(v1.2.0.9037) survey on website

3 years ago · 1b65d76cfb
parent ab2b359e6b
commit 1b65d76cfb
140 changed files with 1259 additions and 891 deletions
--- a/.github/workflows/codecovr.yaml
+++ b/.github/workflows/codecovr.yaml
@ -22,7 +22,6 @@
 on:
  push:
    branches:
-      - premaster
      - master
  pull_request:
    branches:
--- a/4
+++ b/4
@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.2.0.9036
-Date: 2020-07-22
+Version: 1.2.0.9037
+Date: 2020-07-28
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
    person(role = c("aut", "cre"), 
--- a/NEWS.md
+++ b/NEWS.md
@ -1,9 +1,9 @@
-# AMR 1.2.0.9036
-## <small>Last updated: 22 July 2020</small>
+# AMR 1.2.0.9037
+## <small>Last updated: 28 July 2020</small>

 ### New
 * Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
-* [Tidyverse selections](https://tidyselect.r-lib.org/reference/language.html) for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows Tidyverse selections, like `dplyr::select()` and `tidyr::pivot_longer()`:
+* [Tidyverse selection helpers](https://tidyselect.r-lib.org/reference/language.html) for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like `dplyr::select()` and `tidyr::pivot_longer()`:
  ```r
  library(dplyr)
  
@ -33,13 +33,17 @@
  * The `as.ab()` function will now throw a note if more than 1 antimicrobial drug could be retrieved from a single input value.
 * Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded
 * All `*_join_microorganisms()` functions and `bug_drug_combinations()` now return the original data class (e.g. `tibble`s and `data.table`s)
-* Fixed a bug for using grouped versions of `rsi_df()`, `proportion_df()` and `count_df()`, and fixed a bug where not all different antimicrobial results were added as rows
+* For functions `rsi_df()`, `proportion_df()` and `count_df()`:
+  * Fixed a bug for using grouped versions
+  * Fixed a bug where not all different antimicrobial results were added as rows
+  * Fixed a bug when only calculating counts (`count_df()`) when all antibiotics in the data set have only `NA`s
 * Improved auto-determination for columns of types `<mo>` and `<Date>`
 * Fixed a bug in `bug_drug_combinations()` for when only one antibiotic was in the input data
 * Changed the summary for class `<rsi>`, to highlight the %SI vs. %R
 * Improved error handling, giving more useful info when functions return an error
 * Any progress bar will now only show in interactive mode (i.e. not in R Markdown)
 * Speed improvement for `mdro()` and `filter_ab_class()`
+* New option `arrows_textangled` for `ggplot_pca()` to indicate whether the text at the end of the arrows should be angled (defaults to `TRUE`, as it was in previous versions)

 ### Other
 * Moved primary location of this project from GitLab to [GitHub](https://github.com/msberends/AMR), giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@ -72,6 +72,15 @@ addin_insert_like <- function() {
 }

 check_dataset_integrity <- function() {
+  # check if user overwrote our data sets in their global environment
+  data_in_pkg <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE]
+  data_in_globalenv <- ls(envir = globalenv())
+  overwritten <- data_in_pkg[data_in_pkg %in% data_in_globalenv]
+  stop_if(length(overwritten) > 0,
+          "the following data set is overwritten by your global environment and prevents the AMR package from working correctly:\n",
+          paste0("'", overwritten, "'", collapse = ", "),
+          ".\nPlease rename your object before using this function.", call = FALSE)
+  # check if other packages did not overwrite our data sets
  tryCatch({
    check_microorganisms <- all(c("mo", "fullname", "kingdom", "phylum",
                                  "class", "order", "family", "genus", 
@ -86,13 +95,6 @@ check_dataset_integrity <- function() {
  }, error = function(e)
    stop_('please use the command \'library("AMR")\' before using this function, to load the required reference data.', call = FALSE)
  )
-  data_in_pkg <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
-  data_in_globalenv <- ls(envir = globalenv())
-  overwritten <- data_in_pkg[data_in_pkg %in% data_in_globalenv]
-  stop_if(length(overwritten) > 0,
-          "the following data set is overwritten by your global environment and prevents the AMR package from working correctly:\n",
-          paste0("'", overwritten, "'", collapse = ", "),
-          ".\nPlease rename your object before using this function.", call = FALSE)
  invisible(TRUE)
 }

--- a/R/amr.R
+++ b/R/amr.R
@ -23,12 +23,14 @@
 #'
 #' Welcome to the `AMR` package.
