(v1.7.1.9038) dplyr grouping fix on windows?

(v1.7.1.9037) dplyr grouping fix on windows?
(v1.7.1.9036) dplyr grouping fix on windows?
2021-09-01 16:52:55 +02:00 · 2021-08-31 17:06:44 +02:00 · 2021-08-30 16:49:46 +02:00 · 2021-08-30 15:43:12 +02:00 · 2021-08-30 15:07:18 +02:00 · 2021-08-30 15:01:32 +02:00
100 changed files with 583 additions and 982 deletions
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@ -52,39 +52,33 @@ jobs:
      fail-fast: false
      matrix:
        config:
-          # these are the developmental version of R - we allow those tests to fail
-          - {os: macOS-latest,   r: 'devel',   allowfail: false}
-          - {os: windows-latest, r: 'devel',   allowfail: false}
-          - {os: ubuntu-20.04,   r: 'devel',   allowfail: false,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          
          # test all systems against all released versions of R >= 3.0, we support them all!
+          - {os: macOS-latest,   r: 'devel',   allowfail: true}
          - {os: macOS-latest,   r: '4.1',     allowfail: false}
-          - {os: windows-latest, r: '4.1',     allowfail: false}
-          - {os: ubuntu-20.04,   r: '4.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: macOS-latest,   r: '4.0',     allowfail: false}
-          - {os: windows-latest, r: '4.0',     allowfail: false}
-          - {os: ubuntu-20.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: macOS-latest,   r: '3.6',     allowfail: false}
-          - {os: windows-latest, r: '3.6',     allowfail: false}
-          - {os: ubuntu-20.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: macOS-latest,   r: '3.5',     allowfail: false}
-          - {os: windows-latest, r: '3.5',     allowfail: false}
-          - {os: ubuntu-20.04,   r: '3.5',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: macOS-latest,   r: '3.4',     allowfail: false}
-          - {os: windows-latest, r: '3.4',     allowfail: false}
-          - {os: ubuntu-20.04,   r: '3.4',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: macOS-latest,   r: '3.3',     allowfail: false}
-          - {os: windows-latest, r: '3.3',     allowfail: false}
-          - {os: ubuntu-20.04,   r: '3.3',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: macOS-latest,   r: '3.2',     allowfail: false}
-          - {os: windows-latest, r: '3.2',     allowfail: false}
+          - {os: ubuntu-20.04,   r: 'devel',   allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '4.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '3.5',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '3.4',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '3.3',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: ubuntu-20.04,   r: '3.2',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          # - {os: macOS-latest,   r: '3.1',     allowfail: false}
-          # - {os: windows-latest, r: '3.1',     allowfail: false}
          - {os: ubuntu-20.04,   r: '3.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          # - {os: macOS-latest,   r: '3.0',     allowfail: false}
-          # - {os: windows-latest, r: '3.0',     allowfail: false}
          - {os: ubuntu-20.04,   r: '3.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: windows-latest, r: 'devel',   allowfail: true}
+          - {os: windows-latest, r: '4.1',     allowfail: false}
+          - {os: windows-latest, r: '4.0',     allowfail: false}
+          - {os: windows-latest, r: '3.6',     allowfail: false}
+          - {os: windows-latest, r: '3.5',     allowfail: false}
+          - {os: windows-latest, r: '3.4',     allowfail: false}
+          - {os: windows-latest, r: '3.3',     allowfail: false}
+          - {os: windows-latest, r: '3.2',     allowfail: false}

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@ -171,5 +165,5 @@ jobs:
        if: always()
        uses: actions/upload-artifact@v2
        with:
-          name: artifacts-r-${{ matrix.config.r }}-${{ matrix.config.os }}
+          name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
          path: AMR.Rcheck
--- a/12
+++ b/12
@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.7.1.9028
-Date: 2021-08-20
+Version: 1.7.1.9038
+Date: 2021-09-01
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
    data analysis and to work with microbial and antimicrobial properties by
@ -18,19 +18,19 @@ Authors@R: c(
         comment = c(ORCID = "0000-0001-5809-5995")),
  person(given = c("Alexander", "W."),
         family = "Friedrich", 
-         role = c("aut", "ths"),
+         role = "ths",
         comment = c(ORCID = "0000-0003-4881-038X")),
  person(given = c("Bhanu", "N.", "M."),
         family = "Sinha", 
-         role = c("aut", "ths"),
+         role = "ths",
         comment = c(ORCID = "0000-0003-1634-0010")),
  person(given = c("Casper", "J."),
         family = "Albers", 
-         role = c("aut", "ths"),
+         role = "ths",
         comment = c(ORCID = "0000-0002-9213-6743")),
  person(given = "Corinna",
         family = "Glasner", 
-         role = c("aut", "ths"),
+         role = "ths",
         comment = c(ORCID = "0000-0003-1241-1328")),
  person(given = c("Judith", "M."),
         family = "Fonville", 
--- a/NEWS.md
+++ b/NEWS.md
@ -1,5 +1,5 @@
-# `AMR` 1.7.1.9028
-## <small>Last updated: 20 August 2021</small>
+# `AMR` 1.7.1.9038
+## <small>Last updated:  1 September 2021</small>

 ### Breaking changes
 * Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
@ -12,11 +12,12 @@
 ### Changed
 * The `antibiotics` data set now contains **all ATC codes** that are available through the [WHOCC website](https://www.whocc.no), regardless of drugs being present in more than one ATC group. This means that:
  * Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)
-  * `antibiotics$atc` is now a `list` instead of a `character`, and this `atc` column was moved to the 5th position of the `antibiotics` data set
-  * `ab_atc()` does not always return a character vector with length 1, and returns a `list` if the input is larger than length 1
+  * `antibiotics$atc` is now a `list` containing `character` vectors, and this `atc` column was moved to the 5th position of the `antibiotics` data set
+  * `ab_atc()` does not always return a character vector of length 1, and returns a `list` if the input is larger than length 1
+  * `ab_info()` has a slightly different output
  * Some DDDs (daily defined doses) were added or updated according to newly included ATC codes
 * Antibiotic selectors
-  * They now also work in R-3.0 and R-3.1, supporting every version of R since 2013
+  * They now also work in R-3.0 and R-3.1, supporting every version of R since 2013 like the rest of the package
  * Added more selectors for antibiotic classes: `aminopenicillins()`, `antifungals()`, `antimycobacterials()`, `lincosamides()`, `lipoglycopeptides()`, `polymyxins()`, `quinolones()`, `streptogramins()`, `trimethoprims()` and `ureidopenicillins()`
  * Added specific selectors for certain types for treatment: `administrable_per_os()` and `administrable_iv()`, which are based on available Defined Daily Doses (DDDs), as defined by the WHOCC. These are ideal for e.g. analysing pathogens in primary care where IV treatment is not an option. They can be combined with other AB selectors, e.g. to select penicillins that are only administrable per os (i.e., orally):
    ```r
@ -30,8 +31,7 @@
    ```
  * Fix for using selectors multiple times in one call (e.g., using them in `dplyr::filter()` and immediately after in `dplyr::select()`)
  * Added argument `only_treatable`, which defaults to `TRUE` and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)
-* Fixed the Gram stain (`mo_gramstain()`) determination of the class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as *Negativicoccus* and *Veillonella*.
-* Fix for duplicate ATC codes in the `antibiotics` data set
+* Fixed the Gram stain (`mo_gramstain()`) determination of the taxonomic class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as *Negativicoccus* and *Veillonella*.
 * Fix to prevent introducing `NA`s for old MO codes when running `as.mo()` on them
 * Added more informative error messages when any of the `proportion_*()` and `count_*()` functions fail
 * When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using `as.mo()`
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@ -298,7 +298,7 @@ stop_ifnot_installed <- function(package) {

 pkg_is_available <- function(pkg, also_load = TRUE) {
  if (also_load == TRUE) {
-    out <- suppressWarnings(require(pkg, character.only = TRUE, warn.conflicts = FALSE, quietly = TRUE))
+    out <- suppressWarnings(require(pkg, character.only = TRUE, warn.conflicts = FALSE))
  } else {
    out <- requireNamespace(pkg, quietly = TRUE)
  }
--- a/R/ab_property.R
+++ b/R/ab_property.R
@ -288,7 +288,7 @@ ab_ddd <- function(x, administration = "oral", ...) {
  units <- list(...)$units
  if (!is.null(units) && isTRUE(units)) {
    if (message_not_thrown_before("ab_ddd", entire_session = TRUE)) {
-      warning_("Using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` instead. ",
+      warning_("Using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` to retrieve units instead. ",
               "This warning will be shown once per session.", call = FALSE)
    }
    ddd_prop <- paste0(ddd_prop, "_units")
@ -297,7 +297,7 @@ ab_ddd <- function(x, administration = "oral", ...) {
  }
  out <- ab_validate(x = x, property = ddd_prop)
  
