">  </span><span class="kw"><a href="https://www.rdocumentation.org/packages/dplyr/topics/pull">pull</a></span>(mo)</a>
 <a class="sourceLine" id="cb4-6" data-line-number="6">  </a>
 <a class="sourceLine" id="cb4-7" data-line-number="7"><span class="co"># got the right length?</span></a>
 <a class="sourceLine" id="cb4-8" data-line-number="8"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/length">length</a></span>(x)</a>
 <a class="sourceLine" id="cb4-9" data-line-number="9"><span class="co"># [1] 500000</span></a>
 <a class="sourceLine" id="cb4-10" data-line-number="10"></a>
 <a class="sourceLine" id="cb4-11" data-line-number="11"><span class="co"># and how many unique values do we have?</span></a>
-<a class="sourceLine" id="cb4-12" data-line-number="12"><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</a>
+<a class="sourceLine" id="cb4-12" data-line-number="12"><span class="kw"><a href="https://www.rdocumentation.org/packages/dplyr/topics/n_distinct">n_distinct</a></span>(x)</a>
 <a class="sourceLine" id="cb4-13" data-line-number="13"><span class="co"># [1] 96</span></a>
 <a class="sourceLine" id="cb4-14" data-line-number="14"></a>
 <a class="sourceLine" id="cb4-15" data-line-number="15"><span class="co"># only 96, but distributed in 500,000 results. now let's see:</span></a>

docs/articles/freq.html

@@ -40,7 +40,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -76,6 +76,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -178,7 +185,7 @@
       <h1>How to create frequency tables</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">26 January 2019</h4>
+            <h4 class="date">28 January 2019</h4>
       
       
       <div class="hidden name"><code>freq.Rmd</code></div>
@@ -197,7 +204,7 @@
 <a href="#frequencies-of-one-variable" class="anchor"></a>Frequencies of one variable</h2>
 <p>To only show and quickly review the content of one variable, you can just select this variable in various ways. Let’s say we want to get the frequencies of the <code>gender</code> variable of the <code>septic_patients</code> dataset:</p>
 <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
-<p><strong>Frequency table of <code>gender</code></strong></p>
+<p><strong>Frequency table</strong></p>
 <table class="table">
 <thead><tr class="header">
 <th align="left"></th>
@@ -248,7 +255,7 @@
 <p>So now the <code>genus</code> and <code>species</code> variables are available. A frequency table of these combined variables can be created like this:</p>
 <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1">my_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb5-2" data-line-number="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species, <span class="dt">nmax =</span> <span class="dv">15</span>)</a></code></pre></div>
-<p><strong>Frequency table of <code>genus</code> and <code>species</code></strong></p>
+<p><strong>Frequency table</strong></p>
 <table class="table">
 <thead><tr class="header">
 <th align="left"></th>
@@ -392,7 +399,7 @@
 <a class="sourceLine" id="cb6-2" data-line-number="2">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
 <a class="sourceLine" id="cb6-3" data-line-number="3"><span class="st">  </span><span class="kw">distinct</span>(patient_id, <span class="dt">.keep_all =</span> <span class="ot">TRUE</span>) <span class="op">%&gt;%</span><span class="st"> </span></a>
 <a class="sourceLine" id="cb6-4" data-line-number="4"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age, <span class="dt">nmax =</span> <span class="dv">5</span>, <span class="dt">header =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
-<p><strong>Frequency table of <code>age</code></strong><br>
+<p><strong>Frequency table</strong><br>
 Class: numeric<br>
 Length: 981 (of which NA: 0 = 0.00%)<br>
 Unique: 73</p>
@@ -471,7 +478,7 @@ Outliers: 15 (unique count: 12)</p>
 <p><code>sort.count</code> is <code>TRUE</code> by default. Compare this default behaviour…</p>
 <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb7-2" data-line-number="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id)</a></code></pre></div>
-<p><strong>Frequency table of <code>hospital_id</code></strong></p>
+<p><strong>Frequency table</strong></p>
 <table class="table">
 <thead><tr class="header">
 <th align="left"></th>
@@ -519,7 +526,7 @@ Outliers: 15 (unique count: 12)</p>
 <p>… with this, where items are now sorted on count:</p>
 <div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb8-2" data-line-number="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">sort.count =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
-<p><strong>Frequency table of <code>hospital_id</code></strong></p>
+<p><strong>Frequency table</strong></p>
 <table class="table">
 <thead><tr class="header">
 <th align="left"></th>
@@ -567,7 +574,7 @@ Outliers: 15 (unique count: 12)</p>
 <p>All classes will be printed into the header (default is <code>FALSE</code> when using markdown like this document). Variables with the new <code>rsi</code> class of this AMR package are actually ordered factors and have three classes (look at <code>Class</code> in the header):</p>
 <div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb9-2" data-line-number="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(amox, <span class="dt">header =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
-<p><strong>Frequency table of <code>amox</code></strong><br>
+<p><strong>Frequency table</strong><br>
 Class: factor &gt; ordered &gt; rsi (numeric)<br>
 Levels: S &lt; I &lt; R<br>
 Length: 2,000 (of which NA: 828 = 41.40%)<br>
@@ -616,7 +623,7 @@ Unique: 3</p>
 <p>Frequencies of dates will show the oldest and newest date in the data, and the amount of days between them:</p>
 <div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb10-2" data-line-number="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(date, <span class="dt">nmax =</span> <span class="dv">5</span>, <span class="dt">header =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
-<p><strong>Frequency table of <code>date</code></strong><br>
+<p><strong>Frequency table</strong><br>
 Class: Date (numeric)<br>
 Length: 2,000 (of which NA: 0 = 0.00%)<br>
 Unique: 1,140</p>
@@ -698,7 +705,7 @@ Median: 31 July 2009 (47.39%)</p>
 <p>With the <code>na.rm</code> parameter (defaults to <code>TRUE</code>, but they will always be shown into the header), you can include <code>NA</code> values in the frequency table:</p>
 <div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb13-2" data-line-number="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(amox, <span class="dt">na.rm =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
-<p><strong>Frequency table of <code>amox</code></strong></p>
+<p><strong>Frequency table</strong></p>
 <table class="table">
 <thead><tr class="header">
 <th align="left"></th>
@@ -751,7 +758,7 @@ Median: 31 July 2009 (47.39%)</p>
 <p>The default frequency tables shows row indices. To remove them, use <code>row.names = FALSE</code>:</p>
 <div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb14-2" data-line-number="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">row.names =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
-<p><strong>Frequency table of <code>hospital_id</code></strong></p>
+<p><strong>Frequency table</strong></p>
 <table class="table">
 <thead><tr class="header">
 <th align="left">Item</th>
@@ -799,7 +806,7 @@ Median: 31 July 2009 (47.39%)</p>
 <p>The <code>markdown</code> parameter is <code>TRUE</code> at default in non-interactive sessions, like in reports created with R Markdown. This will always print all rows, unless <code>nmax</code> is set.</p>
 <div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb15-2" data-line-number="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">markdown =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
-<p><strong>Frequency table of <code>hospital_id</code></strong></p>
+<p><strong>Frequency table</strong></p>
 <table class="table">
 <thead><tr class="header">
 <th align="left"></th>

