(v0.7.0.9010) mo_synonyms, plot/barplot fixes

.gitlab-ci.yml

@@ -20,7 +20,7 @@
 # ==================================================================== #
 
 # to check with R-Hub:
-# rhub::check_for_cran(devtools::build(args = c('--no-build-vignettes')))
+# chck <- rhub::check_for_cran(devtools::build(args = c('--no-build-vignettes')))
 
 stages:
   - build
@@ -124,18 +124,10 @@ coverage:
 pages:
   stage: deploy
   when: always
-  #cache:
-  #  key: "$CI_COMMIT_REF_SLUG"
-   # paths:
-    #  - installed_deps/
   only:
     - master
   script:
     - mv docs public
-    # install missing and outdated packages
-    #- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
-    #- Rscript -e "devtools::install(build = TRUE, upgrade = FALSE)"
-    #- R -e "pkgdown::build_site(examples = FALSE, lazy = TRUE, override = list(destination = 'public'))"
   artifacts:
     paths:
       - public

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.7.0.9009
+Version: 0.7.0.9010
-Date: 2019-06-13
+Date: 2019-06-16
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(

NAMESPACE

@@ -154,6 +154,7 @@ export(mo_renamed)
 export(mo_shortname)
 export(mo_species)
 export(mo_subspecies)
+export(mo_synonyms)
 export(mo_taxonomy)
 export(mo_type)
 export(mo_uncertainties)

NEWS.md

@@ -1,7 +1,7 @@
-# AMR 0.7.0.9009
+# AMR 0.7.0.9010
 
 #### New
-* Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combinations of existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:
+* Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:
   ```r
   septic_patients %>%
     select(AMX, CIP) %>%
@@ -12,14 +12,31 @@
   # 3 Ciprofloxacin              SI  0.8381831      1181
   # 4 Ciprofloxacin               R  0.1618169       228
   ```
-* Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*:
+* Support for all scientifically published pathotypes of *E. coli* to date. Supported are: 
+
+  * AIEC (Adherent-Invasive *E. coli*) 
+  * ATEC (Atypical Entero-pathogenic *E. coli*) 
+  * DAEC (Diffusely Adhering *E. coli*) 
+  * EAEC (Entero-Aggresive *E. coli*) 
+  * EHEC (Entero-Haemorrhagic *E. coli*) 
+  * EIEC (Entero-Invasive *E. coli*) 
+  * EPEC (Entero-Pathogenic *E. coli*) 
+  * ETEC (Entero-Toxigenic *E. coli*) 
+  * NMEC (Neonatal Meningitis‐causing *E. coli*) 
+  * STEC (Shiga-toxin producing *E. coli*) 
+  * UPEC (Uropathogenic *E. coli*)
+  
+  All these lead to the microbial ID of *E. coli*:
   ```r
   as.mo("UPEC")
   # B_ESCHR_COL
-  mo_fullname("UPEC")
+  mo_name("UPEC")
   # "Escherichia coli"
+  mo_gramstain("EHEC")
+  # "Gram-negative"
   ```
 * Function `mo_info()` as an analogy to `ab_info()`. The `mo_info()` prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism
+* Function `mo_synonyms()` to get all previously accepted taxonomic names of a microorganism
 
 #### Changed
 * Column names of output `count_df()` and `portion_df()` are now lowercase
@@ -36,6 +53,7 @@
 * Removed antibiotic code `PVM1` from the `antibiotics` data set as this was a duplicate of `PME`
 * Fixed bug where not all old taxonomic named would not be printed when using a vector as input for `as.mo()`
 * Manually added *Trichomonas vaginalis* from the kingdom of Protozoa, which is missing from the Catalogue of Life
+* Small improvements to `plot()` and `barplot()` for MIC and RSI classes
 
 #### Other
 * Fixed a note thrown by CRAN tests

R/count.R

@@ -33,7 +33,7 @@
 #'
 #' The function \code{count_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and counts the amounts of S, I and R. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.
 #'
-#' The function \code{rsi_df} works exactly like \code{count_df}, but add the percentage of S, I and R.
+#' The function \code{rsi_df} works exactly like \code{count_df}, but adds the percentage of S, I and R.
 #' @source Wickham H. \strong{Tidy Data.} The Journal of Statistical Software, vol. 59, 2014. \url{http://vita.had.co.nz/papers/tidy-data.html}
 #' @seealso \code{\link{portion}_*} to calculate microbial resistance and susceptibility.
 #' @keywords resistance susceptibility rsi antibiotics isolate isolates