 #' @details
-#' `AMR` is a free and open-source R package 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 License version 2.0 (GPL-2), as published by the Free Software Foundation.
+#' `AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
+#' 
+#' After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
+#' 
+#' This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. 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 License version 2.0 (GPL-2), as published by the Free Software Foundation.
 #'
 #' This package can be used for:
-#' - Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the [Catalogue of Life](http://www.catalogueoflife.org)
+#' - Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature
 #' - Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines
 #' - Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records
 #' - Determining first isolates to be used for AMR analysis
@ -37,15 +39,16 @@
 #' - Calculating (empirical) susceptibility of both mono therapy and combination therapies
 #' - Predicting future antimicrobial resistance using regression models
 #' - Getting properties for any microorganism (like Gram stain, species, genus or family)
-#' - Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name)
+#' - Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)
 #' - Plotting antimicrobial resistance
-#' - Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code
-#' - Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code
+#' - Applying EUCAST expert rules
+#' - Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code
+#' - Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code
 #' - Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI
 #' - Principal component analysis for AMR
-
+#' 
 #' @section Read more on our website!:
-#' On our website <https://msberends.github.io/AMR> you can find [a comprehensive tutorial](https://msberends.github.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.github.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.github.io/AMR/articles/WHONET.html).
+#' On our website <https://msberends.github.io/AMR> you can find [a comprehensive tutorial](https://msberends.github.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.github.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.github.io/AMR/articles/WHONET.html). As we would like to better understand the backgrounds and needs of our users, please [participate in our survey](https://msberends.github.io/AMR/survey.html)!
 #' @section Contact Us:
 #' For suggestions, comments or questions, please contact us at:
 #'
--- a/R/filter_ab_class.R
+++ b/R/filter_ab_class.R
@ -33,8 +33,7 @@
 #' @seealso [antibiotic_class_selectors()] for the `select()` equivalent.
 #' @export
 #' @examples
-#' \dontrun{
-#' library(dplyr)
+#' if (require(dplyr)) {
 #'
 #' # filter on isolates that have any result for any aminoglycoside
 #' example_isolates %>% filter_ab_class("aminoglycoside")
@ -64,6 +63,12 @@
 #'   filter_aminoglycosides("R", "all") %>%
 #'   filter_fluoroquinolones("R", "all")
 #' }
+#' 
+#' \dontrun{
+#' # with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:
+#' example_isolates %>% filter_carbapenems("R", "all")
+#' example_isolates %>% filter(across(carbapenems(), ~. == "R"))
+#' }
 filter_ab_class <- function(x,
                            ab_class,
                            result = NULL,
--- a/R/ggplot_pca.R
+++ b/R/ggplot_pca.R
@ -40,6 +40,7 @@
 #' @param arrows_colour the colour of the arrow and their text
 #' @param arrows_size the size (thickness) of the arrow lines
 #' @param arrows_textsize the size of the text at the end of the arrows
+#' @param arrows_textangled a logical whether the text at the end of the arrows should be angled
 #' @param arrows_alpha the alpha (transparency) of the arrows and their text
 #' @param base_textsize the text size for all plot elements except the labels and arrows
 #' @param ... Parameters passed on to functions
@ -58,20 +59,25 @@
 #' # `example_isolates` is a dataset available in the AMR package.
 #' # See ?example_isolates.
 #'
-#' \dontrun{
 #' # See ?pca for more info about Principal Component Analysis (PCA).