docs/articles/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -114,6 +114,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -226,6 +233,7 @@
         <li><a href="EUCAST.html">How to apply EUCAST rules</a></li>
         <li><a href="G_test.html">How to use the *G*-test</a></li>
         <li><a href="Predict.html">How to predict antimicrobial resistance</a></li>
+        <li><a href="WHONET.html">How to work with WHONET data</a></li>
         <li><a href="ab_property.html">How to get properties of an antibiotic</a></li>
         <li><a href="benchmarks.html">Benchmarks</a></li>
         <li><a href="freq.html">How to create frequency tables</a></li>

docs/articles/mo_property.html

@@ -40,7 +40,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -76,6 +76,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -178,7 +185,7 @@
       <h1>How to get properties of a microorganism</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">26 January 2019</h4>
+            <h4 class="date">28 January 2019</h4>
       
       
       <div class="hidden name"><code>mo_property.Rmd</code></div>

docs/authors.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -114,6 +114,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/index.html

@@ -42,7 +42,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -78,6 +78,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -182,7 +189,7 @@
 </h1></div>
 <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>
 <hr>
-<p><code>AMR</code> is a free and open-source <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 properties by using evidence-based methods.</p>
+<p><code>AMR</code> is a free and open-source <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 properties by using evidence-based methods. It supports any table format, including WHONET/EARS-Net data.</p>
 <p>We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but <strong>not</strong> patent) purposes under the terms of the GNU General Public Licence version 2.0 (GPL-2), as published by the Free Software Foundation. Read the full licence <a href="./LICENSE-text.html">here</a>.</p>
 <p>This package can be used for:</p>
 <ul>
@@ -222,28 +229,30 @@
 <li>Software developers</li>
 <li>Web application / Shiny developers</li>
 </ul>
-<div id="get-this-package" class="section level3">
+<div id="get-this-package" class="section level2">
-<h3 class="hasAnchor">
+<h2 class="hasAnchor">
-<a href="#get-this-package" class="anchor"></a>Get this package</h3>
+<a href="#get-this-package" class="anchor"></a>Get this package</h2>
 <p>This package is available on the official R network (CRAN), which has a peer-reviewed submission process. Install this package in R with:</p>
 <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"AMR"</span>)</a></code></pre></div>
 <p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
+<p>The latest and unpublished development version can be installed with (precaution: may be unstable):</p>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"devtools"</span>)</a>
+<a class="sourceLine" id="cb2-2" data-line-number="2">devtools<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/devtools/topics/reexports">install_gitlab</a></span>(<span class="st">"msberends/AMR"</span>)</a></code></pre></div>
 </div>
-<div id="get-started" class="section level3">
+<div id="get-started" class="section level2">
-<h3 class="hasAnchor">
+<h2 class="hasAnchor">
-<a href="#get-started" class="anchor"></a>Get started</h3>
+<a href="#get-started" class="anchor"></a>Get started</h2>
 <p>To find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click the links in the ‘How to’ menu.</p>
 </div>
-<div id="short-introduction" class="section level3">
+<div id="short-introduction" class="section level2">
-<h3 class="hasAnchor">
+<h2 class="hasAnchor">
-<a href="#short-introduction" class="anchor"></a>Short introduction</h3>
+<a href="#short-introduction" class="anchor"></a>Short introduction</h2>
-<div id="microbial-taxonomic-reference-data" class="section level4">
+<div id="whonet-ears-net" class="section level4">
 <h4 class="hasAnchor">
-<a href="#microbial-taxonomic-reference-data" class="anchor"></a>Microbial (taxonomic) reference data</h4>
+<a href="#whonet-ears-net" class="anchor"></a>WHONET / EARS-Net</h4>
-<p><img src="reference/figures/logo_itis.jpg" height="60px"></p>
+<p><img src="./whonet.png"></p>
-<p>This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href="https://www.itis.gov" class="uri">https://www.itis.gov</a>).</p>
+<p>We support data (exported files) from WHONET. The <code>AMR</code> package contains a data set <code>antibiotics</code> which also contains all EARS-Net antibiotic abbreviations. Furthermore, when using WHONET data as input for analysis all input parameters will be set automatically.</p>
-<p>All ~20,000 (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since ITIS honours the taxonomic branching order of bacterial phyla according to Cavalier-Smith (2002), which defines that all bacteria are classified into either subkingdom Negibacteria or subkingdom Posibacteria.</p>
+<p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
-<p>Read more about the data from ITIS <a href="./reference/ITIS.html">in our manual</a>.</p>
 </div>
 <div id="antimicrobial-reference-data" class="section level4">
 <h4 class="hasAnchor">
@@ -254,6 +263,14 @@
 <p>This package contains <strong>all ~500 antimicrobial 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" class="uri">https://www.whocc.no</a>) and the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register of the European Commission</a>.</p>
 <p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
 </div>
+<div id="microbial-taxonomic-reference-data" class="section level4">
+<h4 class="hasAnchor">
+<a href="#microbial-taxonomic-reference-data" class="anchor"></a>Microbial (taxonomic) reference data</h4>
+<p><img src="reference/figures/logo_itis.jpg" height="60px"></p>
+<p>This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href="https://www.itis.gov" class="uri">https://www.itis.gov</a>).</p>
+<p>All ~20,000 (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since ITIS honours the taxonomic branching order of bacterial phyla according to Cavalier-Smith (2002), which defines that all bacteria are classified into either subkingdom Negibacteria or subkingdom Posibacteria.</p>
+<p>Read more about the data from ITIS <a href="./reference/ITIS.html">in our manual</a>.</p>
+</div>
 <div id="overview-of-functions" class="section level4">
 <h4 class="hasAnchor">
 <a href="#overview-of-functions" class="anchor"></a>Overview of functions</h4>