R/mic.R

@@ -242,34 +242,38 @@ summary.mic <- function(object, ...) {
 
 #' @exportMethod plot.mic
 #' @export
-#' @importFrom dplyr %>% group_by summarise
+#' @importFrom graphics barplot axis
-#' @importFrom graphics plot text
 #' @noRd
-plot.mic <- function(x, ...) {
+plot.mic <- function(x,
-  x_name <- deparse(substitute(x))
+                     main = paste('MIC values of', deparse(substitute(x))),
-  create_barplot_mic(x, x_name, ...)
+                     ylab = 'Frequency',
+                     xlab = 'MIC value',
+                     axes = FALSE,
+                     ...) {
+  barplot(table(droplevels.factor(x)),
+          ylab = ylab,
+          xlab = xlab,
+          axes = axes,
+          main = main,
+          ...)
+  axis(2, seq(0, max(table(droplevels.factor(x)))))
 }
 
 #' @exportMethod barplot.mic
 #' @export
 #' @importFrom graphics barplot axis
 #' @noRd
-barplot.mic <- function(height, ...) {
+barplot.mic <- function(height,
-  x_name <- deparse(substitute(height))
+                        main = paste('MIC values of', deparse(substitute(height))),
-  create_barplot_mic(height, x_name, ...)
-}
-
-#' @importFrom graphics barplot axis
-#' @importFrom dplyr %>% group_by summarise
-create_barplot_mic <- function(x, x_name, ...) {
-  data <- data.frame(mic = droplevels(x), cnt = 1) %>%
-    group_by(mic) %>%
-    summarise(cnt = sum(cnt))
-  barplot(table(droplevels.factor(x)),
                         ylab = 'Frequency',
                         xlab = 'MIC value',
-          main = paste('MIC values of', x_name),
                         axes = FALSE,
+                        ...) {
+  barplot(table(droplevels.factor(height)),
+          ylab = ylab,
+          xlab = xlab,
+          axes = axes,
+          main = main,
           ...)
-  axis(2, seq(0, max(data$cnt)))
+  axis(2, seq(0, max(table(droplevels.factor(height)))))
 }

R/misc.R

@@ -307,5 +307,14 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
 }
 
 "%or%" <- function(x, y) {
-  ifelse(!is.na(x), x, ifelse(!is.na(y), y, NA))
+  if (is.null(x) | is.null(y)) {
+    if (is.null(x)) {
+      return(y)
+    } else {
+      return(x)
+    }
+  }
+  ifelse(!is.na(x),
+         x,
+         ifelse(!is.na(y), y, NA))
 }

R/mo_property.R

@@ -73,6 +73,7 @@
 #' mo_type("E. coli")            # "Bacteria" (equal to kingdom, but may be translated)
 #' mo_rank("E. coli")            # "species"
 #' mo_url("E. coli")             # get the direct url to the online database entry
+#' mo_synonyms("E. coli")        # get previously accepted taxonomic names
 #'
 #' ## scientific reference
 #' mo_ref("E. coli")             # "Castellani et al., 1919"
@@ -312,12 +313,24 @@ mo_taxonomy <- function(x, language = get_locale(),  ...) {
              subspecies = mo_subspecies(x, language = language))
 }
 
+#' @rdname mo_property
+#' @export
+mo_synonyms <- function(x, ...) {
+  x <- AMR::as.mo(x, ...)
+  col_id <- AMR::microorganisms[which(AMR::microorganisms$mo == x), "col_id"]
+  if (is.na(col_id) | !col_id %in% AMR::microorganisms.old$col_id_new) {
+    return(NULL)
+  }
+  sort(AMR::microorganisms.old[which(AMR::microorganisms.old$col_id_new == col_id), "fullname"])
+}
+
 #' @rdname mo_property
 #' @export
 mo_info <- function(x, language = get_locale(),  ...) {
   x <- AMR::as.mo(x, ...)
   c(mo_taxonomy(x, language = language),
-    list(url = unname(mo_url(x, open = FALSE)),
+    list(synonyms = mo_synonyms(x),
+         url = unname(mo_url(x, open = FALSE)),
          ref = mo_ref(x)))
 }
 

R/portion.R

@@ -40,7 +40,7 @@
 #'
 #' The function \code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each group and each variable with class \code{"rsi"}.
 #'
-#' The function \code{rsi_df} works exactly like \code{portion_df}, but add the number of isolates.
+#' The function \code{rsi_df} works exactly like \code{portion_df}, but adds the number of isolates.
 #' \if{html}{
 #    (created with https://www.latex4technics.com/)
 #'   \cr\cr