-  if (any(ab_name(x, language = NULL) %like% "/" & is.na(out)) ) {
+  if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
    warning_("DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package. ",
             "Please refer to the WHOCC website:\n",
             "www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE)
@ -330,17 +330,18 @@ ab_info <- function(x, language = get_locale(), ...) {
  
  x <- as.ab(x, ...)
  list(ab = as.character(x),
-             atc = ab_atc(x),
-             cid = ab_cid(x),
-             name = ab_name(x, language = language),
-             group = ab_group(x, language = language),
-             atc_group1 = ab_atc_group1(x, language = language),
-             atc_group2 = ab_atc_group2(x, language = language),
-             tradenames = ab_tradenames(x),
-             ddd = list(oral = list(amount = ab_ddd(x, administration = "oral"),
-                                    units = ab_ddd_units(x, administration = "oral")),
-                        iv = list(amount = ab_ddd(x, administration = "iv"),
-                                  units = ab_ddd_units(x, administration = "iv"))))
+       cid = ab_cid(x),
+       name = ab_name(x, language = language),
+       group = ab_group(x, language = language),
+       atc = ab_atc(x),
+       atc_group1 = ab_atc_group1(x, language = language),
+       atc_group2 = ab_atc_group2(x, language = language),
+       tradenames = ab_tradenames(x),
+       loinc = ab_loinc(x),
+       ddd = list(oral = list(amount = ab_ddd(x, administration = "oral"),
+                              units = ab_ddd_units(x, administration = "oral")),
+                  iv = list(amount = ab_ddd(x, administration = "iv"),
+                            units = ab_ddd_units(x, administration = "iv"))))
 }


--- a/R/first_isolate.R
+++ b/R/first_isolate.R
@ -23,9 +23,9 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #

-#' Determine First (Weighted) Isolates
+#' Determine First Isolates
 #'
-#' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler *et al.* in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use [is_new_episode()] that also supports grouping with the `dplyr` package.
+#' Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler *et al.* in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use [is_new_episode()] that also supports grouping with the `dplyr` package.
 #' @inheritSection lifecycle Stable Lifecycle
 #' @param x a [data.frame] containing isolates. Can be left blank for automatic determination, see *Examples*.
 #' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column with a date class
@ -34,7 +34,7 @@
 #' @param col_testcode column name of the test codes. Use `col_testcode = NULL` to **not** exclude certain test codes (such as test codes for screening). In that case `testcodes_exclude` will be ignored.
 #' @param col_specimen column name of the specimen type or group
 #' @param col_icu column name of the logicals (`TRUE`/`FALSE`) whether a ward or department is an Intensive Care Unit (ICU)
-#' @param col_keyantimicrobials (only useful when `method = "phenotype-based"`) column name of the key antimicrobials to determine first (weighted) isolates, see [key_antimicrobials()]. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use `col_keyantimicrobials = FALSE` to prevent this. Can also be the output of [key_antimicrobials()].
+#' @param col_keyantimicrobials (only useful when `method = "phenotype-based"`) column name of the key antimicrobials to determine first isolates, see [key_antimicrobials()]. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use `col_keyantimicrobials = FALSE` to prevent this. Can also be the output of [key_antimicrobials()].
 #' @param episode_days episode in days after which a genus/species combination will be determined as 'first isolate' again. The default of 365 days is based on the guideline by CLSI, see *Source*. 
 #' @param testcodes_exclude a [character] vector with test codes that should be excluded (case-insensitive)
 #' @param icu_exclude a [logical] to indicate whether ICU isolates should be excluded (rows with value `TRUE` in the column set with `col_icu`)
@ -102,9 +102,9 @@
 #' 
 #' This is a more reliable method, since it also *weighs* the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:
 #' 
-#' 1. Using `type = "points"` and argument `points_threshold`
+#' 1. Using `type = "points"` and argument `points_threshold` (default)
 #' 
-#'    This method weighs *all* antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as 0.5 points, a difference from S to R (or vice versa) counts as 1 point. When the sum of points exceeds `points_threshold`, which defaults to `2`, an isolate will be selected as a first weighted isolate.
+#'    This method weighs *all* antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as `0.5` points, a difference from S to R (or vice versa) counts as `1` point. When the sum of points exceeds `points_threshold`, which defaults to `2`, an isolate will be selected as a first weighted isolate.
 #'    
 #'    All antimicrobials are internally selected using the [all_antimicrobials()] function. The output of this function does not need to be passed to the [first_isolate()] function.
 #' 
@ -218,7 +218,7 @@ first_isolate <- function(x = NULL,
  meet_criteria(col_icu, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
  # method
  method <- coerce_method(method)
-  meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based", "p", "e", "i"))
+  meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based"))
  # key antimicrobials
  if (length(col_keyantimicrobials) > 1) {
    meet_criteria(col_keyantimicrobials, allow_class = "character", has_length = nrow(x))
@ -256,11 +256,11 @@ first_isolate <- function(x = NULL,
    method <- "episode-based"
  }
  if (info == TRUE & message_not_thrown_before("first_isolate.method")) {
-    message_(paste0("Determining first isolates using the '", font_bold(method), "' method",
+    message_(paste0("Determining first isolates ",
                    ifelse(method %in% c("episode-based", "phenotype-based"),
                           ifelse(is.infinite(episode_days),
-                                  " without a specified episode length",
-                                  paste(" and an episode length of", episode_days, "days")),
+                                  "without a specified episode length",
+                                  paste("using an episode length of", episode_days, "days")),
                           "")),
             as_note = FALSE,
             add_fn = font_black)
@ -360,7 +360,7 @@ first_isolate <- function(x = NULL,
  }
  # remove testcodes
  if (!is.null(testcodes_exclude) & info == TRUE & message_not_thrown_before("first_isolate.excludingtestcodes")) {
-    message_("Excluding test codes: ", toString(paste0("'", testcodes_exclude, "'")),
+    message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE),
             add_fn = font_black,
             as_note = FALSE)
  }
@ -454,9 +454,7 @@ first_isolate <- function(x = NULL,
                                           episode_days = episode_days),
                                    use.names = FALSE)
  
-  weighted.notice <- ""
  if (!is.null(col_keyantimicrobials)) {
-    weighted.notice <- "weighted "
    if (info == TRUE & message_not_thrown_before("first_isolate.type")) {
      if (type == "keyantimicrobials") {
        message_("Basing inclusion on key antimicrobials, ",
@ -583,16 +581,16 @@ first_isolate <- function(x = NULL,
    }
    # mark up number of found
    n_found <- format(n_found, big.mark = big.mark, decimal.mark = decimal.mark)
-    if (p_found_total != p_found_scope) {
-      msg_txt <- paste0("=> Found ",
-                        font_bold(paste0(n_found, " first ", weighted.notice, "isolates")),
-                        " (", method, ", ", p_found_scope, " within scope and ", p_found_total, " of total where a microbial ID was available)")
-    } else {
-      msg_txt <- paste0("=> Found ",
-                        font_bold(paste0(n_found, " first ", weighted.notice, "isolates")),
-                        " (", method, ", ", p_found_total, " of total where a microbial ID was available)")
-    }
-    message_(msg_txt, add_fn = font_black, as_note = FALSE)
+    message_(paste0("=> Found ",
+                    font_bold(paste0(n_found,
+                                     ifelse(method == "isolate-based", "", paste0(" '", method, "'")),
+                                     " first isolates")),
+                    " (",
+                    ifelse(p_found_total != p_found_scope,
+                           paste0(p_found_scope, " within scope and "),
+                           ""),
+                    p_found_total, " of total where a microbial ID was available)"),
+             add_fn = font_black, as_note = FALSE)
  }
  
  x$newvar_first_isolate
@ -619,7 +617,7 @@ filter_first_isolate <- function(x = NULL,
  meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
  meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = FALSE)
  method <- coerce_method(method)
-  meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based", "p", "e", "i"))
+  meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based"))
  
  subset(x, first_isolate(x = x,
                          col_date = col_date,
@ -637,7 +635,7 @@ coerce_method <- function(method) {
  method <- tolower(as.character(method[1L]))
  method[method %like% "^(p$|pheno)"] <- "phenotype-based"
  method[method %like% "^(e$|episode)"] <- "episode-based"
-  method[method %like% "^patient"] <- "patient-based"
+  method[method %like% "^pat"] <- "patient-based"
  method[method %like% "^(i$|iso)"] <- "isolate-based"
  method
 }
--- a/R/guess_ab_col.R
+++ b/R/guess_ab_col.R
@ -179,7 +179,7 @@ get_column_abx <- function(x,
                        } else {
                          return(NA_character_)
                        }
-                      })
+                      }, USE.NAMES = FALSE)
  
  x_columns <- x_columns[!is.na(x_columns)]
  x <- x[, x_columns, drop = FALSE] # without drop = FALSE, x will become a vector when x_columns is length 1
@ -192,13 +192,27 @@ get_column_abx <- function(x,
  