-#' library(dplyr)
-#' pca_model <- example_isolates %>% 
-#'   filter(mo_genus(mo) == "Staphylococcus") %>% 
-#'   group_by(species = mo_shortname(mo)) %>%
-#'   summarise_if (is.rsi, resistance) %>%
-#'   pca(FLC, AMC, CXM, GEN, TOB, TMP, SXT, CIP, TEC, TCY, ERY)
+#' if (require("dplyr")) {
+#'   pca_model <- example_isolates %>% 
+#'     filter(mo_genus(mo) == "Staphylococcus") %>% 
+#'     group_by(species = mo_shortname(mo)) %>%
+#'     summarise_if (is.rsi, resistance) %>%
+#'     pca(FLC, AMC, CXM, GEN, TOB, TMP, SXT, CIP, TEC, TCY, ERY)
+#'     
+#'   # old (base R)
+#'   biplot(pca_model)
 #'   
-#' # old
-#' biplot(pca_model)
-#' 
-#' # new 
-#' ggplot_pca(pca_model)
+#'   # new 
+#'   ggplot_pca(pca_model)
+#'   
+#'   if (require("ggplot2")) {
+#'     ggplot_pca(pca_model) +
+#'       scale_colour_viridis_d() +
+#'       labs(title = "Title here")
+#'   }
 #' }
 ggplot_pca <- function(x,
                       choices = 1:2,
@ -91,26 +97,28 @@ ggplot_pca <- function(x,
                       arrows_colour = "darkblue",
                       arrows_size = 0.5,
                       arrows_textsize = 3,
+                       arrows_textangled = TRUE,
                       arrows_alpha = 0.75,
                       base_textsize = 10,
                       ...) {
  
  stop_ifnot_installed("ggplot2")
  stop_ifnot(length(choices) == 2, "`choices` must be of length 2")
-  stop_ifnot(is.logical(scale), "`scale` must be TRUE or FALSE")
-  stop_ifnot(is.logical(pc.biplot), "`pc.biplot` must be TRUE or FALSE")
-  stop_ifnot(is.numeric(choices), "`choices` must be numeric")
-  stop_ifnot(is.numeric(labels_textsize), "`labels_textsize` must be numeric")
-  stop_ifnot(is.numeric(labels_text_placement), "`labels_text_placement` must be numeric")
-  stop_ifnot(is.logical(ellipse), "`ellipse` must be TRUE or FALSE")
-  stop_ifnot(is.numeric(ellipse_prob), "`ellipse_prob` must be numeric")
-  stop_ifnot(is.numeric(ellipse_size), "`ellipse_size` must be numeric")
-  stop_ifnot(is.numeric(ellipse_alpha), "`ellipse_alpha` must be numeric")
  stop_ifnot(is.logical(arrows), "`arrows` must be TRUE or FALSE")
+  stop_ifnot(is.logical(arrows_textangled), "`arrows_textangled` must be TRUE or FALSE")
+  stop_ifnot(is.logical(ellipse), "`ellipse` must be TRUE or FALSE")
+  stop_ifnot(is.logical(pc.biplot), "`pc.biplot` must be TRUE or FALSE")
+  stop_ifnot(is.logical(scale), "`scale` must be TRUE or FALSE")
+  stop_ifnot(is.numeric(arrows_alpha), "`arrows_alpha` must be numeric")
  stop_ifnot(is.numeric(arrows_size), "`arrows_size` must be numeric")
  stop_ifnot(is.numeric(arrows_textsize), "`arrows_textsize` must be numeric")
-  stop_ifnot(is.numeric(arrows_alpha), "`arrows_alpha` must be numeric")
  stop_ifnot(is.numeric(base_textsize), "`base_textsize` must be numeric")
+  stop_ifnot(is.numeric(choices), "`choices` must be numeric")
+  stop_ifnot(is.numeric(ellipse_alpha), "`ellipse_alpha` must be numeric")
+  stop_ifnot(is.numeric(ellipse_prob), "`ellipse_prob` must be numeric")
+  stop_ifnot(is.numeric(ellipse_size), "`ellipse_size` must be numeric")
+  stop_ifnot(is.numeric(labels_text_placement), "`labels_text_placement` must be numeric")
+  stop_ifnot(is.numeric(labels_textsize), "`labels_textsize` must be numeric")
  
  calculations <- pca_calculations(pca_model = x,
                                   groups = groups, 
@ -206,12 +214,20 @@ ggplot_pca <- function(x,
                                                          type = "open"), 
                                   colour = arrows_colour, 
                                   size = arrows_size,
-                                   alpha = arrows_alpha) +
-      ggplot2::geom_text(data = df.v, 
-                         ggplot2::aes(label = varname, x = xvar, y = yvar, angle = angle, hjust = hjust), 
-                         colour = arrows_colour,
-                         size = arrows_textsize,
-                         alpha = arrows_alpha)
+                                   alpha = arrows_alpha)
+    if (arrows_textangled == TRUE) {
+      g <- g + ggplot2::geom_text(data = df.v, 
+                                  ggplot2::aes(label = varname, x = xvar, y = yvar, angle = angle, hjust = hjust), 
+                                  colour = arrows_colour,
+                                  size = arrows_textsize,
+                                  alpha = arrows_alpha)
+    } else {
+      g <- g + ggplot2::geom_text(data = df.v, 
+                                  ggplot2::aes(label = varname, x = xvar, y = yvar, hjust = hjust), 
+                                  colour = arrows_colour,
+                                  size = arrows_textsize,
+                                  alpha = arrows_alpha)
+    }
  }
  
  # Add caption label about total explained variance
--- a/R/rsi.R
+++ b/R/rsi.R
@ -37,7 +37,7 @@
 #' 
 #' Supported guidelines to be used as input for the `guideline` parameter are: `r paste0('"', sort(unique(AMR::rsi_translation$guideline)), '"', collapse = ", ")`. Simply using `"CLSI"` or `"EUCAST"` for input will automatically select the latest version of that guideline. 