R/rsi.R

@@ -387,9 +387,14 @@ summary.rsi <- function(object, ...) {
 #' @importFrom dplyr %>% group_by summarise filter mutate if_else n_distinct
 #' @importFrom graphics plot text
 #' @noRd
-plot.rsi <- function(x, ...) {
+plot.rsi <- function(x,
-  x_name <- deparse(substitute(x))
+                     lwd = 2,
-
+                     ylim = NULL,
+                     ylab = 'Percentage',
+                     xlab = 'Antimicrobial Interpretation',
+                     main = paste('Susceptibility Analysis of', deparse(substitute(x))),
+                     axes = FALSE,
+                     ...) {
   suppressWarnings(
     data <- data.frame(x = x,
                        y = 1,
@@ -415,13 +420,12 @@ plot.rsi <- function(x, ...) {
 
   plot(x = data$x,
        y = data$s,
-       lwd = 2,
+       lwd = lwd,
-       col = c('green', 'orange', 'red'),
        ylim = c(0, ymax),
-       ylab = 'Percentage',
+       ylab = ylab,
-       xlab = 'Antimicrobial Interpretation',
+       xlab = xlab,
-       main = paste('Susceptibility Analysis of', x_name),
+       main = main,
-       axes = FALSE,
+       axes = axes,
        ...)
   # x axis
   axis(side = 1, at = 1:n_distinct(data$x), labels = levels(data$x), lwd = 0)
@@ -439,24 +443,32 @@ plot.rsi <- function(x, ...) {
 #' @importFrom dplyr %>% group_by summarise
 #' @importFrom graphics barplot axis
 #' @noRd
-barplot.rsi <- function(height, ...) {
+barplot.rsi <- function(height,
-  x <- height
-  x_name <- deparse(substitute(height))
-
-  suppressWarnings(
-    data <- data.frame(rsi = x, cnt = 1) %>%
-      group_by(rsi) %>%
-      summarise(cnt = sum(cnt)) %>%
-      droplevels()
-  )
-
-  barplot(table(x),
                         col = c('green3', 'orange2', 'red3'),
-          xlab = 'Antimicrobial Interpretation',
+                        xlab = ifelse(beside, 'Antimicrobial Interpretation', ''),
-          main = paste('Susceptibility Analysis of', x_name),
+                        main = paste('Susceptibility Analysis of', deparse(substitute(height))),
                         ylab = 'Frequency',
+                        beside = TRUE,
+                        axes = beside,
+                        ...) {
+
+  if (axes == TRUE) {
+    par(mar =  c(5, 4, 4, 2) + 0.1)
+  } else {
+    par(mar =  c(2, 4, 4, 2) + 0.1)
+  }
+
+  barplot(as.matrix(table(height)),
+          col = col,
+          xlab = xlab,
+          main = main,
+          ylab = ylab,
+          beside = beside,
           axes = FALSE,
           ...)
   # y axis, 0-100%
-  axis(side = 2, at = seq(0, max(data$cnt) + max(data$cnt) * 1.1, by = 25))
+  axis(side = 2, at = seq(0, max(table(height)) + max(table(height)) * 1.1, by = 25))
+  if (axes == TRUE && beside == TRUE) {
+    axis(side = 1, labels = levels(height), at = c(1, 2, 3) + 0.5, lwd = 0)
+  }
 }

docs/LICENSE-text.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
       </span>
     </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="Latest development version">0.7.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
       </span>
     </div>
 

docs/news/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
       </span>
     </div>
 