docs/news/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -114,6 +114,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -229,6 +236,12 @@
 <ul>
 <li>
 <strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</li>
+<li>Support for data from <a href="https://whonet.org/">WHONET</a> and <a href="https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net">EARS-Net</a> (European Antimicrobial Resistance Surveillance Network):
+<ul>
+<li>Exported files from WHONET can be read and used in this package. For functions like <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, all parameters will be filled in automatically.</li>
+<li>This package now knows all antibiotic abbrevations by EARS-Net (which are also being used by WHONET) - the <code>antibiotics</code> data set now contains a column <code>ears_net</code>.</li>
+</ul>
+</li>
 <li>
 <p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
 <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">ab_property -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_property</a></span>()</a>
@@ -318,6 +331,8 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
 <li>Function <code><a href="../reference/mo_property.html">mo_taxonomy()</a></code> now contains the kingdom too</li>
 <li>Reduce false positives for <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code>
 </li>
+<li>New colours for <code><a href="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code>
+</li>
 <li>Summaries of class <code>mo</code> will now return the top 3 and the unique count, e.g. using <code><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary(mo)</a></code>
 </li>
 <li>Small text updates to summaries of class <code>rsi</code> and <code>mic</code>
@@ -325,7 +340,7 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
 <li>Frequency tables (<code><a href="../reference/freq.html">freq()</a></code> function):
 <ul>
 <li>
-<p>Support for tidyverse quasiquotation! So now you can create frequency tables of function outcomes:</p>
+<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
 <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
 <a class="sourceLine" id="cb5-2" data-line-number="2"><span class="co"># OLD WAY</span></a>
 <a class="sourceLine" id="cb5-3" data-line-number="3">septic_patients <span class="op">%&gt;%</span></a>
@@ -776,7 +791,7 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
 <ul>
 <li>Full support for Windows, Linux and macOS</li>
 <li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
-<li>Function <code>n_rsi</code> to count cases where antibiotic test results were available, to be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">dplyr::summarise</a></code>, see ?rsi</li>
+<li>Function <code>n_rsi</code> to count cases where antibiotic test results were available, to be used in conjunction with <code><a href="https://www.rdocumentation.org/packages/dplyr/topics/summarise">dplyr::summarise</a></code>, see ?rsi</li>
 <li>Function <code>guess_bactid</code> to <strong>determine the ID</strong> of a microorganism based on genus/species or known abbreviations like MRSA</li>
 <li>Function <code>guess_atc</code> to <strong>determine the ATC</strong> of an antibiotic based on name, trade name, or known abbreviations</li>
 <li>Function <code>freq</code> to create <strong>frequency tables</strong>, with additional info in a header</li>

docs/pkgdown.yml

@@ -6,6 +6,7 @@ articles:
   EUCAST: EUCAST.html
   G_test: G_test.html
   Predict: Predict.html
+  WHONET: WHONET.html
   ab_property: ab_property.html
   benchmarks: benchmarks.html
   freq: freq.html

docs/reference/AMR-deprecated.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/AMR.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/ITIS.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/WHOCC.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/abname.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/age.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/age_groups.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -296,11 +303,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 <span class='co'># resistance of ciprofloxacine per age group</span>
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</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='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
          <span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</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='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>age_group</span>,
          <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
 <span class='co'># }</span></pre>

docs/reference/antibiotics.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -231,8 +238,9 @@
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 488 observations and 16 variables:</p><dl class='dl-horizontal'>
+    <p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 488 observations and 17 variables:</p><dl class='dl-horizontal'>
-  <dt><code>atc</code></dt><dd><p>ATC code, like <code>J01CR02</code></p></dd>
+  <dt><code>atc</code></dt><dd><p>ATC code (Anatomical Therapeutic Chemical), like <code>J01CR02</code></p></dd>
+  <dt><code>ears_net</code></dt><dd><p>EARS-Net code (European Antimicrobial Resistance Surveillance Network), like <code>AMC</code></p></dd>
   <dt><code>certe</code></dt><dd><p>Certe code, like <code>amcl</code></p></dd>
   <dt><code>umcg</code></dt><dd><p>UMCG code, like <code>AMCL</code></p></dd>
   <dt><code>abbr</code></dt><dd><p>Abbreviation as used by many countries, used internally by <code><a href='as.atc.html'>as.atc</a></code></p></dd>
@@ -253,6 +261,7 @@
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
 