 #' 
-#' The repository of this package [contains a machine readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This **allows for easy implementation of these rules in laboratory information systems (LIS)**.
+#' The repository of this package [contains a machine readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**.
 #'
 #' After using [as.rsi()], you can use [eucast_rules()] to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
 #'
--- a/R/rsi_calc.R
+++ b/R/rsi_calc.R
@ -214,7 +214,7 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
    out <- data.frame(antibiotic = character(0),
                      interpretation = character(0),
                      value = double(0),
-                      isolates <- integer(0),
+                      isolates = integer(0),
                      stringsAsFactors = FALSE)
    if (data_has_groups) {
      group_values <- unique(.data[, which(colnames(.data) %in% groups), drop = FALSE])
--- a/R/sysdata.rda
+++ b/R/sysdata.rda
--- a/README.md
+++ b/README.md
@ -3,7 +3,13 @@
 # `AMR` (for R)
 <img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />

-This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.github.io/AMR](https://msberends.github.io/AMR) to read about this package.
+`AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
+ 
+After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
+
+This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. 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 License version 2.0 (GPL-2), as published by the Free Software Foundation.
+
+This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.github.io/AMR](https://msberends.github.io/AMR) to read more about this package.

 *NOTE: this source code is on GitHub (https://github.com/msberends/AMR), but also automatically mirrored to GitLab (https://gitlab.com/msberends/AMR).*

--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@ -70,20 +70,20 @@ navbar:
        href: "articles/benchmarks.html"
    - text: "Manual"
      icon: "fa-book-open"
-      href: "reference/"
+      href: "reference/index.html"
    - text: "Authors"
      icon: "fa-users"
      href: "authors.html"
    - text: "Changelog"
      icon: "far fa-newspaper"
-      href: "news/"
+      href: "news/index.html"
  right:
    - text: "Source Code"
      icon: "fab fa-github"
      href: "https://github.com/msberends/AMR"
-    - text: "Licence"
-      icon: "fa-book"
-      href: "LICENSE-text.html"
+    - text: "Survey"
+      icon: "fa-clipboard-list"
+      href: "survey.html"

 reference:
  - title: "Cleaning your data"
@ -156,7 +156,7 @@ reference:
    - "`catalogue_of_life_version`"
    - "`WHOCC`"
    - "`lifecycle`"
-  - title: Other functions
+  - title: "Other functions"
    desc: >
      These functions are mostly for internal use, but some of
      them may also be suitable for your analysis. Especially the
@ -164,7 +164,7 @@ reference:
    contents:
    - "`get_locale`"
    - "`like`"
-  - title: Deprecated functions
+  - title: "Deprecated functions"
    desc: >
      These functions are deprecated, meaning that they will still
      work but show a warning with every use and will be removed
--- a/data-raw/create_survey_page.R
+++ b/data-raw/create_survey_page.R
@ -0,0 +1,6 @@
+
+license_text <- readLines("docs/LICENSE-text.html")
+license_text <- paste(license_text, collapse = "|||")
+license_text <- gsub("licen(s|c)e", "Survey", license_text, ignore.case = TRUE)
+license_text <- gsub("<pre>.*</pre>", '<p>If no form is showing below, please <a href="https://forms.office.com/Pages/ResponsePage.aspx?id=-SJRM_TUZ02i_M1twg3ecDlnO1BBtdxGi-GnYu7DKfdUNTFLQ0xVSUlRVVlXTlVTNjZFMjdRUVpCSy4u" target="_blank">click here to open it</a>.</p><iframe width="100%" height= "500px" src= "https://forms.office.com/Pages/ResponsePage.aspx?id=-SJRM_TUZ02i_M1twg3ecDlnO1BBtdxGi-GnYu7DKfdUNTFLQ0xVSUlRVVlXTlVTNjZFMjdRUVpCSy4u&embed=true" frameborder= "0" marginwidth= "0" marginheight= "0" style= "border: none; max-width:100%; max-height:100vh" allowfullscreen webkitallowfullscreen mozallowfullscreen msallowfullscreen> </iframe>', license_text)
+writeLines(unlist(strsplit(license_text, "|||", fixed = TRUE)), "docs/survey.html")
--- a/data-raw/eucast_rules.tsv
+++ b/data-raw/eucast_rules.tsv
@ -177,7 +177,7 @@ genus_species	is	Clostridium innocuum			VAN	R	Table 04: Intrinsic resistance in
 genus_species	like	^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)	PEN	S	aminopenicillins, cephalosporins_except_CAZ, carbapenems	S	Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci	Expert Rules
 genus	is	Enterococcus	AMP	R	ureidopenicillins, carbapenems	R	Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci	Expert Rules