@@ -232,16 +232,16 @@
       
     </div>
 
-    <div id="amr-0709009" class="section level1">
+    <div id="amr-0709010" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0709009" class="anchor"></a>AMR 0.7.0.9009<small> Unreleased </small>
+<a href="#amr-0709010" class="anchor"></a>AMR 0.7.0.9010<small> Unreleased </small>
 </h1>
 <div id="new" class="section level4">
 <h4 class="hasAnchor">
 <a href="#new" class="anchor"></a>New</h4>
 <ul>
 <li>
-<p>Function <code><a href="../reference/portion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combinations of existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/portion.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
+<p>Function <code><a href="../reference/portion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/portion.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
 <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb1-2" title="2"><span class="st">  </span><span class="kw">select</span>(AMX, CIP) <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb1-3" title="3"><span class="st">  </span><span class="kw"><a href="../reference/portion.html">rsi_df</a></span>()</a>
@@ -252,13 +252,30 @@
 <a class="sourceLine" id="cb1-8" title="8"><span class="co"># 4 Ciprofloxacin               R  0.1618169       228</span></a></code></pre></div>
 </li>
 <li>
-<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date. Supported are: AIEC (Adherent-Invasive <em>E. coli</em>), ATEC (Atypical Entero-pathogenic <em>E. coli</em>), DAEC (Diffusely Adhering <em>E. coli</em>), EAEC (Entero-Aggresive <em>E. coli</em>), EHEC (Entero-Haemorrhagic <em>E. coli</em>), EIEC (Entero-Invasive <em>E. coli</em>), EPEC (Entero-Pathogenic <em>E. coli</em>), ETEC (Entero-Toxigenic <em>E. coli</em>), NMEC (Neonatal Meningitis‐causing <em>E. coli</em>), STEC (Shiga-toxin producing <em>E. coli</em>) and UPEC (Uropathogenic <em>E. coli</em>). All these lead to the microbial ID of <em>E. coli</em>:</p>
+<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date. Supported are:</p>
+<ul>
+<li>AIEC (Adherent-Invasive <em>E. coli</em>)</li>
+<li>ATEC (Atypical Entero-pathogenic <em>E. coli</em>)</li>
+<li>DAEC (Diffusely Adhering <em>E. coli</em>)</li>
+<li>EAEC (Entero-Aggresive <em>E. coli</em>)</li>
+<li>EHEC (Entero-Haemorrhagic <em>E. coli</em>)</li>
+<li>EIEC (Entero-Invasive <em>E. coli</em>)</li>
+<li>EPEC (Entero-Pathogenic <em>E. coli</em>)</li>
+<li>ETEC (Entero-Toxigenic <em>E. coli</em>)</li>
+<li>NMEC (Neonatal Meningitis‐causing <em>E. coli</em>)</li>
+<li>STEC (Shiga-toxin producing <em>E. coli</em>)</li>
+<li>UPEC (Uropathogenic <em>E. coli</em>)</li>
+</ul>
+<p>All these lead to the microbial ID of <em>E. coli</em>:</p>
 <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)</a>
 <a class="sourceLine" id="cb2-2" title="2"><span class="co"># B_ESCHR_COL</span></a>
-<a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"UPEC"</span>)</a>
+<a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)</a>
-<a class="sourceLine" id="cb2-4" title="4"><span class="co"># "Escherichia coli"</span></a></code></pre></div>
+<a class="sourceLine" id="cb2-4" title="4"><span class="co"># "Escherichia coli"</span></a>
+<a class="sourceLine" id="cb2-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)</a>
+<a class="sourceLine" id="cb2-6" title="6"><span class="co"># "Gram-negative"</span></a></code></pre></div>
 </li>
-<li><p>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</p></li>
+<li>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</li>
+<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
 </ul>
 </div>
 <div id="changed" class="section level4">
@@ -283,6 +300,7 @@
 <li>Fixed bug where not all old taxonomic named would not be printed when using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code>
 </li>
 <li>Manually added <em>Trichomonas vaginalis</em> from the kingdom of Protozoa, which is missing from the Catalogue of Life</li>
+<li>Small improvements to <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> and <code><a href="https://www.rdocumentation.org/packages/graphics/topics/barplot">barplot()</a></code> for MIC and RSI classes</li>
 </ul>
 </div>
 <div id="other" class="section level4">
@@ -1121,7 +1139,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
     <div id="tocnav">
       <h2>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
-        <li><a href="#amr-0709009">0.7.0.9009</a></li>
+        <li><a href="#amr-0709010">0.7.0.9010</a></li>
         <li><a href="#amr-070">0.7.0</a></li>
         <li><a href="#amr-061">0.6.1</a></li>
         <li><a href="#amr-060">0.6.0</a></li>

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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/WHONET.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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/ab_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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

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="Latest development version">0.7.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 

docs/reference/as.ab.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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/as.disk.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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/availability.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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/catalogue_of_life.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="Latest development version">0.7.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 

docs/reference/catalogue_of_life_version.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="Latest development version">0.7.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 

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="Latest development version">0.7.0.9008</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 

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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/extended-functions.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">0.7.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/filter_ab_class.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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -166,13 +166,6 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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="Latest development version">0.7.0.9008</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 

docs/reference/guess_ab_col.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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
       </span>
     </div>
 
@@ -373,7 +373,7 @@
       </tr><tr>
         
         <td>
-          <p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
+          <p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
         </td>
         <td><p>Property of a microorganism</p></td>
       </tr><tr>

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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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="Latest development version">0.7.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 

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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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="Latest development version">0.7.0.9008</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 

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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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="Latest development version">0.7.0.9005</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9010</span>
       </span>
     </div>
 