     <p>- World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
+<p>Table antibiotic coding EARSS (from WHONET 5.3): <a href='http://www.madsonline.dk/Tutorials/landskoder_antibiotika_WM.pdf'>http://www.madsonline.dk/Tutorials/landskoder_antibiotika_WM.pdf</a></p>
 <p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016: <a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf</a></p>
 <p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <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>
     

docs/reference/as.atc.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/as.mic.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/as.mo.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -364,16 +371,16 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
 <span class='co'># the select function of tidyverse is also supported:</span>
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>microorganism_name</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>microorganism_name</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'>as.mo</span>()
 
 <span class='co'># and can even contain 2 columns, which is convenient for genus/species combinations:</span>
 <span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'>as.mo</span>()
 <span class='co'># although this works easier and does the same:</span>
 <span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'>as.mo</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)))
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'>as.mo</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)))
 <span class='co'># }</span></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

docs/reference/as.rsi.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -277,11 +284,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 <span class='co'># using dplyr's mutate</span>
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>peni</span>:<span class='no'>rifa</span>), <span class='no'>as.rsi</span>)
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise_all'>mutate_at</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/vars'>vars</a></span>(<span class='no'>peni</span>:<span class='no'>rifa</span>), <span class='no'>as.rsi</span>)
 
 <span class='co'># fastest way to transform all columns with already valid AB results to class `rsi`:</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>,
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise_all'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>,
             <span class='no'>as.rsi</span>)
 <span class='co'># }</span></pre>
   </div>

docs/reference/atc_online.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/atc_property.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/count.html

@@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -117,6 +117,13 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -282,7 +289,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     <p>These functions are meant to count isolates. Use the <code><a href='portion.html'>portion</a>_*</code> functions to calculate microbial resistance.</p>
-<p><code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
+<p><code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://www.rdocumentation.org/packages/dplyr/topics/n_distinct'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
 <p><code>count_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 counts the amounts of 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 variable with class <code>"rsi"</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>
@@ -321,13 +328,13 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='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://www.rdocumentation.org/packages/dplyr/topics/group_by'>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'>count_R</span>(<span class='no'>cipr</span>),
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>summarise</a></span>(<span class='kw'>R</span>  <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>cipr</span>),
             <span class='kw'>I</span>  <span class='kw'>=</span> <span class='fu'>count_I</span>(<span class='no'>cipr</span>),
             <span class='kw'>S</span>  <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>cipr</span>),
             <span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>cipr</span>), <span class='co'># the actual total; sum of all three</span>
             <span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>cipr</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 amount of tested isolates!</span>
+            <span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/n'>n</a></span>())          <span class='co'># NOT the amount of tested isolates!</span>
 
 <span class='co'># Count 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>
@@ -345,13 +352,13 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 
 <span class='co'># Get portions S/I/R immediately of all rsi columns</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'>count_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'>septic_patients</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'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</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://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
 
 <span class='co'># }</span></pre>

docs/reference/eucast_rules.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/first_isolate.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -368,11 +375,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='co'># Filter on first isolates:</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'>first_isolate</span>(<span class='no'>.</span>,
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'>first_isolate</span>(<span class='no'>.</span>,
                                        <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
                                        <span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>,
                                        <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</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='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>)
 
 <span class='co'># Which can be shortened to:</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
@@ -383,14 +390,14 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 
 <span class='co'># Now let's see if first isolates matter:</span>
 <span class='no'>A</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</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://www.rdocumentation.org/packages/dplyr/topics/group_by'>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'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>),            <span class='co'># gentamicin availability</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>),            <span class='co'># gentamicin availability</span>
             <span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>))  <span class='co'># gentamicin resistance</span>
 
 <span class='no'>B</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
   <span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%&gt;%</span>       <span class='co'># the 1st isolate filter</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://www.rdocumentation.org/packages/dplyr/topics/group_by'>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'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>),            <span class='co'># gentamicin availability</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>),            <span class='co'># gentamicin availability</span>
             <span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>))  <span class='co'># gentamicin resistance</span>
 
 <span class='co'># Have a look at A and B.</span>

docs/reference/freq.html

@@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
       </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="Released version">0.5.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -117,6 +117,13 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -385,8 +392,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 
 <span class='co'># you could also use `select` or `pull` to get your variables</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'>freq</span>()
 
 
@@ -402,20 +409,20 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 
 <span class='co'># group a variable and analyse another</span>
 <span class='no'>septic_patients</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://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'>freq</span>(<span class='no'>gender</span>)
 
 
 <span class='co'># get top 10 bugs of hospital A as a vector</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>hospital_id</span> <span class='kw'>==</span> <span class='st'>"A"</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'>freq</span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'>top_freq</span>(<span class='fl'>10</span>)
 
 
 <span class='co'># save frequency table to an object</span>
 <span class='no'>years</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%&gt;%</span>
   <span class='fu'>freq</span>(<span class='no'>year</span>)
 
 
@@ -466,11 +473,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 <span class='co'># only get selected columns</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
   <span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</span>)
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>item</span>, <span class='no'>percent</span>)
 