 genus	is	Enterococcus	AMX	R	ureidopenicillins, carbapenems	R	Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci	Expert Rules
-family	is	Enterobacteriaceae	TIC, PIP	R, S	PIP	R	Table 09: Interpretive rules for B-lactam agents and Gram-negative rods	Expert Rules
+order	is	Enterobacterales	TIC, PIP	R, S	PIP	R	Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (at the time: Enterobacteriaceae)	Expert Rules
 genus	like	.*	ERY	S	AZM, CLR	S	Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins	Expert Rules
 genus	like	.*	ERY	I	AZM, CLR	I	Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins	Expert Rules
 genus	like	.*	ERY	R	AZM, CLR	R	Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins	Expert Rules
--- a/docs/404.html
+++ b/docs/404.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9036</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
      </span>
    </div>

@ -176,7 +176,7 @@
  </ul>
 </li>
 <li>
-  <a href="reference/">
+  <a href="reference/index.html">
    <span class="fa fa-book-open"></span>
     
    Manual
@ -190,7 +190,7 @@
  </a>
 </li>
 <li>
-  <a href="news/">
+  <a href="news/index.html">
    <span class="far fa far fa-newspaper"></span>
     
    Changelog
@ -206,10 +206,10 @@
  </a>
 </li>
 <li>
-  <a href="LICENSE-text.html">
-    <span class="fa fa-book"></span>
+  <a href="survey.html">
+    <span class="fa fa-clipboard-list"></span>
     
-    Licence
+    Survey
  </a>
 </li>
      </ul>
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9036</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
      </span>
    </div>

@ -176,7 +176,7 @@
  </ul>
 </li>
 <li>
-  <a href="reference/">
+  <a href="reference/index.html">
    <span class="fa fa-book-open"></span>
     
    Manual
@ -190,7 +190,7 @@
  </a>
 </li>
 <li>
-  <a href="news/">
+  <a href="news/index.html">
    <span class="far fa far fa-newspaper"></span>
     
    Changelog
@ -206,10 +206,10 @@
  </a>
 </li>
 <li>
-  <a href="LICENSE-text.html">
-    <span class="fa fa-book"></span>
+  <a href="survey.html">
+    <span class="fa fa-clipboard-list"></span>
     
-    Licence
+    Survey
  </a>
 </li>
      </ul>
--- a/docs/articles/AMR.html
+++ b/docs/articles/AMR.html
@ -39,7 +39,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9030</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
      </span>
    </div>

@ -134,7 +134,7 @@
  </ul>
 </li>
 <li>
-  <a href="../reference/">
+  <a href="../reference/index.html">
    <span class="fa fa-book-open"></span>
     
    Manual
@ -148,7 +148,7 @@
  </a>
 </li>
 <li>
-  <a href="../news/">
+  <a href="../news/index.html">
    <span class="far fa far fa-newspaper"></span>
     
    Changelog
@ -164,10 +164,10 @@
  </a>
 </li>
 <li>
-  <a href="../LICENSE-text.html">
-    <span class="fa fa-book"></span>
+  <a href="../survey.html">
+    <span class="fa fa-clipboard-list"></span>
     
-    Licence
+    Survey
  </a>
 </li>
      </ul>
@ -186,7 +186,7 @@
      <h1 data-toc-skip>How to conduct AMR analysis</h1>
                        <h4 class="author">Matthijs S. Berends</h4>
            
-            <h4 class="date">09 July 2020</h4>
+            <h4 class="date">24 July 2020</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
      <div class="hidden name"><code>AMR.Rmd</code></div>
@ -195,7 +195,7 @@

    
    
-<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 09 July 2020.</p>
+<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 24 July 2020.</p>
 <div id="introduction" class="section level1">
 <h1 class="hasAnchor">
 <a href="#introduction" class="anchor"></a>Introduction</h1>
@ -226,21 +226,21 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2020-07-09</td>
+<td align="center">2020-07-24</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 </tr>
 <tr class="even">
-<td align="center">2020-07-09</td>
+<td align="center">2020-07-24</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">R</td>
 </tr>
 <tr class="odd">
-<td align="center">2020-07-09</td>
+<td align="center">2020-07-24</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@ -336,66 +336,66 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2016-01-30</td>
-<td align="center">Y5</td>
-<td align="center">Hospital A</td>
+<td align="center">2014-06-04</td>
+<td align="center">V5</td>
+<td align="center">Hospital B</td>
 <td align="center">Escherichia coli</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2010-11-13</td>
-<td align="center">Y1</td>
-<td align="center">Hospital D</td>
+<td align="center">2015-09-20</td>
+<td align="center">M6</td>
+<td align="center">Hospital A</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">F</td>
+<td align="center">M</td>
 </tr>
 <tr class="odd">
-<td align="center">2016-07-21</td>