@@ -277,6 +277,8 @@
 
 <span class='fu'>mo_taxonomy</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
 
+<span class='fu'>mo_synonyms</span>(<span class='no'>x</span>, <span class='no'>...</span>)
+
 <span class='fu'>mo_info</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
 
 <span class='fu'>mo_url</span>(<span class='no'>x</span>, <span class='kw'>open</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
@@ -377,6 +379,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 <span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>)            <span class='co'># "Bacteria" (equal to kingdom, but may be translated)</span>
 <span class='fu'>mo_rank</span>(<span class='st'>"E. coli"</span>)            <span class='co'># "species"</span>
 <span class='fu'>mo_url</span>(<span class='st'>"E. coli"</span>)             <span class='co'># get the direct url to the online database entry</span>
+<span class='fu'>mo_synonyms</span>(<span class='st'>"E. coli"</span>)        <span class='co'># get previously accepted taxonomic names</span>
 
 <span class='co'>## scientific reference</span>
 <span class='fu'>mo_ref</span>(<span class='st'>"E. coli"</span>)             <span class='co'># "Castellani et al., 1919"</span>

docs/reference/mo_source.html

@@ -81,7 +81,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -166,13 +166,6 @@ This is the fastest way to have your organisation (or analysis) specific codes p
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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="Latest development version">0.7.0.9008</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/rsi_translation.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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -166,13 +166,6 @@ When negative: the left tail is longer; the mass of the distribution is concentr
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/translate.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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9009</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

git_merge.sh

@@ -13,15 +13,15 @@
 git add .
 git commit -a -m "website update" --quiet
 git checkout master --quiet
-echo "changed branch to master"
+echo "• changed branch to master"
 # import everything from premaster
 git merge premaster --quiet
 # and send it to git
 git push --quiet
-echo "pushed changes to master"
+echo "• pushed changes to master"
 # return to premaster
 git checkout premaster --quiet
-echo "changed branch back to premaster"
+echo "• changed branch back to premaster"
 git status --short
 
 

man/count.Rd

@@ -62,7 +62,7 @@ The function \code{n_rsi} is an alias of \code{count_all}. They can be used to c
 
 The function \code{count_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and counts the amounts of S, I and R. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.
 
-The function \code{rsi_df} works exactly like \code{count_df}, but add the percentage of S, I and R.
+The function \code{rsi_df} works exactly like \code{count_df}, but adds the percentage of S, I and R.
 }
 \section{Interpretation of S, I and R}{
 

man/mo_property.Rd

@@ -20,6 +20,7 @@
 \alias{mo_year}
 \alias{mo_rank}
 \alias{mo_taxonomy}
+\alias{mo_synonyms}
 \alias{mo_info}
 \alias{mo_url}
 \title{Property of a microorganism}
@@ -60,6 +61,8 @@ mo_rank(x, ...)
 
 mo_taxonomy(x, language = get_locale(), ...)
 
+mo_synonyms(x, ...)
+
 mo_info(x, language = get_locale(), ...)
 
 mo_url(x, open = FALSE, ...)
@@ -147,6 +150,7 @@ mo_gramstain("E. coli")       # "Gram-negative"
 mo_type("E. coli")            # "Bacteria" (equal to kingdom, but may be translated)
 mo_rank("E. coli")            # "species"
 mo_url("E. coli")             # get the direct url to the online database entry
+mo_synonyms("E. coli")        # get previously accepted taxonomic names
 
 ## scientific reference
 mo_ref("E. coli")             # "Castellani et al., 1919"

man/portion.Rd

@@ -73,7 +73,7 @@ These functions are not meant to count isolates, but to calculate the portion of
 
 The function \code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each group and each variable with class \code{"rsi"}.
 
-The function \code{rsi_df} works exactly like \code{portion_df}, but add the number of isolates.
+The function \code{rsi_df} works exactly like \code{portion_df}, but adds the number of isolates.
 \if{html}{
   \cr\cr
   To calculate the probability (\emph{p}) of susceptibility of one antibiotic, we use this formula:

tests/testthat/test-mo_property.R

@@ -22,34 +22,37 @@
 context("mo_property.R")
 