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
   <span class='fu'>freq</span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(-<span class='no'>count</span>, -<span class='no'>cum_count</span>)
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(-<span class='no'>count</span>, -<span class='no'>cum_count</span>)
 
 
 <span class='co'># check differences between frequency tables</span>

docs/reference/g.test.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/get_locale.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/ggplot_rsi.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -223,7 +230,7 @@
 
     <div class="ref-description">
     
-    <p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> functions.</p>
+    <p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code> functions.</p>
     
     </div>
 
@@ -314,7 +321,7 @@
     <p>At default, the names of antibiotics will be shown on the plots using <code><a href='abname.html'>abname</a></code>. This can be set with the option <code>get_antibiotic_names</code> (a logical value), so change it e.g. to <code>FALSE</code> with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>options(get_antibiotic_names = FALSE)</a></code>.</p>
 <p><strong>The functions</strong><br />
 <code>geom_rsi</code> will take any variable from the data that has an <code>rsi</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) using <code>fun</code> (<code><a href='count.html'>count_df</a></code> at default, can also be <code><a href='portion.html'>portion_df</a></code>) and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
-<p><code>facet_rsi</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://ggplot2.tidyverse.org/reference/facet_wrap.html'>facet_wrap</a></code>.</p>
+<p><code>facet_rsi</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/facet_wrap'>facet_wrap</a></code>.</p>
 <p><code>scale_y_percent</code> transforms the y axis to a 0 to 100% range using <code>scale_continuous</code>.</p>
 <p><code>scale_rsi_colours</code> sets colours to the bars: green for S, yellow for I and red for R, using <code>scale_brewer</code>.</p>
 <p><code>theme_rsi</code> is a <code>ggplot <a href='https://ggplot2.tidyverse.org/reference/theme.html'>theme</a></code> with minimal distraction.</p>
@@ -334,12 +341,12 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>ggplot2</span>)
 
 <span class='co'># get antimicrobial results for drugs against a UTI:</span>
-<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>)) +
+<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>)) +
   <span class='fu'>geom_rsi</span>()
 
 <span class='co'># prettify the plot using some additional functions:</span>
 <span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span>[, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"amox"</span>, <span class='st'>"nitr"</span>, <span class='st'>"fosf"</span>, <span class='st'>"trim"</span>, <span class='st'>"cipr"</span>)]
-<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>df</span>) +
+<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>df</span>) +
   <span class='fu'>geom_rsi</span>() +
   <span class='fu'>scale_y_percent</span>() +
   <span class='fu'>scale_rsi_colours</span>() +
@@ -348,17 +355,17 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 
 <span class='co'># or better yet, simplify this using the wrapper function - a single command:</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'>ggplot_rsi</span>()
 
 <span class='co'># get only portions and no counts:</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'>ggplot_rsi</span>(<span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>portion_df</span>)
 
 <span class='co'># add other ggplot2 parameters as you like:</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'>ggplot_rsi</span>(<span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
              <span class='kw'>colour</span> <span class='kw'>=</span> <span class='st'>"black"</span>,
              <span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>1</span>,
@@ -367,56 +374,56 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 
 <span class='co'># resistance of ciprofloxacine per age group</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</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='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
          <span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
   <span class='co'># `age_group` is also a function of this package:</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'><a href='age_groups.html'>age_groups</a></span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'><a href='age_groups.html'>age_groups</a></span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>age_group</span>,
          <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
 <span class='co'># }</span><span class='co'># NOT RUN {</span>
 <span class='co'># for colourblind mode, use divergent colours from the viridis package:</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'>ggplot_rsi</span>() + <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_fill_viridis_d</a></span>()
+  <span class='fu'>ggplot_rsi</span>() + <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/scale_viridis'>scale_fill_viridis_d</a></span>()
 
 
 <span class='co'># it also supports groups (don't forget to use the group var on `x` or `facet`):</span>
 <span class='no'>septic_patients</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'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</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://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>hospital_id</span>,
              <span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>,
              <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>) +
-  <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/labs'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
        <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Hospital"</span>)
 
 <span class='co'># genuine analysis: check 2 most prevalent microorganisms</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
   <span class='co'># create new bacterial ID's, with all CoNS under the same group (Becker et al.)</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
   <span class='co'># filter on top three bacterial ID's</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>%in%</span> <span class='fu'><a href='freq.html'>top_freq</a></span>(<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>.</span>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>%in%</span> <span class='fu'><a href='freq.html'>top_freq</a></span>(<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>.</span>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%&gt;%</span>
   <span class='co'># determine first isolates</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>,
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>,
                                        <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
                                        <span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>,
                                        <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</span>)) <span class='kw'>%&gt;%</span>
   <span class='co'># filter on first isolates</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='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%&gt;%</span>
   <span class='co'># get short MO names (like "E. coli")</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
   <span class='co'># select this short name and some antiseptic drugs</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='no'>cfur</span>, <span class='no'>gent</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>mo</span>, <span class='no'>cfur</span>, <span class='no'>gent</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
   <span class='co'># group by MO</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>mo</span>) <span class='kw'>%&gt;%</span>
   <span class='co'># plot the thing, putting MOs on the facet</span>
   <span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>,
              <span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>mo</span>,
              <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
              <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>) +
-  <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Top Three Microorganisms In Blood Culture Isolates"</span>,
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/labs'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Top Three Microorganisms In Blood Culture Isolates"</span>,
        <span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='st'>"Only First Isolates, CoNS grouped according to Becker et al. (2014)"</span>,
        <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Microorganisms"</span>)
 <span class='co'># }</span></pre>

docs/reference/guess_ab_col.html

@@ -47,7 +47,7 @@
   <script src="../extra.js"></script>
 <meta property="og:title" content="Guess antibiotic column — guess_ab_col" />
 