-<td align="center">U10</td>
-<td align="center">Hospital B</td>
-<td align="center">Escherichia coli</td>
-<td align="center">I</td>
+<td align="center">2017-05-14</td>
+<td align="center">Q6</td>
+<td align="center">Hospital C</td>
+<td align="center">Streptococcus pneumoniae</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2013-03-14</td>
-<td align="center">Q1</td>
-<td align="center">Hospital B</td>
-<td align="center">Staphylococcus aureus</td>
-<td align="center">R</td>
+<td align="center">2017-03-12</td>
+<td align="center">O3</td>
+<td align="center">Hospital D</td>
+<td align="center">Klebsiella pneumoniae</td>
+<td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="odd">
-<td align="center">2013-04-22</td>
-<td align="center">O8</td>
+<td align="center">2017-12-27</td>
+<td align="center">P8</td>
 <td align="center">Hospital B</td>
-<td align="center">Staphylococcus aureus</td>
+<td align="center">Escherichia coli</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2017-11-14</td>
-<td align="center">J4</td>
-<td align="center">Hospital A</td>
-<td align="center">Streptococcus pneumoniae</td>
-<td align="center">S</td>
+<td align="center">2013-11-30</td>
+<td align="center">B10</td>
+<td align="center">Hospital B</td>
+<td align="center">Staphylococcus aureus</td>
+<td align="center">I</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -432,18 +432,18 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,300</td>
-<td align="right">51.5%</td>
-<td align="right">10,300</td>
-<td align="right">51.5%</td>
+<td align="right">10,487</td>
+<td align="right">52.44%</td>
+<td align="right">10,487</td>
+<td align="right">52.44%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,700</td>
-<td align="right">48.5%</td>
+<td align="right">9,513</td>
+<td align="right">47.57%</td>
 <td align="right">20,000</td>
-<td align="right">100.0%</td>
+<td align="right">100.00%</td>
 </tr>
 </tbody>
 </table>
@ -481,7 +481,7 @@ Longest: 1</p>
 <span class="co"># NOTE: Using column `bacteria` as input for `col_mo`.</span>
 <span class="co"># NOTE: Using column `date` as input for `col_date`.</span>
 <span class="co"># NOTE: Using column `patient_id` as input for `col_patient_id`.</span></pre></body></html></div>
-<p>So only 28.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
+<p>So only 28.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb16"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data</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</span> <span class="kw">==</span> <span class="fl">TRUE</span>)</pre></body></html></div>
 <p>For future use, the above two syntaxes can be shortened with the <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> function:</p>
@ -491,7 +491,7 @@ Longest: 1</p>
 <div id="first-weighted-isolates" class="section level2">
 <h2 class="hasAnchor">
 <a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
-<p>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 Y2, sorted on date:</p>
+<p>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 J1, sorted on date:</p>
 <table class="table">
 <thead><tr class="header">
 <th align="center">isolate</th>
@ -507,19 +507,19 @@ Longest: 1</p>
 <tbody>
 <tr class="odd">
 <td align="center">1</td>
-<td align="center">2010-03-16</td>
-<td align="center">Y2</td>
+<td align="center">2010-04-08</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
-<td align="center">R</td>
-<td align="center">R</td>
+<td align="center">I</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2</td>
-<td align="center">2010-08-04</td>
-<td align="center">Y2</td>
+<td align="center">2010-06-01</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -529,21 +529,21 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">3</td>
-<td align="center">2010-10-06</td>
-<td align="center">Y2</td>
+<td align="center">2010-06-21</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
-<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">4</td>
-<td align="center">2010-11-11</td>
-<td align="center">Y2</td>
+<td align="center">2010-07-08</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -551,30 +551,30 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">5</td>
-<td align="center">2010-11-23</td>
-<td align="center">Y2</td>
+<td align="center">2011-01-29</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
-<td align="center">R</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">6</td>
-<td align="center">2011-04-01</td>
-<td align="center">Y2</td>
+<td align="center">2011-02-23</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
 <td align="center">S</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">TRUE</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">FALSE</td>