 test_that("mo_property works", {
-  expect_equal(mo_kingdom("E. coli"), "Bacteria")
+  expect_equal(mo_kingdom("Escherichia coli"), "Bacteria")
-  expect_equal(mo_phylum("E. coli"), "Proteobacteria")
+  expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
-  expect_equal(mo_class("E. coli"), "Gammaproteobacteria")
+  expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
-  expect_equal(mo_order("E. coli"), "Enterobacteriales")
+  expect_equal(mo_order("Escherichia coli"), "Enterobacteriales")
-  expect_equal(mo_family("E. coli"), "Enterobacteriaceae")
+  expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
-  expect_equal(mo_genus("E. coli"), "Escherichia")
+  expect_equal(mo_genus("Escherichia coli"), "Escherichia")
-  expect_equal(mo_species("E. coli"), "coli")
+  expect_equal(mo_species("Escherichia coli"), "coli")
-  expect_equal(mo_subspecies("E. coli"), "")
+  expect_equal(mo_subspecies("Escherichia coli"), "")
-  expect_equal(mo_fullname("E. coli"), "Escherichia coli")
+  expect_equal(mo_fullname("Escherichia coli"), "Escherichia coli")
-  expect_equal(mo_name("E. coli"), "Escherichia coli")
+  expect_equal(mo_name("Escherichia coli"), "Escherichia coli")
-  expect_equal(mo_type("E. coli", language = "en"), "Bacteria")
+  expect_equal(mo_type("Escherichia coli", language = "en"), "Bacteria")
-  expect_equal(mo_gramstain("E. coli", language = "en"), "Gram-negative")
+  expect_equal(mo_gramstain("Escherichia coli", language = "en"), "Gram-negative")
-  expect_equal(class(mo_taxonomy("E. coli")), "list")
+  expect_equal(class(mo_taxonomy("Escherichia coli")), "list")
-  expect_equal(names(mo_taxonomy("E. coli")), c("kingdom", "phylum", "class", "order",
+  expect_equal(names(mo_taxonomy("Escherichia coli")), c("kingdom", "phylum", "class", "order",
                                                 "family", "genus", "species", "subspecies"))
-  expect_equal(names(mo_info("E. coli")), c("kingdom", "phylum", "class", "order",
+  expect_equal(mo_synonyms("Escherichia coli"), NULL)
+  expect_gt(length(mo_synonyms("C. albicans")), 1)
+  expect_equal(names(mo_info("Escherichia coli")), c("kingdom", "phylum", "class", "order",
                                             "family", "genus", "species", "subspecies",
-                                            "url", "ref"))
+                                            "synonyms", "url", "ref"))
 
-  expect_equal(mo_ref("E. coli"), "Castellani et al., 1919")
+  expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
-  expect_equal(mo_authors("E. coli"), "Castellani et al.")
+  expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
-  expect_equal(mo_year("E. coli"), 1919)
+  expect_equal(mo_year("Escherichia coli"), 1919)
 
-  expect_equal(mo_shortname("MRSA"), "S. aureus")
+  expect_equal(mo_shortname("Escherichia coli"), "E. coli")
-  expect_equal(mo_shortname("MRSA", Becker = TRUE), "S. aureus")
+  expect_equal(mo_shortname("Staphylococcus aureus"), "S. aureus")
-  expect_equal(mo_shortname("MRSA", Becker = "all", language = "en"), "CoPS")
+  expect_equal(mo_shortname("Staphylococcus aureus", Becker = TRUE), "S. aureus")
-  expect_equal(mo_shortname("S. agalac"), "S. agalactiae")
+  expect_equal(mo_shortname("Staphylococcus aureus", Becker = "all", language = "en"), "CoPS")
-  expect_equal(mo_shortname("S. agalac", Lancefield = TRUE), "GBS")
+  expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
+  expect_equal(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE), "GBS")
 
   expect_true(mo_url("Escherichia coli") %like% "www.catalogueoflife.org")
 
@@ -58,28 +61,28 @@ test_that("mo_property works", {
   expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
 
   # check languages
-  expect_equal(mo_type("E. coli", language = "de"), "Bakterien")
+  expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
-  expect_equal(mo_gramstain("E. coli", language = "nl"), "Gram-negatief")
+  expect_equal(mo_gramstain("Escherichia coli", language = "nl"), "Gram-negatief")
 
-  expect_output(print(mo_gramstain("E. coli", language = "en")))
+  expect_output(print(mo_gramstain("Escherichia coli", language = "en")))
-  expect_output(print(mo_gramstain("E. coli", language = "de")))
+  expect_output(print(mo_gramstain("Escherichia coli", language = "de")))
-  expect_output(print(mo_gramstain("E. coli", language = "nl")))
+  expect_output(print(mo_gramstain("Escherichia coli", language = "nl")))
-  expect_output(print(mo_gramstain("E. coli", language = "es")))
+  expect_output(print(mo_gramstain("Escherichia coli", language = "es")))
-  expect_output(print(mo_gramstain("E. coli", language = "pt")))
+  expect_output(print(mo_gramstain("Escherichia coli", language = "pt")))
-  expect_output(print(mo_gramstain("E. coli", language = "it")))
+  expect_output(print(mo_gramstain("Escherichia coli", language = "it")))
-  expect_output(print(mo_gramstain("E. coli", language = "fr")))
+  expect_output(print(mo_gramstain("Escherichia coli", language = "fr")))
 