  # add from self-defined dots (...):
  # such as get_column_abx(example_isolates %>% rename(thisone = AMX), amox = "thisone")
+  all_okay <- TRUE
  dots <- list(...)
  if (length(dots) > 0) {
    newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
    if (any(is.na(newnames))) {
-      warning_("Invalid antibiotic reference(s): ", toString(names(dots)[is.na(newnames)]),
+      if (info == TRUE) {
+        message_(" WARNING", add_fn = list(font_yellow, font_bold), as_note = FALSE)
+      }
+      warning_("Invalid antibiotic reference(s): ", vector_and(names(dots)[is.na(newnames)], quotes = FALSE),
               call = FALSE,
               immediate = TRUE)
+      all_okay <- FALSE
+    }
+    unexisting_cols <- which(!vapply(FUN.VALUE = logical(1), dots, function(col) all(col %in% x_columns)))
+    if (length(unexisting_cols) > 0) {
+      if (info == TRUE) {
+        message_(" ERROR", add_fn = list(font_red, font_bold), as_note = FALSE)
+      }
+      stop_("Column(s) not found: ", vector_and(unlist(dots[[unexisting_cols]]), quotes = FALSE),
+            call = FALSE)
+      all_okay <- FALSE
    }
    # turn all NULLs to NAs
    dots <- unlist(lapply(dots, function(dot) if (is.null(dot)) NA else dot))
@ -211,7 +225,7 @@ get_column_abx <- function(x,
  }
  
  if (length(out) == 0) {
-    if (info == TRUE) {
+    if (info == TRUE & all_okay == TRUE) {
      message_("No columns found.")
    }
    pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
@ -232,7 +246,7 @@ get_column_abx <- function(x,
  }
  
  # succeeded with auto-guessing
-  if (info == TRUE) {
+  if (info == TRUE & all_okay == TRUE) {
    message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
  }
  
--- a/data-raw/AMR_latest.tar.gz
+++ b/data-raw/AMR_latest.tar.gz
--- a/data-raw/_install_deps.R
+++ b/data-raw/_install_deps.R
@ -24,13 +24,13 @@
 # ==================================================================== #

 # some old R instances have trouble installing tinytest, so we ship it too
-install.packages("data-raw/tinytest_1.2.4.10.tar.gz", dependencies = c("Depends", "Imports"))
+install.packages("data-raw/tinytest_1.3.1.tar.gz", dependencies = c("Depends", "Imports"))
 install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)

 pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
                     unlist(strsplit(unlist(packageDescription("AMR",
                                                               fields = c("Suggests", "Enhances"))),
-                                     ", ?")))
+                                     split = ", ?")))
 cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n")

 to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
@ -39,7 +39,11 @@ if (length(to_install) == 0) {
 }
 for (i in seq_len(length(to_install))) {
  cat("Installing package", to_install[i], "\n")
-  tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = c("Depends", "Imports"), quiet = FALSE),
+  tryCatch(install.packages(to_install[i],
+                            # type = ifelse(.Platform$OS.type == "unix", "source", "binary"),
+                            repos = "https://cran.rstudio.com/",
+                            dependencies = c("Depends", "Imports"),
+                            quiet = FALSE),
           # message = function(m) invisible(),
           warning = function(w) message(w$message),
           error = function(e) message(e$message))
@ -51,9 +55,10 @@ if (length(to_update) == 0) {
  message("\nNothing to update\n")
 }
 for (i in seq_len(length(to_update))) {
-  cat("Updating package", to_update[i], "\n")
+  cat("Updating package '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
  tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),
           # message = function(m) invisible(),
           warning = function(w) message(w$message),
           error = function(e) message(e$message))
+  cat("Updated to '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
 }
--- a/data-raw/tinytest_1.3.1.tar.gz
+++ b/data-raw/tinytest_1.3.1.tar.gz
--- a/docs/404.html
+++ b/docs/404.html
@ -43,7 +43,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -173,13 +173,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="https://msberends.github.io/AMR/survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
 </div>
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@ -92,7 +92,7 @@
      </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">1.7.1.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
      </span>
    </div>

--- a/docs/articles/AMR.html
+++ b/docs/articles/AMR.html
@ -44,7 +44,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -174,13 +174,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
 </div>
@ -198,7 +191,7 @@
      <h1 data-toc-skip>How to conduct AMR data analysis</h1>
                        <h4 data-toc-skip class="author">Matthijs S. Berends</h4>
            
-            <h4 data-toc-skip class="date">17 August 2021</h4>
+            <h4 data-toc-skip class="date">29 August 2021</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
      <div class="hidden name"><code>AMR.Rmd</code></div>
@ -207,7 +200,7 @@

    
    