-<meta property="og:description" content="This tries to find a column name in a data set based on information from the antibiotics data set. You can look for an antibiotic (trade) name or abbreviation and it will search the data.frame for any column containing a name or ATC code of that antibiotic." />
+<meta property="og:description" content="This tries to find a column name in a data set based on information from the antibiotics data set. Also supports WHONET abbreviations. You can look for an antibiotic (trade) name or abbreviation and it will search the data.frame for any column containing a name or ATC code of that antibiotic." />
 
 <meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
 <meta name="twitter:card" content="summary" />
@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -223,7 +230,7 @@
 
     <div class="ref-description">
     
-    <p>This tries to find a column name in a data set based on information from the <code><a href='antibiotics.html'>antibiotics</a></code> data set. You can look for an antibiotic (trade) name or abbreviation and it will search the <code>data.frame</code> for any column containing a name or ATC code of that antibiotic.</p>
+    <p>This tries to find a column name in a data set based on information from the <code><a href='antibiotics.html'>antibiotics</a></code> data set. Also supports WHONET abbreviations. You can look for an antibiotic (trade) name or abbreviation and it will search the <code>data.frame</code> for any column containing a name or ATC code of that antibiotic.</p>
     
     </div>
 
@@ -266,6 +273,16 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 <span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"J01AA07"</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 <span class='co'># using column `tetr` for col "J01AA07"</span>
 <span class='co'># [1] "tetr"</span>
+
+<span class='co'># WHONET codes</span>
+<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>AMP_ND10</span> <span class='kw'>=</span> <span class='st'>"R"</span>,
+                 <span class='kw'>AMC_ED20</span> <span class='kw'>=</span> <span class='st'>"S"</span>)
+<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"ampicillin"</span>)
+<span class='co'># [1] "AMP_ND10"</span>
+<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"J01CR02"</span>)
+<span class='co'># [1] "AMC_ED20"</span>
+<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='fu'><a href='as.atc.html'>as.atc</a></span>(<span class='st'>"augmentin"</span>))
+<span class='co'># [1] "AMC_ED20"</span>
 <span class='co'># }</span></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

docs/reference/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -114,6 +114,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/join.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/key_antibiotics.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -334,8 +341,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='co'># set key antibiotics to a new variable</span>
 <span class='no'>my_patients</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>keyab</span> <span class='kw'>=</span> <span class='fu'>key_antibiotics</span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>keyab</span> <span class='kw'>=</span> <span class='fu'>key_antibiotics</span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(
     <span class='co'># now calculate first isolates</span>
     <span class='kw'>first_regular</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
     <span class='co'># and first WEIGHTED isolates</span>

docs/reference/kurtosis.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/like.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -295,7 +302,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='join.html'>left_join_microorganisms</a></span>() <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)
 <span class='co'># }</span></pre>
   </div>

docs/reference/mdro.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -618,7 +625,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
 
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>EUCAST</span> <span class='kw'>=</span> <span class='fu'>mdro</span>(<span class='no'>.</span>),
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>EUCAST</span> <span class='kw'>=</span> <span class='fu'>mdro</span>(<span class='no'>.</span>),
          <span class='kw'>BRMO</span> <span class='kw'>=</span> <span class='fu'>brmo</span>(<span class='no'>.</span>))
 <span class='co'># }</span></pre>
   </div>

docs/reference/microorganisms.codes.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/microorganisms.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/microorganisms.old.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/mo_failures.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/mo_property.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/mo_renamed.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/mo_source.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/p.symbol.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/portion.html

@@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -117,6 +117,13 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -340,17 +347,17 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_SI</span>(<span class='no'>amox</span>)
 
 <span class='no'>septic_patients</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://www.rdocumentation.org/packages/dplyr/topics/group_by'>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_S</span>(<span class='no'>cipr</span>),
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>),
             <span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>)) <span class='co'># n_rsi works like n_distinct in dplyr</span>
 
 <span class='no'>septic_patients</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://www.rdocumentation.org/packages/dplyr/topics/group_by'>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'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>portion_R</span>(<span class='no'>cipr</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'>cipr</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'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
             <span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>), <span class='co'># works like n_distinct in dplyr</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 amount of tested isolates!</span>
+            <span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/n'>n</a></span>())     <span class='co'># NOT the amount 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>
@@ -365,8 +372,8 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 
 
 <span class='no'>septic_patients</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://www.rdocumentation.org/packages/dplyr/topics/group_by'>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_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>summarise</a></span>(<span class='kw'>cipro_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</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'>cipr</span>),
             <span class='kw'>genta_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>gent</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'>gent</span>),
@@ -375,22 +382,22 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 
 <span class='co'># Get portions S/I/R immediately of all rsi columns</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</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'>septic_patients</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'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</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://www.rdocumentation.org/packages/dplyr/topics/group_by'>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='co'># }</span><span class='co'># NOT RUN {</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='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>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'>amox</span>, <span class='no'>metr</span>),  <span class='co'># amoxicillin with metronidazole</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>amox</span>, <span class='no'>metr</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'>amox</span>, <span class='no'>metr</span>))
 <span class='co'># }</span></pre>
   </div>

docs/reference/read.4D.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/resistance_predict.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>
@@ -341,7 +348,7 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'>resistance_predict</span>(<span class='st'>"peni"</span>)
 <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>x</span>)
 
@@ -350,27 +357,27 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
 <span class='kw'>if</span> (!<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>require</a></span>(<span class='no'>ggplot2</span>)) {
 
   <span class='no'>data</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
-    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
+    <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
     <span class='fu'>resistance_predict</span>(<span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"amox"</span>,
                        <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
                        <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
                        <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>15</span>)
 