-  expect_error(mo_gramstain("E. coli", language = "UNKNOWN"))
+  expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
 
   # manual property function
-  expect_error(mo_property("E. coli", property = c("tsn", "fullname")))
+  expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))
-  expect_error(mo_property("E. coli", property = "UNKNOWN"))
+  expect_error(mo_property("Escherichia coli", property = "UNKNOWN"))
-  expect_identical(mo_property("E. coli", property = "fullname"),
+  expect_identical(mo_property("Escherichia coli", property = "fullname"),
-                   mo_fullname("E. coli"))
+                   mo_fullname("Escherichia coli"))
-  expect_identical(mo_property("E. coli", property = "genus"),
+  expect_identical(mo_property("Escherichia coli", property = "genus"),
-                   mo_genus("E. coli"))
+                   mo_genus("Escherichia coli"))
-  expect_identical(mo_property("E. coli", property = "species"),
+  expect_identical(mo_property("Escherichia coli", property = "species"),
-                   mo_species("E. coli"))
+                   mo_species("Escherichia coli"))
 
   expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
   expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
@@ -87,14 +90,13 @@ test_that("mo_property works", {
 
   # outcome of mo_fullname must always return the fullname from the data set
   library(dplyr)
-  a <- microorganisms %>%
+  x <- microorganisms %>%
     transmute(mo,
               # fullname from the original data:
               f1 = fullname,
               # newly created fullname based on MO code:
               f2 = mo_fullname(mo, language = "en")) %>%
     filter(f1 != f2)
-
+  expect_equal(nrow(x), 0)
-  expect_equal(nrow(a), 0)
 
 })

vignettes/AMR.Rmd

@@ -78,7 +78,7 @@ patients_table <- data.frame(patient_id = patients,
 The first 135 patient IDs are now male, the other 125 are female.
 
 ## Dates
-Let's pretend that our data consists of blood cultures isolates from 1 January 2010 until 1 January 2018. 
+Let's pretend that our data consists of blood cultures isolates from between 1 January 2010 and 1 January 2018. 
 
 ```{r create dates}
 dates <- seq(as.Date("2010-01-01"), as.Date("2018-01-01"), by = "day")
@@ -131,7 +131,7 @@ Using the `left_join()` function from the `dplyr` package, we can 'map' the gend
 data <- data %>% left_join(patients_table)
 ```
 
-The resulting data set contains 5,000 blood culture isolates. With the `head()` function we can preview the first 6 values of this data set:
+The resulting data set contains `r format(nrow(data), big.mark = ",")` blood culture isolates. With the `head()` function we can preview the first 6 values of this data set:
 
 ```{r preview data set 1, eval = FALSE}
 head(data)
@@ -154,7 +154,7 @@ data %>% freq(gender) # this would be the same: freq(data$gender)
 data %>% freq(gender, markdown = FALSE, header = TRUE)
 ```
 
-So, we can draw at least two conclusions immediately. From a data scientist perspective, the data looks clean: only values `M` and `F`. From a researcher perspective: there are slightly more men. Nothing we didn't already know.
+So, we can draw at least two conclusions immediately. From a data scientists perspective, the data looks clean: only values `M` and `F`. From a researchers perspective: there are slightly more men. Nothing we didn't already know.
 
 The data is already quite clean, but we still need to transform some variables. The `bacteria` column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The `mutate()` function of the `dplyr` package makes this really easy:
 
@@ -219,7 +219,6 @@ data_1st <- data %>%
 ```
 
 ## First *weighted* isolates
-We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Imagine this data, sorted on date:
 
 ```{r, echo = FALSE, message = FALSE, warning = FALSE, results = 'asis'}
 weighted_df <- data %>%
@@ -232,7 +231,11 @@ weighted_df <- data %>%
   .[1:min(10, nrow(.)),] %>% 
   mutate(isolate = row_number()) %>% 
   select(isolate, everything())
+```
 