-<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/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 17 August 2021.</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/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 29 August 2021.</p>
 <div id="introduction" class="section level1">
 <h1 class="hasAnchor">
 <a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h1>
@ -238,21 +231,21 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2021-08-17</td>
+<td align="center">2021-08-29</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">2021-08-17</td>
+<td align="center">2021-08-29</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">2021-08-17</td>
+<td align="center">2021-08-29</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@ -349,68 +342,68 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2012-12-11</td>
-<td align="center">B5</td>
-<td align="center">Hospital D</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">R</td>
-<td align="center">M</td>
-</tr>
-<tr class="even">
-<td align="center">2012-01-03</td>
-<td align="center">D5</td>
-<td align="center">Hospital B</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">S</td>
-<td align="center">M</td>
-</tr>
-<tr class="odd">
-<td align="center">2013-03-20</td>
-<td align="center">E3</td>
+<td align="center">2012-06-29</td>
+<td align="center">E6</td>
 <td align="center">Hospital A</td>
 <td align="center">Escherichia coli</td>
-<td align="center">I</td>
-<td align="center">I</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">M</td>
-</tr>
-<tr class="even">
-<td align="center">2017-02-14</td>
-<td align="center">L5</td>
-<td align="center">Hospital B</td>
-<td align="center">Klebsiella 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">M</td>
 </tr>
-<tr class="odd">
-<td align="center">2010-04-27</td>
-<td align="center">Y6</td>
+<tr class="even">
+<td align="center">2014-08-25</td>
+<td align="center">D8</td>
 <td align="center">Hospital D</td>
-<td align="center">Escherichia coli</td>
+<td align="center">Klebsiella pneumoniae</td>
+<td align="center">R</td>
+<td align="center">I</td>
 <td align="center">S</td>
 <td align="center">S</td>
+<td align="center">M</td>
+</tr>
+<tr class="odd">
+<td align="center">2017-01-14</td>
+<td align="center">V1</td>
+<td align="center">Hospital C</td>
+<td align="center">Streptococcus pneumoniae</td>
+<td align="center">I</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">2011-08-04</td>
-<td align="center">O2</td>
+<td align="center">2010-10-15</td>
+<td align="center">X2</td>
 <td align="center">Hospital B</td>
 <td align="center">Staphylococcus aureus</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>
+</tr>
+<tr class="odd">
+<td align="center">2011-04-05</td>
+<td align="center">H6</td>
+<td align="center">Hospital A</td>
+<td align="center">Streptococcus pneumoniae</td>
+<td align="center">S</td>
+<td align="center">I</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">M</td>
+</tr>
+<tr class="even">
+<td align="center">2012-01-10</td>
+<td align="center">Y7</td>
+<td align="center">Hospital D</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">R</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
@ -446,16 +439,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,443</td>
-<td align="right">52.22%</td>
-<td align="right">10,443</td>
-<td align="right">52.22%</td>
+<td align="right">10,326</td>
+<td align="right">51.63%</td>
+<td align="right">10,326</td>
+<td align="right">51.63%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,557</td>
-<td align="right">47.79%</td>
+<td align="right">9,674</td>
+<td align="right">48.37%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@ -510,9 +503,9 @@ Longest: 1</p>
 <span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
 <span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
 <span class="co"># 2</span>
-<span class="co"># =&gt; Found 10,606 first weighted isolates (phenotype-based, 53.0% of total</span>
+<span class="co"># =&gt; Found 10,571 first weighted isolates (phenotype-based, 52.9% of total</span>
 <span class="co">#    where a microbial ID was available)</span></code></pre></div>
-<p>So only 53.0% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
+<p>So only 52.9% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
@ -520,7 +513,7 @@ Longest: 1</p>
 <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
-<p>So we end up with 10,606 isolates for analysis. Now our data looks like:</p>
+<p>So we end up with 10,571 isolates for analysis. Now our data looks like:</p>
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
 <table style="width:100%;" class="table">
@ -559,27 +552,11 @@ Longest: 1</p>
 <tbody>
 <tr class="odd">
 <td align="left">1</td>
-<td align="center">2012-12-11</td>
-<td align="center">B5</td>
-<td align="center">Hospital D</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">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">TRUE</td>
-</tr>
-<tr class="even">
-<td align="left">2</td>
-<td align="center">2012-01-03</td>
-<td align="center">D5</td>
-<td align="center">Hospital B</td>
+<td align="center">2012-06-29</td>
+<td align="center">E6</td>
+<td align="center">Hospital A</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>
@ -589,14 +566,14 @@ Longest: 1</p>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="odd">
-<td align="left">4</td>
-<td align="center">2017-02-14</td>
-<td align="center">L5</td>
-<td align="center">Hospital B</td>
+<tr class="even">
+<td align="left">2</td>
+<td align="center">2014-08-25</td>
+<td align="center">D8</td>
+<td align="center">Hospital D</td>
 <td align="center">B_KLBSL_PNMN</td>
 <td align="center">R</td>
-<td align="center">S</td>
+<td align="center">I</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
@ -605,52 +582,68 @@ Longest: 1</p>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
-<td align="left">7</td>
-<td align="center">2012-03-07</td>
-<td align="center">I8</td>
-<td align="center">Hospital B</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">M</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="left">9</td>
-<td align="center">2010-12-20</td>
-<td align="center">H10</td>
+<td align="left">4</td>
+<td align="center">2010-10-15</td>
+<td align="center">X2</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STPHY_AURS</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">S</td>
-<td align="center">M</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">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">11</td>
-<td align="center">2014-01-24</td>
-<td align="center">M2</td>
-<td align="center">Hospital B</td>
-<td align="center">B_ESCHR_COLI</td>
+<td align="left">6</td>
+<td align="center">2012-01-10</td>
+<td align="center">Y7</td>
+<td align="center">Hospital D</td>
+<td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">R</td>
+<td align="center">R</td>
+<td align="center">F</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="left">8</td>
+<td align="center">2016-02-07</td>
+<td align="center">V2</td>
+<td align="center">Hospital A</td>
+<td align="center">B_KLBSL_PNMN</td>
+<td align="center">R</td>
 <td align="center">S</td>
-<td align="center">M</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="left">10</td>
+<td align="center">2016-11-08</td>
+<td align="center">D4</td>
+<td align="center">Hospital A</td>
+<td align="center">B_STPHY_AURS</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</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>
 </tbody>
@ -674,8 +667,8 @@ Longest: 1</p>
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
-Length: 10,606<br>
-Available: 10,606 (100.0%, NA: 0 = 0.0%)<br>
+Length: 10,571<br>
+Available: 10,571 (100.0%, NA: 0 = 0.0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@ -692,33 +685,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">4,494</td>
-<td align="right">42.37%</td>
-<td align="right">4,494</td>
-<td align="right">42.37%</td>
+<td align="right">4,507</td>
+<td align="right">42.64%</td>
+<td align="right">4,507</td>
+<td align="right">42.64%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">2,785</td>
-<td align="right">26.26%</td>
-<td align="right">7,279</td>
-<td align="right">68.63%</td>
+<td align="right">2,799</td>
+<td align="right">26.48%</td>
+<td align="right">7,306</td>
+<td align="right">69.11%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,106</td>
-<td align="right">19.86%</td>
-<td align="right">9,385</td>
-<td align="right">88.49%</td>
+<td align="right">2,087</td>
+<td align="right">19.74%</td>
+<td align="right">9,393</td>
+<td align="right">88.86%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,221</td>
-<td align="right">11.51%</td>
-<td align="right">10,606</td>
+<td align="right">1,178</td>
+<td align="right">11.14%</td>
+<td align="right">10,571</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@ -765,8 +758,83 @@ Longest: 24</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2012-12-11</td>
-<td align="center">B5</td>
+<td align="center">2010-10-15</td>
+<td align="center">X2</td>
+<td align="center">Hospital B</td>
+<td align="center">B_STPHY_AURS</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-positive</td>
+<td align="center">Staphylococcus</td>
+<td align="center">aureus</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td align="center">2012-01-10</td>
+<td align="center">Y7</td>
+<td align="center">Hospital D</td>
+<td align="center">B_STRPT_PNMN</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">F</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">2014-02-02</td>
+<td align="center">K7</td>
+<td align="center">Hospital A</td>
+<td align="center">B_STPHY_AURS</td>
+<td align="center">S</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">Staphylococcus</td>
+<td align="center">aureus</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td align="center">2011-08-05</td>
+<td align="center">V3</td>
+<td align="center">Hospital B</td>
+<td align="center">B_STRPT_PNMN</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-positive</td>
+<td align="center">Streptococcus</td>
+<td align="center">pneumoniae</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="odd">
+<td align="center">2014-06-16</td>
+<td align="center">Z8</td>
+<td align="center">Hospital B</td>
+<td align="center">B_STRPT_PNMN</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-positive</td>
+<td align="center">Streptococcus</td>
+<td align="center">pneumoniae</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td align="center">2017-08-23</td>
+<td align="center">J10</td>
 <td align="center">Hospital D</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
@ -779,81 +847,6 @@ Longest: 24</p>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
-<td align="center">2011-06-11</td>
-<td align="center">L7</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">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">TRUE</td>
-</tr>
-<tr class="odd">
-<td align="center">2012-12-19</td>
-<td align="center">A10</td>
-<td align="center">Hospital B</td>
-<td align="center">B_STRPT_PNMN</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">R</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">TRUE</td>
-</tr>
-<tr class="even">
-<td align="center">2014-12-05</td>
-<td align="center">M6</td>
-<td align="center">Hospital B</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">R</td>
-<td align="center">M</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">2017-05-14</td>
-<td align="center">L8</td>
-<td align="center">Hospital C</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">R</td>
-<td align="center">M</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="even">
-<td align="center">2010-12-14</td>
-<td align="center">Q1</td>
-<td align="center">Hospital C</td>
-<td align="center">B_STPHY_AURS</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-positive</td>
-<td align="center">Staphylococcus</td>
-<td align="center">aureus</td>
-<td align="center">TRUE</td>
-</tr>
 </tbody>
 </table>
 <p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
@ -875,50 +868,50 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">2137</td>
-<td align="center">139</td>
-<td align="center">2218</td>
-<td align="center">4494</td>
+<td align="center">2196</td>
+<td align="center">119</td>
+<td align="center">2192</td>
+<td align="center">4507</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">AMC</td>
-<td align="center">3298</td>
-<td align="center">157</td>
-<td align="center">1039</td>
-<td align="center">4494</td>
+<td align="center">3378</td>
+<td align="center">151</td>
+<td align="center">978</td>
+<td align="center">4507</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">3230</td>
+<td align="center">3282</td>
 <td align="center">0</td>
-<td align="center">1264</td>
-<td align="center">4494</td>
+<td align="center">1225</td>
+<td align="center">4507</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">3946</td>
+<td align="center">3929</td>
 <td align="center">0</td>
-<td align="center">548</td>
-<td align="center">4494</td>
+<td align="center">578</td>
+<td align="center">4507</td>
 </tr>
 <tr class="odd">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMX</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">1221</td>
-<td align="center">1221</td>
+<td align="center">1178</td>
+<td align="center">1178</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">967</td>
-<td align="center">44</td>
-<td align="center">210</td>
-<td align="center">1221</td>
+<td align="center">930</td>
+<td align="center">45</td>
+<td align="center">203</td>
+<td align="center">1178</td>
 </tr>
 </tbody>
 </table>
@ -941,34 +934,34 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">3946</td>
+<td align="center">3929</td>
 <td align="center">0</td>
-<td align="center">548</td>
-<td align="center">4494</td>
+<td align="center">578</td>
+<td align="center">4507</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">GEN</td>
-<td align="center">1088</td>
+<td align="center">1052</td>
 <td align="center">0</td>
-<td align="center">133</td>
-<td align="center">1221</td>
+<td align="center">126</td>
+<td align="center">1178</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">GEN</td>
-<td align="center">2490</td>
+<td align="center">2473</td>
 <td align="center">0</td>
-<td align="center">295</td>
-<td align="center">2785</td>
+<td align="center">326</td>
+<td align="center">2799</td>
 </tr>
 <tr class="even">
 <td align="center">S. pneumoniae</td>
 <td align="center">GEN</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">2106</td>
-<td align="center">2106</td>
+<td align="center">2087</td>
+<td align="center">2087</td>
 </tr>
 </tbody>
 </table>
@ -982,7 +975,7 @@ Longest: 24</p>
 <p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
 <div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
-<span class="co"># [1] 0.5427117</span></code></pre></div>
+<span class="co"># [1] 0.5403462</span></code></pre></div>
 <p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> 
@ -996,19 +989,19 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5356582</td>
+<td align="center">0.5487147</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5408108</td>
+<td align="center">0.5436519</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5371153</td>
+<td align="center">0.5257549</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5614714</td>
+<td align="center">0.5338095</td>
 </tr>
 </tbody>
 </table>
@ -1027,23 +1020,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5356582</td>
-<td align="center">3183</td>
+<td align="center">0.5487147</td>
+<td align="center">3151</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5408108</td>
-<td align="center">3700</td>
+<td align="center">0.5436519</td>
+<td align="center">3631</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5371153</td>
-<td align="center">1657</td>
+<td align="center">0.5257549</td>
+<td align="center">1689</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5614714</td>
-<td align="center">2066</td>
+<td align="center">0.5338095</td>
+<td align="center">2100</td>
 </tr>
 </tbody>
 </table>
@ -1064,27 +1057,27 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.7688028</td>
-<td align="center">0.8780596</td>
-<td align="center">0.9815309</td>
+<td align="center">0.7830042</td>
+<td align="center">0.8717550</td>
+<td align="center">0.9764810</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.8280098</td>
-<td align="center">0.8910729</td>
-<td align="center">0.9754300</td>
+<td align="center">0.8276740</td>
+<td align="center">0.8930390</td>
+<td align="center">0.9787776</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.7921005</td>
-<td align="center">0.8940754</td>
-<td align="center">0.9795332</td>
+<td align="center">0.7874241</td>
+<td align="center">0.8835298</td>
+<td align="center">0.9828510</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.5351377</td>
+<td align="center">0.5318639</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5351377</td>
+<td align="center">0.5318639</td>
 </tr>
 </tbody>
 </table>
@ -1109,23 +1102,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="left">Hospital A</td>
-<td align="right">53.6%</td>
-<td align="right">26.4%</td>
+<td align="right">54.9%</td>
+<td align="right">25.8%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital B</td>
-<td align="right">54.1%</td>
-<td align="right">24.6%</td>
+<td align="right">54.4%</td>
+<td align="right">27.8%</td>
 </tr>
 <tr class="odd">
 <td align="left">Hospital C</td>
-<td align="right">53.7%</td>
-<td align="right">27.5%</td>
+<td align="right">52.6%</td>
+<td align="right">25.0%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital D</td>
-<td align="right">56.1%</td>
-<td align="right">29.0%</td>
+<td align="right">53.4%</td>
+<td align="right">24.3%</td>
 </tr>
 </tbody>
 </table>
@ -1209,16 +1202,16 @@ Longest: 24</p>
 <code class="sourceCode R"><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
 <span class="va">mic_values</span>
 <span class="co"># Class &lt;mic&gt;</span>
-<span class="co">#   [1] 0.25   16     0.0625 32     0.025  1      256    64     0.002  0.005 </span>
-<span class="co">#  [11] 0.01   0.005  8      0.01   0.025  128    0.01   8      0.005  256   </span>
-<span class="co">#  [21] 0.005  8      0.0625 0.125  0.005  16     8      2      0.5    4     </span>
-<span class="co">#  [31] 2      32     0.25   0.25   8      0.025  0.25   8      64     1     </span>
-<span class="co">#  [41] 0.005  0.01   0.005  256    0.025  0.5    2      0.025  0.5    0.005 </span>
-<span class="co">#  [51] 0.0625 128    4      1      0.0625 0.002  16     0.002  8      0.005 </span>
-<span class="co">#  [61] 1      1      8      32     0.002  32     0.25   8      4      0.001 </span>
-<span class="co">#  [71] 2      16     16     0.025  0.005  0.0625 2      128    0.001  2     </span>
-<span class="co">#  [81] 64     0.025  16     64     2      128    8      0.5    4      256   </span>
-<span class="co">#  [91] 0.5    32     0.001  0.01   2      64     4      32     4      0.0625</span></code></pre></div>
+<span class="co">#   [1] 1      128    0.01   0.25   0.01   16     0.001  0.125  0.25   0.01  </span>
+<span class="co">#  [11] 0.005  16     0.0625 64     &gt;=256  0.5    0.01   16     0.5    0.0625</span>
+<span class="co">#  [21] 0.001  0.5    0.0625 4      2      8      0.5    0.0625 0.125  128   </span>
+<span class="co">#  [31] 0.002  0.25   2      8      0.125  0.0625 0.125  16     128    0.002 </span>
+<span class="co">#  [41] 1      0.005  2      32     0.01   0.0625 &gt;=256  64     16     0.005 </span>
+<span class="co">#  [51] 2      0.001  &gt;=256  32     64     &gt;=256  128    0.01   0.005  0.001 </span>
+<span class="co">#  [61] 0.01   0.125  2      0.125  &gt;=256  32     64     0.01   2      0.25  </span>
+<span class="co">#  [71] 0.01   64     0.5    128    0.001  64     128    0.002  &gt;=256  64    </span>
+<span class="co">#  [81] 0.01   8      0.5    4      16     0.025  0.025  0.001  0.125  0.025 </span>
+<span class="co">#  [91] 2      64     64     128    32     128    0.001  32     2      0.005</span></code></pre></div>
 <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># base R:</span>
 <span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></code></pre></div>
@ -1247,10 +1240,10 @@ Longest: 24</p>
 <span class="co">#   to review it.</span>
 <span class="va">disk_values</span>
 <span class="co"># Class &lt;disk&gt;</span>
-<span class="co">#   [1] 26 25 28 21 24 22 21 27 22 21 31 25 26 17 28 29 18 31 21 30 23 28 22 18 28</span>
-<span class="co">#  [26] 21 25 26 18 30 22 28 25 28 25 21 29 26 19 21 19 26 31 17 25 22 21 27 24 26</span>
-<span class="co">#  [51] 20 17 18 27 31 31 20 31 26 22 25 22 19 22 27 19 25 27 30 17 24 27 22 28 18</span>
-<span class="co">#  [76] 26 30 29 25 23 26 29 19 25 25 24 25 30 29 25 29 17 26 21 20 29 26 23 29 31</span></code></pre></div>
+<span class="co">#   [1] 30 29 25 23 27 18 23 21 31 26 17 30 18 31 30 25 22 19 18 26 31 19 21 25 29</span>
+<span class="co">#  [26] 22 26 30 20 20 18 19 18 29 22 17 27 21 24 18 17 23 27 18 19 31 18 29 30 25</span>
+<span class="co">#  [51] 27 23 21 20 31 19 19 25 25 23 23 19 17 25 21 30 20 31 26 23 29 27 30 29 24</span>
+<span class="co">#  [76] 20 23 23 27 20 24 19 28 24 31 29 26 23 20 29 23 18 17 27 21 28 28 17 23 17</span></code></pre></div>
 <div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># base R:</span>
 <span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></code></pre></div>
--- a/docs/articles/AMR_files/figure-html/disk_plots-1.png
+++ b/docs/articles/AMR_files/figure-html/disk_plots-1.png
--- a/docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
+++ b/docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
--- a/docs/articles/AMR_files/figure-html/mic_plots-1.png
+++ b/docs/articles/AMR_files/figure-html/mic_plots-1.png
--- a/docs/articles/AMR_files/figure-html/mic_plots-2.png
+++ b/docs/articles/AMR_files/figure-html/mic_plots-2.png
--- a/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
+++ b/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
--- a/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
+++ b/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
--- a/docs/articles/AMR_files/figure-html/plot
+++ b/docs/articles/AMR_files/figure-html/plot
--- a/docs/articles/AMR_files/figure-html/plot
+++ b/docs/articles/AMR_files/figure-html/plot
--- a/docs/articles/AMR_files/figure-html/plot
+++ b/docs/articles/AMR_files/figure-html/plot
--- a/docs/articles/AMR_files/figure-html/plot
+++ b/docs/articles/AMR_files/figure-html/plot
--- a/docs/articles/EUCAST.html
+++ b/docs/articles/EUCAST.html
@ -44,7 +44,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -174,13 +174,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
 </div>
--- a/docs/articles/MDR.html
+++ b/docs/articles/MDR.html
@ -44,7 +44,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -174,13 +174,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
 </div>
@ -364,19 +357,19 @@ Unique: 2</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
 <span class="co">#   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
-<span class="co"># 1          I         I            I          S            R            R</span>
-<span class="co"># 2          I         R            R          R            I            R</span>
-<span class="co"># 3          S         I            R          S            I            I</span>
-<span class="co"># 4          S         S            S          S            I            R</span>
-<span class="co"># 5          R         S            R          I            I            S</span>
-<span class="co"># 6          I         R            S          R            R            I</span>
+<span class="co"># 1          S         I            I          R            I            I</span>
+<span class="co"># 2          S         S            I          I            R            R</span>
+<span class="co"># 3          I         S            S          I            I            R</span>
+<span class="co"># 4          S         R            S          R            S            R</span>
+<span class="co"># 5          R         S            R          S            R            R</span>
+<span class="co"># 6          I         S            S          R            I            S</span>
 <span class="co">#   kanamycin</span>
 <span class="co"># 1         I</span>
 <span class="co"># 2         R</span>
 <span class="co"># 3         I</span>
 <span class="co"># 4         R</span>
 <span class="co"># 5         R</span>
-<span class="co"># 6         S</span></code></pre></div>
+<span class="co"># 6         I</span></code></pre></div>
 <p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></code></pre></div>
@ -419,40 +412,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3227</td>
-<td align="right">64.54%</td>
-<td align="right">3227</td>
-<td align="right">64.54%</td>
+<td align="right">3144</td>
+<td align="right">62.88%</td>
+<td align="right">3144</td>
+<td align="right">62.88%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">990</td>
-<td align="right">19.80%</td>
-<td align="right">4217</td>
-<td align="right">84.34%</td>
+<td align="right">1027</td>
+<td align="right">20.54%</td>
+<td align="right">4171</td>
+<td align="right">83.42%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
 <td align="right">464</td>
 <td align="right">9.28%</td>
-<td align="right">4681</td>
-<td align="right">93.62%</td>
+<td align="right">4635</td>
+<td align="right">92.70%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">223</td>
-<td align="right">4.46%</td>
-<td align="right">4904</td>
-<td align="right">98.08%</td>
+<td align="right">257</td>
+<td align="right">5.14%</td>
+<td align="right">4892</td>
+<td align="right">97.84%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">96</td>
-<td align="right">1.92%</td>
+<td align="right">108</td>
+<td align="right">2.16%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
--- a/docs/articles/PCA.html
+++ b/docs/articles/PCA.html
@ -44,7 +44,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -174,13 +174,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
 </div>
--- a/docs/articles/SPSS.html
+++ b/docs/articles/SPSS.html
@ -44,7 +44,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -174,13 +174,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
 </div>
@ -198,7 +191,7 @@
      <h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
                        <h4 data-toc-skip class="author">Matthijs S. Berends</h4>
            