 </tr>
 <tr class="odd">
 <td align="center">7</td>
-<td align="center">2011-04-27</td>
-<td align="center">Y2</td>
+<td align="center">2011-02-23</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -584,19 +584,19 @@ Longest: 1</p>
 </tr>
 <tr class="even">
 <td align="center">8</td>
-<td align="center">2011-05-27</td>
-<td align="center">Y2</td>
+<td align="center">2011-02-28</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="odd">
 <td align="center">9</td>
-<td align="center">2011-07-05</td>
-<td align="center">Y2</td>
+<td align="center">2011-03-13</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -606,14 +606,14 @@ Longest: 1</p>
 </tr>
 <tr class="even">
 <td align="center">10</td>
-<td align="center">2011-09-25</td>
-<td align="center">Y2</td>
+<td align="center">2011-05-14</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">R</td>
-<td align="center">R</td>
 <td align="center">S</td>
-<td align="center">FALSE</td>
+<td align="center">S</td>
+<td align="center">TRUE</td>
 </tr>
 </tbody>
 </table>
@ -644,20 +644,20 @@ Longest: 1</p>
 <tbody>
 <tr class="odd">
 <td align="center">1</td>
-<td align="center">2010-03-16</td>
-<td align="center">Y2</td>
+<td align="center">2010-04-08</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
-<td align="center">R</td>
-<td align="center">R</td>
+<td align="center">I</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center">TRUE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2</td>
-<td align="center">2010-08-04</td>
-<td align="center">Y2</td>
+<td align="center">2010-06-01</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -668,80 +668,80 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">3</td>
-<td align="center">2010-10-06</td>
-<td align="center">Y2</td>
+<td align="center">2010-06-21</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
-<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
-<td align="center">TRUE</td>
+<td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">4</td>
-<td align="center">2010-11-11</td>
-<td align="center">Y2</td>
+<td align="center">2010-07-08</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
-<td align="center">TRUE</td>
+<td align="center">FALSE</td>
 </tr>
 <tr class="odd">
 <td align="center">5</td>
-<td align="center">2010-11-23</td>
-<td align="center">Y2</td>
+<td align="center">2011-01-29</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
-<td align="center">R</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">6</td>
-<td align="center">2011-04-01</td>
-<td align="center">Y2</td>
+<td align="center">2011-02-23</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
 <td align="center">S</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">TRUE</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">FALSE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">7</td>
-<td align="center">2011-04-27</td>
-<td align="center">Y2</td>
+<td align="center">2011-02-23</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
-<td align="center">TRUE</td>
+<td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">8</td>
-<td align="center">2011-05-27</td>
-<td align="center">Y2</td>
+<td align="center">2011-02-28</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">FALSE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">9</td>
-<td align="center">2011-07-05</td>
-<td align="center">Y2</td>
+<td align="center">2011-03-13</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -752,23 +752,23 @@ Longest: 1</p>
 </tr>
 <tr class="even">
 <td align="center">10</td>
-<td align="center">2011-09-25</td>
-<td align="center">Y2</td>
+<td align="center">2011-05-14</td>
+<td align="center">J1</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">R</td>
-<td align="center">R</td>
 <td align="center">S</td>
-<td align="center">FALSE</td>
+<td align="center">S</td>
+<td align="center">TRUE</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
 </table>
-<p>Instead of 2, now 10 isolates are flagged. In total, 78.3% of all isolates are marked ‘first weighted’ - 49.8% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
+<p>Instead of 2, now 7 isolates are flagged. In total, 78.6% of all isolates are marked ‘first weighted’ - 50.2% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
 <p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
 <div class="sourceCode" id="cb19"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data</span> <span class="kw">%&gt;%</span>
  <span class="fu"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</pre></body></html></div>
-<p>So we end up with 15,664 isolates for analysis.</p>
+<p>So we end up with 15,719 isolates for analysis.</p>
 <p>We can remove unneeded columns:</p>