+We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient `r as.data.frame(weighted_df[1, 'patient_id'])`, sorted on date:
+
+```{r, echo = FALSE, message = FALSE, warning = FALSE, results = 'asis'}
 weighted_df %>% 
   knitr::kable(align = "c")
 ```
@@ -378,10 +381,10 @@ data_1st %>%
   summarise("1. Amoxi/clav" = portion_SI(AMC),
             "2. Gentamicin" = portion_SI(GEN),
             "3. Amoxi/clav + genta" = portion_SI(AMC, GEN)) %>% 
-  tidyr::gather("Antibiotic", "S", -genus) %>%
+  tidyr::gather("antibiotic", "S", -genus) %>%
   ggplot(aes(x = genus,
              y = S,
-             fill = Antibiotic)) +
+             fill = antibiotic)) +
   geom_col(position = "dodge2")
 ```
 
@@ -410,7 +413,7 @@ ggplot(data_1st) +
   geom_rsi(translate_ab = FALSE)
 ```
 
-Omit the `translate_ab = FALSE` to have the antibiotic codes (AMX, AMC, CIP, GEN) translated to official WHO names (amoxicillin, amoxicillin and betalactamase inhibitor, ciprofloxacin, gentamicin).
+Omit the `translate_ab = FALSE` to have the antibiotic codes (AMX, AMC, CIP, GEN) translated to official WHO names (amoxicillin, amoxicillin/clavulanic acid, ciprofloxacin, gentamicin).
 
 If we group on e.g. the `genus` column and add some additional functions from our package, we can create this:
 
@@ -422,7 +425,7 @@ ggplot(data_1st %>% group_by(genus)) +
   # of which we have 4 (earlier created with `as.rsi`)
   geom_rsi(x = "genus") + 
   # split plots on antibiotic
-  facet_rsi(facet = "Antibiotic") +
+  facet_rsi(facet = "antibiotic") +
   # make R red, I yellow and S green
   scale_rsi_colours() +
   # show percentages on y axis
@@ -443,7 +446,7 @@ To simplify this, we also created the `ggplot_rsi()` function, which combines al
 data_1st %>% 
   group_by(genus) %>%
   ggplot_rsi(x = "genus",
-             facet = "Antibiotic",
+             facet = "antibiotic",
              breaks = 0:4 * 25,
              datalabels = FALSE) +
   coord_flip()
@@ -453,33 +456,26 @@ data_1st %>%
 
 The next example uses the included `septic_patients`, which is an anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. It is true, genuine data. This `data.frame` can be used to practice AMR analysis.
 
-We will compare the resistance to fosfomycin (column `FOS`) in hospital A and D. The input for the final `fisher.test()` will be this:
+We will compare the resistance to fosfomycin (column `FOS`) in hospital A and D. The input for the `fisher.test()` can be retrieved with a transformation like this:
 
-```{r, echo = FALSE, results = 'asis'}
+```{r, results = 'markup'}
-septic_patients %>%
+check_FOS <- septic_patients %>%
-  filter(hospital_id %in% c("A", "D")) %>%
-  select(hospital_id, FOS) %>%
-  group_by(hospital_id) %>%
-  count_df(combine_IR = TRUE) %>%
-  tidyr::spread(hospital_id, Value) %>%
-  select(A, D) %>%
-  bind_cols(tibble(" " = c("IR", "S")), .) %>% 
-  as.matrix() %>%
-  knitr::kable()
-```
-
-We can transform the data and apply the test in only a couple of lines: 
-
-```{r}
-septic_patients %>%
   filter(hospital_id %in% c("A", "D")) %>% # filter on only hospitals A and D
   select(hospital_id, FOS) %>%             # select the hospitals and fosfomycin
   group_by(hospital_id) %>%                # group on the hospitals
-  count_df(combine_IR = TRUE) %>%          # count all isolates per group (hospital_id)
+  count_df(combine_SI = TRUE) %>%          # count all isolates per group (hospital_id)
-  tidyr::spread(hospital_id, Value) %>%    # transform output so A and D are columns
+  tidyr::spread(hospital_id, value) %>%    # transform output so A and D are columns
   select(A, D) %>%                         # and select these only
-  as.matrix() %>%                          # transform to good old matrix for fisher.test()
+  as.matrix()                              # transform to good old matrix for fisher.test()
-  fisher.test()                            # do Fisher's Exact Test
+
+check_FOS
 ```
 
-As can be seen, the p value is 0.03, which means that the fosfomycin resistances found in hospital A and D are really different.
+We can apply the test now with:
+
+```{r}
+# do Fisher's Exact Test
+fisher.test(check_FOS)                            
+```
+
+As can be seen, the p value is `r round(fisher.test(check_FOS)$p.value, 3)`, which means that the fosfomycin resistances found in hospital A and D are really different.