-            <h4 data-toc-skip class="date">17 August 2021</h4>
+            <h4 data-toc-skip class="date">29 August 2021</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
      <div class="hidden name"><code>SPSS.Rmd</code></div>
@ -233,7 +226,7 @@
 </li>
 <li>
 <p><strong>R has a huge community.</strong></p>
-<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">414,789 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
+<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">415,751 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
 </li>
 <li>
 <p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>
--- a/docs/articles/WHONET.html
+++ b/docs/articles/WHONET.html
@ -44,7 +44,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -174,13 +174,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
 </div>
--- a/docs/articles/benchmarks.html
+++ b/docs/articles/benchmarks.html
@ -44,7 +44,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -174,13 +174,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
 </div>
@ -231,32 +224,19 @@
  times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span>
 <span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
-<span class="co">#                                   expr   min    lq mean median    uq   max</span>
-<span class="co">#                           as.mo("sau")  12.0  13.0   14   13.0  13.0  45.0</span>
-<span class="co">#                          as.mo("stau")  55.0  58.0   72   60.0  92.0 100.0</span>
-<span class="co">#                          as.mo("STAU")  54.0  59.0   85   91.0  94.0 200.0</span>
-<span class="co">#                        as.mo("staaur")  11.0  12.0   19   13.0  15.0  58.0</span>
-<span class="co">#                        as.mo("STAAUR")  12.0  13.0   21   14.0  16.0  63.0</span>
-<span class="co">#                     as.mo("S. aureus")  24.0  28.0   41   30.0  62.0  73.0</span>
-<span class="co">#                      as.mo("S aureus")  26.0  28.0   37   30.0  33.0  75.0</span>
-<span class="co">#         as.mo("Staphylococcus aureus")   3.1   3.8    4    3.9   4.2   4.7</span>
-<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 250.0 260.0  270  260.0 290.0 300.0</span>
-<span class="co">#       as.mo("Sthafilokkockus aaureuz") 160.0 200.0  200  200.0 200.0 240.0</span>
-<span class="co">#                          as.mo("MRSA")  11.0  13.0   20   13.0  15.0  55.0</span>
-<span class="co">#                          as.mo("VISA")  21.0  22.0   31   23.0  27.0  69.0</span>
-<span class="co">#  neval</span>
-<span class="co">#     25</span>
-<span class="co">#     25</span>
-<span class="co">#     25</span>
-<span class="co">#     25</span>
-<span class="co">#     25</span>
-<span class="co">#     25</span>
-<span class="co">#     25</span>
-<span class="co">#     25</span>
-<span class="co">#     25</span>
-<span class="co">#     25</span>
-<span class="co">#     25</span>
-<span class="co">#     25</span></code></pre></div>
+<span class="co">#                                   expr   min    lq  mean median    uq max neval</span>
+<span class="co">#                           as.mo("sau")  12.0  13.0  15.0   14.0  15.0  48    25</span>
+<span class="co">#                          as.mo("stau")  54.0  57.0  73.0   62.0  92.0  99    25</span>
+<span class="co">#                          as.mo("STAU")  54.0  58.0  73.0   63.0  91.0  98    25</span>
+<span class="co">#                        as.mo("staaur")  13.0  13.0  20.0   14.0  15.0  52    25</span>
+<span class="co">#                        as.mo("STAAUR")  11.0  13.0  18.0   14.0  16.0  47    25</span>
+<span class="co">#                     as.mo("S. aureus")  27.0  30.0  38.0   31.0  36.0  63    25</span>
+<span class="co">#                      as.mo("S aureus")  27.0  29.0  42.0   33.0  60.0  66    25</span>
+<span class="co">#         as.mo("Staphylococcus aureus")   3.8   4.1   6.8    4.2   4.6  36    25</span>
+<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 240.0 250.0 280.0  270.0 300.0 320    25</span>
+<span class="co">#       as.mo("Sthafilokkockus aaureuz") 160.0 190.0 200.0  200.0 210.0 340    25</span>
+<span class="co">#                          as.mo("MRSA")  13.0  13.0  17.0   14.0  15.0  46    25</span>
+<span class="co">#                          as.mo("VISA")  20.0  23.0  34.0   25.0  52.0  59    25</span></code></pre></div>
 <p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
 <p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 200 times slower to determine.</p>
 <p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
@ -278,7 +258,7 @@
 <span class="co"># what do these values look like? They are of class &lt;mo&gt;:</span>
 <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
 <span class="co"># Class &lt;mo&gt;</span>
-<span class="co"># [1] B_STPHY_AURS B_STPHY_CONS B_ESCHR_COLI B_STRPT_PYGN B_STPHY_CONS</span>
+<span class="co"># [1] B_STRPT_PNMN B_KLBSL_PNMN B_ESCHR_COLI B_SERRT_MRCS B_STPHY_CONS</span>
 <span class="co"># [6] B_ESCHR_COLI</span>
  