 <div class="sourceCode" id="cb20"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">&lt;-</span> <span class="no">data_1st</span> <span class="kw">%&gt;%</span>
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">first</span>, <span class="no">keyab</span>))</pre></body></html></div>
@ -776,6 +776,7 @@ Longest: 1</p>
 <div class="sourceCode" id="cb21"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">data_1st</span>)</pre></body></html></div>
 <table class="table">
 <colgroup>
+<col width="2%">
 <col width="8%">
 <col width="8%">
 <col width="8%">
@ -791,6 +792,7 @@ Longest: 1</p>
 <col width="11%">
 </colgroup>
 <thead><tr class="header">
+<th align="left"></th>
 <th align="center">date</th>
 <th align="center">patient_id</th>
 <th align="center">hospital</th>
@ -807,11 +809,12 @@ Longest: 1</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2016-01-30</td>
-<td align="center">Y5</td>
-<td align="center">Hospital A</td>
+<td align="left">1</td>
+<td align="center">2014-06-04</td>
+<td align="center">V5</td>
+<td align="center">Hospital B</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -822,78 +825,83 @@ Longest: 1</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2010-11-13</td>
-<td align="center">Y1</td>
-<td align="center">Hospital D</td>
-<td align="center">B_ESCHR_COLI</td>
+<td align="left">3</td>
+<td align="center">2017-05-14</td>
+<td align="center">Q6</td>
+<td align="center">Hospital C</td>
+<td align="center">B_STRPT_PNMN</td>
+<td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">F</td>
-<td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
+<td align="center">Gram-positive</td>
+<td align="center">Streptococcus</td>
+<td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="center">2016-07-21</td>
-<td align="center">U10</td>
-<td align="center">Hospital B</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">I</td>
-<td align="center">S</td>
+<td align="left">4</td>
+<td align="center">2017-03-12</td>
+<td align="center">O3</td>
+<td align="center">Hospital D</td>
+<td align="center">B_KLBSL_PNMN</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
+<td align="center">Klebsiella</td>
+<td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2013-03-14</td>
-<td align="center">Q1</td>
+<td align="left">5</td>
+<td align="center">2017-12-27</td>
+<td align="center">P8</td>
 <td align="center">Hospital B</td>
-<td align="center">B_STPHY_AURS</td>
-<td align="center">R</td>
-<td align="center">R</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
-<td align="center">Gram-positive</td>
-<td align="center">Staphylococcus</td>
-<td align="center">aureus</td>
+<td align="center">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="center">2013-04-22</td>
-<td align="center">O8</td>
+<td align="left">6</td>
+<td align="center">2013-11-30</td>
+<td align="center">B10</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STPHY_AURS</td>
+<td align="center">I</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">S</td>
-<td align="center">F</td>
+<td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2017-11-14</td>
-<td align="center">J4</td>
-<td align="center">Hospital A</td>
-<td align="center">B_STRPT_PNMN</td>
-<td align="center">S</td>
+<td align="left">8</td>
+<td align="center">2011-06-14</td>
+<td align="center">A2</td>
+<td align="center">Hospital D</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">M</td>
-<td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
-<td align="center">pneumoniae</td>
+<td align="center">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
@ -915,8 +923,8 @@ Longest: 1</p>
 <div class="sourceCode" id="cb23"><html><body><pre class="r"><span class="no">data_1st</span> <span class="kw">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">genus</span>, <span class="no">species</span>)</pre></body></html></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
-Length: 15,664<br>
-Available: 15,664 (100%, NA: 0 = 0%)<br>
+Length: 15,719<br>
+Available: 15,719 (100%, NA: 0 = 0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@ -933,33 +941,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">7,860</td>
-<td align="right">50.18%</td>
-<td align="right">7,860</td>
-<td align="right">50.18%</td>
+<td align="right">7,902</td>
+<td align="right">50.27%</td>
+<td align="right">7,902</td>
+<td align="right">50.27%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">3,867</td>
-<td align="right">24.69%</td>
-<td align="right">11,727</td>
-<td align="right">74.87%</td>
+<td align="right">3,926</td>
+<td align="right">24.98%</td>
+<td align="right">11,828</td>
+<td align="right">75.25%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,386</td>