-  <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>data</span>,
+  <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>data</span>,
-         <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>year</span>)) +
+         <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/aes'>aes</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>year</span>)) +
-    <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_bar.html'>geom_col</a></span>(<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(<span class='kw'>y</span> <span class='kw'>=</span> <span class='no'>value</span>),
+    <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/geom_bar'>geom_col</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/aes'>aes</a></span>(<span class='kw'>y</span> <span class='kw'>=</span> <span class='no'>value</span>),
              <span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"grey75"</span>) +
-    <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_linerange.html'>geom_errorbar</a></span>(<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(<span class='kw'>ymin</span> <span class='kw'>=</span> <span class='no'>se_min</span>,
+    <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/geom_linerange'>geom_errorbar</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/aes'>aes</a></span>(<span class='kw'>ymin</span> <span class='kw'>=</span> <span class='no'>se_min</span>,
                       <span class='kw'>ymax</span> <span class='kw'>=</span> <span class='no'>se_max</span>),
                   <span class='kw'>colour</span> <span class='kw'>=</span> <span class='st'>"grey50"</span>) +
-    <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_continuous.html'>scale_y_continuous</a></span>(<span class='kw'>limits</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>),
+    <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/scale_continuous'>scale_y_continuous</a></span>(<span class='kw'>limits</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>),
                        <span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
                        <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste0</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>, <span class='fl'>10</span>), <span class='st'>"%"</span>)) +
-    <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/expression'>expression</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Forecast of amoxicillin resistance in "</span>,
+    <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/labs'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/expression'>expression</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Forecast of amoxicillin resistance in "</span>,
                                   <span class='fu'><a href='https://www.rdocumentation.org/packages/grDevices/topics/plotmath'>italic</a></span>(<span class='st'>"E. coli"</span>))),
          <span class='kw'>y</span> <span class='kw'>=</span> <span class='st'>"%IR"</span>,
          <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Year"</span>) +
-    <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggtheme.html'>theme_minimal</a></span>(<span class='kw'>base_size</span> <span class='kw'>=</span> <span class='fl'>13</span>)
+    <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggtheme'>theme_minimal</a></span>(<span class='kw'>base_size</span> <span class='kw'>=</span> <span class='fl'>13</span>)
 }
 <span class='co'># }</span></pre>
   </div>

docs/reference/rsi.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/septic_patients.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/skewness.html

@@ -81,7 +81,7 @@ 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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -117,6 +117,13 @@ When negative: the left tail is longer; the mass of the distribution is concentr
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/reference/supplementary_data.html

@@ -80,7 +80,7 @@
       </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="Released version">0.5.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
       </span>
     </div>
 
@@ -116,6 +116,13 @@
         Predict antimicrobial resistance
       </a>
     </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
     <li>
       <a href="../articles/EUCAST.html">
         <span class="fa fa-exchange-alt"></span>

docs/sitemap.xml

@@ -141,6 +141,9 @@
   <url>
     <loc>https://msberends.gitlab.io/AMR/articles/Predict.html</loc>
   </url>
+  <url>
+    <loc>https://msberends.gitlab.io/AMR/articles/WHONET.html</loc>
+  </url>
   <url>
     <loc>https://msberends.gitlab.io/AMR/articles/ab_property.html</loc>
   </url>

index.md

@@ -4,7 +4,7 @@
 
 ----
 
-`AMR` is a free and open-source [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods.
+`AMR` is a free and open-source [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods. It supports any table format, including WHONET/EARS-Net data.
 
 We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).
 This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but **not** patent) purposes under the terms of the GNU General Public Licence version 2.0 (GPL-2), as published by the Free Software Foundation. Read the full licence [here](./LICENSE-text.html).
@@ -48,7 +48,7 @@ Developers
   * Software developers
   * Web application / Shiny developers
 
-### Get this package
+## Get this package
 
 This package is available on the official R network (CRAN), which has a peer-reviewed submission process. Install this package in R with:
 
@@ -58,11 +58,34 @@ install.packages("AMR")
 
 It will be downloaded and installed automatically. For RStudio, click on the menu *Tools* > *Install Packages...* and then type in "AMR" and press <kbd>Install</kbd>.
 
-### Get started
+
+The latest and unpublished development version can be installed with (precaution: may be unstable):
+```r
+install.packages("devtools")
+devtools::install_gitlab("msberends/AMR")
+```
+
+## Get started
 
 To find out how to conduct AMR analysis, please [continue reading here to get started](./articles/AMR.html) or click the links in the 'How to' menu.
 
-### Short introduction
+## Short introduction
+
+#### WHONET / EARS-Net
+
+<img src="./whonet.png">
+
+We support data (exported files) from WHONET. The `AMR` package contains a data set `antibiotics` which also contains all EARS-Net antibiotic abbreviations. Furthermore, when using WHONET data as input for analysis all input parameters will be set automatically.
+
+Read our tutorial about [how to work with WHONET data here](./articles/WHONET.html).
+
+#### Antimicrobial reference data
+
+<div><img src="reference/figures/logo_who.png" height="75px" class="logo_img"><p class="logo_txt">WHO Collaborating Centre for Drug Statistics Methodology</p></div>
+
+This package contains **all ~500 antimicrobial drugs** 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, https://www.whocc.no) and the [Pharmaceuticals Community Register of the European Commission](http://ec.europa.eu/health/documents/community-register/html/atc.htm).
+
+Read more about the data from WHOCC [in our manual](./reference/WHOCC.html).
 