 <span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
@ -295,7 +275,7 @@
 <span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#        expr min  lq mean median  uq max neval</span>
-<span class="co">#  mo_name(x) 163 204  267    233 346 398    10</span></code></pre></div>
+<span class="co">#  mo_name(x) 188 202  260    233 335 408    10</span></code></pre></div>
 <p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.233 seconds. That is 116 nanoseconds on average. You only lose time on your unique input values.</p>
 </div>
 <div id="precalculated-results" class="section level3">
@ -310,10 +290,10 @@
 <span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#  expr   min    lq  mean median    uq   max neval</span>
-<span class="co">#     A  7.93  8.08 14.50   8.35  8.46 70.00    10</span>
-<span class="co">#     B 22.40 22.80 24.30  24.30 24.60 27.20    10</span>
-<span class="co">#     C  1.89  2.00  2.19   2.15  2.30  2.76    10</span></code></pre></div>
-<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0021 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
+<span class="co">#     A  8.09  8.18  8.94   8.69  9.47 10.50    10</span>
+<span class="co">#     B 23.40 24.90 31.90  27.90 28.20 80.70    10</span>
+<span class="co">#     C  2.03  2.20  2.35   2.35  2.48  2.66    10</span></code></pre></div>
+<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0023 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
                         B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
@ -327,14 +307,14 @@
 <span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#  expr  min   lq mean median   uq  max neval</span>
-<span class="co">#     A 1.73 1.78 1.83   1.81 1.90 1.90    10</span>
-<span class="co">#     B 1.73 1.83 1.90   1.89 1.98 2.04    10</span>
-<span class="co">#     C 1.72 1.79 1.88   1.85 1.95 2.08    10</span>
-<span class="co">#     D 1.75 1.75 1.85   1.88 1.91 1.93    10</span>
-<span class="co">#     E 1.70 1.78 1.82   1.80 1.83 2.02    10</span>
-<span class="co">#     F 1.68 1.78 1.79   1.79 1.81 1.91    10</span>
-<span class="co">#     G 1.69 1.75 1.79   1.79 1.81 1.89    10</span>
-<span class="co">#     H 1.68 1.71 1.85   1.76 1.85 2.65    10</span></code></pre></div>
+<span class="co">#     A 1.68 1.72 1.88   1.88 1.97 2.32    10</span>
+<span class="co">#     B 1.64 1.80 1.90   1.95 1.98 2.14    10</span>
+<span class="co">#     C 1.71 1.74 1.88   1.80 2.08 2.21    10</span>
+<span class="co">#     D 1.70 1.79 1.86   1.87 1.96 1.99    10</span>
+<span class="co">#     E 1.73 1.85 1.94   1.91 2.03 2.20    10</span>
+<span class="co">#     F 1.71 1.78 1.91   1.89 2.00 2.25    10</span>
+<span class="co">#     G 1.66 1.78 1.87   1.88 1.98 2.04    10</span>
+<span class="co">#     H 1.73 1.82 2.06   1.98 2.07 2.80    10</span></code></pre></div>
 <p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
 </div>
 <div id="results-in-other-languages" class="section level3">
@ -362,13 +342,13 @@
 <span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#  expr   min    lq  mean median    uq    max neval</span>
-<span class="co">#    en 19.47 20.23 24.54  20.72 21.85  89.57   100</span>
-<span class="co">#    de 30.58 31.52 41.31  32.78 34.76  86.03   100</span>
-<span class="co">#    nl 34.81 35.58 45.89  36.76 39.41  94.01   100</span>
-<span class="co">#    es 34.41 35.12 40.08  36.22 37.33  94.71   100</span>
-<span class="co">#    it 23.93 24.65 27.31  25.15 25.84  81.01   100</span>
-<span class="co">#    fr 23.59 24.40 31.40  25.01 25.62 200.30   100</span>
-<span class="co">#    pt 23.69 24.73 30.23  25.57 26.32  82.19   100</span></code></pre></div>
+<span class="co">#    en 19.64 20.10 28.32  20.72 22.65 104.80   100</span>
+<span class="co">#    de 30.76 31.59 37.06  32.27 33.87  95.10   100</span>
+<span class="co">#    nl 34.88 35.58 43.87  36.41 38.73  94.00   100</span>
+<span class="co">#    es 34.62 35.22 44.72  36.04 37.88  97.92   100</span>
+<span class="co">#    it 24.03 24.59 28.09  25.19 26.12  79.32   100</span>
+<span class="co">#    fr 23.79 24.37 30.37  24.89 26.29 194.10   100</span>
+<span class="co">#    pt 23.85 24.42 28.21  24.90 26.22  83.14   100</span></code></pre></div>
 <p>Currently supported non-English languages are German, Dutch, Spanish, Italian, French and Portuguese.</p>
 </div>
  </div>
--- a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png
+++ b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png
--- a/docs/articles/datasets.html
+++ b/docs/articles/datasets.html
@ -44,7 +44,7 @@
      </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">1.7.1.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9038</span>
      </span>
    </div>

@ -190,7 +190,7 @@
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>Data sets for download / own use</h1>
            
-            <h4 data-toc-skip class="date">20 August 2021</h4>
+            <h4 data-toc-skip class="date">01 September 2021</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
      <div class="hidden name"><code>datasets.Rmd</code></div>
@ -1256,7 +1256,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi

      <footer><div class="copyright">
  <p></p>
-<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
+<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>.</p>
 </div>

 <div class="pkgdown">
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@ -92,7 +92,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -222,13 +222,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/articles/resistance_predict.html
+++ b/docs/articles/resistance_predict.html
@ -44,7 +44,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -174,13 +174,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
 </div>
--- a/docs/articles/welcome_to_AMR.html
+++ b/docs/articles/welcome_to_AMR.html
@ -44,7 +44,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -174,13 +174,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
 </div>
--- a/docs/authors.html
+++ b/docs/authors.html
@ -92,7 +92,7 @@
      </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">1.7.1.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
      </span>
    </div>

@ -241,7 +241,7 @@
    </div>

    <p>Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2021). AMR - An R Package for Working with
-Antimicrobial Resistance Data. Journal of Statistical Software (accepted for publication), https://www.biorxiv.org/content/10.1101/810622v4</p>
+Antimicrobial Resistance Data. Journal of Statistical Software (accepted for publication), https://www.biorxiv.org/content/10.1101/810622v4.</p>
    <pre>@Article{,
  title = {AMR - An R Package for Working with Antimicrobial Resistance Data},
  author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner},
@ -251,6 +251,16 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
  year = {2021},
  url = {https://www.biorxiv.org/content/10.1101/810622v4},
 }</pre>
+    <p>Berends, MS (2021). A New Instrument for Microbial Epidemiology: Empowering Antimicrobial Resistance Data Analysis (PhD thesis). University of Groningen, doi: 10.33612/diss.177417131.</p>
+    <pre>@PhdThesis{,
+  title = {A New Instrument for Microbial Epidemiology: Empowering Antimicrobial Resistance Data Analysis},
+  author = {M S Berends},
+  publisher = {University of Groningen},
+  school = {University of Groningen},
+  doi = {10.33612/diss.177417131},
+  pages = {288},
+  year = {2021},
+}</pre>

    <div class="page-header">
      <h1>Authors</h1>
--- a/docs/extra.js
+++ b/docs/extra.js
@ -98,6 +98,7 @@ $(document).ready(function() {
      x = x.replace(/Author, maintainer/g, "Main developer");
      x = x.replace(/Author, contributor/g, "Main contributor");
      x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
+      x = x.replace("Matthijs", "Dr. Matthijs");
      x = x.replace("Alex", "Prof. Dr. Alex");
      x = x.replace("Bhanu", "Prof. Dr. Bhanu");
      x = x.replace("Casper", "Prof. Dr. Casper");
--- a/docs/index.html
+++ b/docs/index.html
@ -47,7 +47,7 @@
      </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">1.7.1.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
      </span>
    </div>

@ -194,10 +194,12 @@
 <div class="page-header"><h1 class="hasAnchor">
 <a href="#amr-for-r-" class="anchor" aria-hidden="true"></a><code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px">
 </h1></div>
+<blockquote>
+<p>This package formed the basis of two PhD theses, of which the first was published and defended on 25 August 2021. Click here to read it: <a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a>.</p>
+</blockquote>
 <div id="what-is-amr-for-r" class="section level3">
 <h3 class="hasAnchor">
 <a href="#what-is-amr-for-r" class="anchor" aria-hidden="true"></a>What is <code>AMR</code> (for R)?</h3>
-<p><em>(To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.)</em></p>
 <p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
 <p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
 <p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
--- a/docs/news/index.html
+++ b/docs/news/index.html
@ -92,7 +92,7 @@
      </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">1.7.1.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9038</span>
      </span>
    </div>

@ -240,17 +240,17 @@
      <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
    </div>

-    <div id="amr-1719028" class="section level1">
-<h1 class="page-header" data-toc-text="1.7.1.9028">
-<a href="#amr-1719028" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9028</h1>
-<div id="last-updated-20-august-2021" class="section level2">
+    <div id="amr-1719038" class="section level1">
+<h1 class="page-header" data-toc-text="1.7.1.9038">
+<a href="#amr-1719038" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9038</h1>
+<div id="last-updated-1-september-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-20-august-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 20 August 2021</small>
+<a href="#last-updated-1-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 1 September 2021</small>
 </h2>
 <div id="breaking-changes" class="section level3">
 <h3 class="hasAnchor">
 <a href="#breaking-changes" class="anchor" aria-hidden="true"></a>Breaking changes</h3>
-<ul><li>Removed <code><a href="https://msberends.github.io/AMR/reference/AMR-deprecated.html">p_symbol()</a></code> and all <code>filter_*()</code> functions (except for <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>), which were all deprecated in a previous package version</li>
+<ul><li>Removed <code>p_symbol()</code> and all <code>filter_*()</code> functions (except for <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>), which were all deprecated in a previous package version</li>
 <li>Removed the <code>key_antibiotics()</code> and <code>key_antibiotics_equal()</code> functions, which were deprecated and superseded by <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> and <code><a href="../reference/key_antimicrobials.html">antimicrobials_equal()</a></code>
 </li>
 <li>Removed all previously implemented <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot2::ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code>, <code>&lt;rsi&gt;</code> and <code>&lt;resistance_predict&gt;</code> as they did not follow the <code>ggplot2</code> logic. They were replaced with <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">ggplot2::autoplot()</a></code> generics.</li>
@ -266,13 +266,15 @@
 <ul><li>The <code>antibiotics</code> data set now contains <strong>all ATC codes</strong> that are available through the <a href="https://www.whocc.no" class="external-link">WHOCC website</a>, regardless of drugs being present in more than one ATC group. This means that:
 <ul><li>Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)</li>
 <li>
-<code>antibiotics$atc</code> is now a <code>list</code> instead of a <code>character</code>, and this <code>atc</code> column was moved to the 5th position of the <code>antibiotics</code> data set</li>
+<code>antibiotics$atc</code> is now a <code>list</code> containing <code>character</code> vectors, and this <code>atc</code> column was moved to the 5th position of the <code>antibiotics</code> data set</li>
 <li>
-<code><a href="../reference/ab_property.html">ab_atc()</a></code> does not always return a character vector with length 1, and returns a <code>list</code> if the input is larger than length 1</li>
+<code><a href="../reference/ab_property.html">ab_atc()</a></code> does not always return a character vector of length 1, and returns a <code>list</code> if the input is larger than length 1</li>
+<li>
+<code><a href="../reference/ab_property.html">ab_info()</a></code> has a slightly different output</li>
 <li>Some DDDs (daily defined doses) were added or updated according to newly included ATC codes</li>
 </ul></li>
 <li>Antibiotic selectors
-<ul><li><p>They now also work in R-3.0 and R-3.1, supporting every version of R since 2013</p></li>
+<ul><li><p>They now also work in R-3.0 and R-3.1, supporting every version of R since 2013 like the rest of the package</p></li>
 <li><p>Added more selectors for antibiotic classes: <code><a href="../reference/antibiotic_class_selectors.html">aminopenicillins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">antifungals()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">antimycobacterials()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lipoglycopeptides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">polymyxins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">quinolones()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">streptogramins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">trimethoprims()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">ureidopenicillins()</a></code></p></li>
 <li>
 <p>Added specific selectors for certain types for treatment: <code><a href="../reference/antibiotic_class_selectors.html">administrable_per_os()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">administrable_iv()</a></code>, which are based on available Defined Daily Doses (DDDs), as defined by the WHOCC. These are ideal for e.g. analysing pathogens in primary care where IV treatment is not an option. They can be combined with other AB selectors, e.g. to select penicillins that are only administrable per os (i.e., orally):</p>
@ -291,8 +293,7 @@
 <li><p>Fix for using selectors multiple times in one call (e.g., using them in <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">dplyr::filter()</a></code> and immediately after in <code><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">dplyr::select()</a></code>)</p></li>
 <li><p>Added argument <code>only_treatable</code>, which defaults to <code>TRUE</code> and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)</p></li>
 </ul></li>
-<li>Fixed the Gram stain (<code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) determination of the class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as <em>Negativicoccus</em> and <em>Veillonella</em>.</li>
-<li>Fix for duplicate ATC codes in the <code>antibiotics</code> data set</li>
+<li>Fixed the Gram stain (<code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) determination of the taxonomic class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as <em>Negativicoccus</em> and <em>Veillonella</em>.</li>
 <li>Fix to prevent introducing <code>NA</code>s for old MO codes when running <code><a href="../reference/as.mo.html">as.mo()</a></code> on them</li>
 <li>Added more informative error messages when any of the <code>proportion_*()</code> and <code>count_*()</code> functions fail</li>
 <li>When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using <code><a href="../reference/as.mo.html">as.mo()</a></code>
@ -608,7 +609,7 @@
 </li>
 <li><p>For all function arguments in the code, it is now defined what the exact type of user input should be (inspired by the <a href="https://github.com/moodymudskipper/typed" class="external-link"><code>typed</code></a> package). If the user input for a certain function does not meet the requirements for a specific argument (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 420 arguments were defined.</p></li>
 <li><p>Fix for <code><a href="../reference/mo_source.html">set_mo_source()</a></code>, that previously would not remember the file location of the original file</p></li>
-<li><p>Deprecated function <code><a href="https://msberends.github.io/AMR/reference/AMR-deprecated.html">p_symbol()</a></code> that not really fits the scope of this package. It will be removed in a future version. See <a href="https://github.com/msberends/AMR/blob/v1.4.0/R/p_symbol.R" class="external-link">here</a> for the source code to preserve it.</p></li>
+<li><p>Deprecated function <code>p_symbol()</code> that not really fits the scope of this package. It will be removed in a future version. See <a href="https://github.com/msberends/AMR/blob/v1.4.0/R/p_symbol.R" class="external-link">here</a> for the source code to preserve it.</p></li>
 <li><p>Updated coagulase-negative staphylococci determination with Becker <em>et al.</em> 2020 (PMID 32056452), meaning that the species <em>S. argensis</em>, <em>S. caeli</em>, <em>S. debuckii</em>, <em>S. edaphicus</em> and <em>S. pseudoxylosus</em> are now all considered CoNS</p></li>
 <li><p>Fix for using argument <code>reference_df</code> in <code><a href="../reference/as.mo.html">as.mo()</a></code> and <code>mo_*()</code> functions that contain old microbial codes (from previous package versions)</p></li>
 <li><p>Fixed a bug where <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code> would not return the results based on the MO matching score</p></li>
@ -841,7 +842,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <div id="other-5" class="section level3">
 <h3 class="hasAnchor">
 <a href="#other-5" class="anchor" aria-hidden="true"></a>Other</h3>
-<ul><li>Removed previously deprecated function <code>p.symbol()</code> - it was replaced with <code><a href="https://msberends.github.io/AMR/reference/AMR-deprecated.html">p_symbol()</a></code>
+<ul><li>Removed previously deprecated function <code>p.symbol()</code> - it was replaced with <code>p_symbol()</code>
 </li>
 <li>Removed function <code>read.4d()</code>, that was only useful for reading data from an old test database.</li>
 </ul></div>
@ -1195,7 +1196,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Improved <code>filter_ab_class()</code> to be more reliable and to support 5th generation cephalosporins</li>
 <li>Function <code><a href="../reference/availability.html">availability()</a></code> now uses <code>portion_R()</code> instead of <code>portion_IR()</code>, to comply with EUCAST insights</li>
 <li>Functions <code><a href="../reference/age.html">age()</a></code> and <code><a href="../reference/age_groups.html">age_groups()</a></code> now have a <code>na.rm</code> argument to remove empty values</li>
-<li>Renamed function <code>p.symbol()</code> to <code><a href="https://msberends.github.io/AMR/reference/AMR-deprecated.html">p_symbol()</a></code> (the former is now deprecated and will be removed in a future version)</li>
+<li>Renamed function <code>p.symbol()</code> to <code>p_symbol()</code> (the former is now deprecated and will be removed in a future version)</li>
 <li>Using negative values for <code>x</code> in <code><a href="../reference/age_groups.html">age_groups()</a></code> will now introduce <code>NA</code>s and not return an error anymore</li>
 <li>Fix for determining the system’s language</li>
 <li>Fix for <code>key_antibiotics()</code> on foreign systems</li>
@ -2043,7 +2044,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