 #### Microbial (taxonomic) reference data
 
@@ -74,14 +97,6 @@ All ~20,000 (sub)species from **the taxonomic kingdoms Bacteria, Fungi and Proto
 
 Read more about the data from ITIS [in our manual](./reference/ITIS.html).
 
-#### Antimicrobial reference data
-
-<div><img src="reference/figures/logo_who.png" height="75px" class="logo_img"><p class="logo_txt">WHO Collaborating Centre for Drug Statistics Methodology</p></div>
-
-This package contains **all ~500 antimicrobial drugs** 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, https://www.whocc.no) and the [Pharmaceuticals Community Register of the European Commission](http://ec.europa.eu/health/documents/community-register/html/atc.htm).
-
-Read more about the data from WHOCC [in our manual](./reference/WHOCC.html).
-
 #### Overview of functions
 
 The `AMR` package basically does four important things:

man/antibiotics.Rd

@@ -4,9 +4,10 @@
 \name{antibiotics}
 \alias{antibiotics}
 \title{Data set with ~500 antibiotics}
-\format{A \code{\link{data.frame}} with 488 observations and 16 variables:
+\format{A \code{\link{data.frame}} with 488 observations and 17 variables:
 \describe{
-  \item{\code{atc}}{ATC code, like \code{J01CR02}}
+  \item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical), like \code{J01CR02}}
+  \item{\code{ears_net}}{EARS-Net code (European Antimicrobial Resistance Surveillance Network), like \code{AMC}}
   \item{\code{certe}}{Certe code, like \code{amcl}}
   \item{\code{umcg}}{UMCG code, like \code{AMCL}}
   \item{\code{abbr}}{Abbreviation as used by many countries, used internally by \code{\link{as.atc}}}
@@ -26,6 +27,8 @@
 \source{
 - World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
 
+Table antibiotic coding EARSS (from WHONET 5.3): \url{http://www.madsonline.dk/Tutorials/landskoder_antibiotika_WM.pdf}
+
 EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016: \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
 
 European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}

man/guess_ab_col.Rd

@@ -14,7 +14,7 @@ guess_ab_col(tbl = NULL, col = NULL, verbose = FALSE)
 \item{verbose}{a logical to indicate whether additional info should be printed}
 }
 \description{
-This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. You can look for an antibiotic (trade) name or abbreviation and it will search the \code{data.frame} for any column containing a name or ATC code of that antibiotic.
+This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. Also supports WHONET abbreviations. You can look for an antibiotic (trade) name or abbreviation and it will search the \code{data.frame} for any column containing a name or ATC code of that antibiotic.
 }
 \section{Read more on our website!}{
 
@@ -34,4 +34,14 @@ guess_ab_col(df, "J01AA07") # ATC code of Tetracycline
 guess_ab_col(df, "J01AA07", verbose = TRUE)
 # using column `tetr` for col "J01AA07"
 # [1] "tetr"
+
+# WHONET codes
+df <- data.frame(AMP_ND10 = "R",
+                 AMC_ED20 = "S")
+guess_ab_col(df, "ampicillin")
+# [1] "AMP_ND10"
+guess_ab_col(df, "J01CR02")
+# [1] "AMC_ED20"
+guess_ab_col(df, as.atc("augmentin"))
+# [1] "AMC_ED20"
 }

tests/testthat/test-atc.R

@@ -22,7 +22,7 @@
 context("atc.R")
 
 test_that("as.atc works", {
-  expect_equal(suppressWarnings(as.character(guess_atc(c("J01FA01",
+  expect_equal(suppressWarnings(as.character(as.atc(c("J01FA01",
                                                          "Erythromycin",
                                                          "eryt",
                                                          "ERYT",
@@ -45,4 +45,8 @@ test_that("as.atc works", {
   expect_equal(as.character(as.atc(c("nitro", "cipro"))),
                c("J01XE01", "J01MA02"))
 
+  # EARS-Net
+  expect_equal(as.character(as.atc("AMX")),
+               "J01CA04")
+
 })

tests/testthat/test-first_isolate.R

@@ -160,7 +160,7 @@ test_that("first isolates work", {
 
   # look for columns itself
   expect_message(first_isolate(septic_patients))
-  expect_error(first_isolate(septic_patients %>%
+  expect_message(first_isolate(septic_patients %>%
                                mutate(mo = as.character(mo)) %>%
                                left_join_microorganisms()))
 

tests/testthat/test-guess_ab_col.R

@@ -33,4 +33,13 @@ test_that("guess_ab_col works", {
                "tetr")
   expect_equal(guess_ab_col(septic_patients, "TETR"),
                "tetr")
+
+  df <- data.frame(AMP_ND10 = "R",
+                   AMC_ED20 = "S")
+  expect_equal(guess_ab_col(df, "ampicillin"),
+               "AMP_ND10")
+  expect_equal(guess_ab_col(df, "J01CR02"),
+               "AMC_ED20")
+  expect_equal(guess_ab_col(df, as.atc("augmentin")),
+               "AMC_ED20")
 })

vignettes/WHONET.Rmd

@@ -0,0 +1,26 @@
+---
+title: "How to work with WHONET data"
+author: "Matthijs S. Berends"
+date: '`r format(Sys.Date(), "%d %B %Y")`'
+output:
+  rmarkdown::html_vignette:
+    toc: true
+    toc_depth: 3
+vignette: >
+  %\VignetteIndexEntry{How to work with WHONET data}
+  %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{knitr::rmarkdown}
+editor_options:
+  chunk_output_type: console
+---
+
+```{r setup, include = FALSE, results = 'markup'}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#",
+  fig.width = 7.5,
+  fig.height = 4.5
+)
+```
+
+*(will be available soon)*