      <footer>
      <div class="copyright">
-  <p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
+  <p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>.</p></p>
 </div>

 <div class="pkgdown">
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@ -12,7 +12,7 @@ articles:
  datasets: datasets.html
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-08-17T12:31Z
+last_built: 2021-08-29T21:41Z
 urls:
  reference: https://msberends.github.io/AMR/reference
  article: https://msberends.github.io/AMR/articles
--- a/docs/reference/AMR-deprecated.html
+++ b/docs/reference/AMR-deprecated.html
@ -93,7 +93,7 @@
      </button>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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--- a/docs/reference/AMR.html
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@ -93,7 +93,7 @@
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@ -223,13 +223,6 @@
     
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@ -93,7 +93,7 @@
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--- a/docs/reference/WHONET.html
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@ -93,7 +93,7 @@
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@ -223,13 +223,6 @@
     
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--- a/docs/reference/ab_from_text.html
+++ b/docs/reference/ab_from_text.html
@ -93,7 +93,7 @@
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@ -223,13 +223,6 @@
     
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--- a/docs/reference/ab_property.html
+++ b/docs/reference/ab_property.html
@ -93,7 +93,7 @@
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@ -223,13 +223,6 @@
     
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--- a/docs/reference/age.html
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@ -93,7 +93,7 @@
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--- a/docs/reference/age_groups.html
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@ -93,7 +93,7 @@
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--- a/docs/reference/antibiotic_class_selectors.html
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@ -93,7 +93,7 @@
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--- a/docs/reference/antibiotics.html
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@ -93,7 +93,7 @@
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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--- a/docs/reference/as.ab.html
+++ b/docs/reference/as.ab.html
@ -93,7 +93,7 @@
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@ -223,13 +223,6 @@
     
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--- a/docs/reference/as.disk.html
+++ b/docs/reference/as.disk.html
@ -93,7 +93,7 @@
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@ -223,13 +223,6 @@
     
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--- a/docs/reference/as.mic.html
+++ b/docs/reference/as.mic.html
@ -93,7 +93,7 @@
      </button>
      <span class="navbar-brand">
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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@ -223,13 +223,6 @@
     
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--- a/docs/reference/as.mo.html
+++ b/docs/reference/as.mo.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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@ -223,13 +223,6 @@
     
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-    <span class="fa fa-clipboard-list"></span>
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--- a/docs/reference/as.rsi.html
+++ b/docs/reference/as.rsi.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
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@ -223,13 +223,6 @@
     
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--- a/docs/reference/atc_online.html
+++ b/docs/reference/atc_online.html
@ -93,7 +93,7 @@
      </button>
      <span class="navbar-brand">
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9026</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
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--- a/docs/reference/availability.html
+++ b/docs/reference/availability.html
@ -93,7 +93,7 @@
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      <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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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@ -223,13 +223,6 @@
     
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 </li>
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--- a/docs/reference/bug_drug_combinations.html
+++ b/docs/reference/bug_drug_combinations.html
@ -93,7 +93,7 @@
      </button>
      <span class="navbar-brand">
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
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@ -223,13 +223,6 @@
     
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--- a/docs/reference/catalogue_of_life.html
+++ b/docs/reference/catalogue_of_life.html
@ -93,7 +93,7 @@
      </button>
      <span class="navbar-brand">
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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@ -223,13 +223,6 @@
     
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-    <span class="fa fa-clipboard-list"></span>
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--- a/docs/reference/catalogue_of_life_version.html
+++ b/docs/reference/catalogue_of_life_version.html
@ -93,7 +93,7 @@
      </button>
      <span class="navbar-brand">
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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@ -223,13 +223,6 @@
     
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-  </a>
 </li>
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--- a/docs/reference/count.html
+++ b/docs/reference/count.html
@ -94,7 +94,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
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@ -224,13 +224,6 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
     
    Source Code
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--- a/docs/reference/custom_eucast_rules.html
+++ b/docs/reference/custom_eucast_rules.html
@ -93,7 +93,7 @@
      </button>
      <span class="navbar-brand">
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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@ -223,13 +223,6 @@
     
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--- a/docs/reference/dosage.html
+++ b/docs/reference/dosage.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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@ -223,13 +223,6 @@
     
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-     
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 </li>
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--- a/docs/reference/eucast_rules.html
+++ b/docs/reference/eucast_rules.html
@ -94,7 +94,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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@ -224,13 +224,6 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
     
    Source Code
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 </li>
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--- a/docs/reference/example_isolates.html
+++ b/docs/reference/example_isolates.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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@ -223,13 +223,6 @@
     
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 </li>
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--- a/docs/reference/example_isolates_unclean.html
+++ b/docs/reference/example_isolates_unclean.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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@ -223,13 +223,6 @@
     
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--- a/docs/reference/first_isolate.html
+++ b/docs/reference/first_isolate.html
@ -6,7 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">

-<title>Determine First (Weighted) Isolates — first_isolate • AMR (for R)</title>
+<title>Determine First Isolates — first_isolate • AMR (for R)</title>

 <!-- favicons -->
 <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,8 +48,8 @@
  <link href="../extra.css" rel="stylesheet">
  <script src="../extra.js"></script>

-<meta property="og:title" content="Determine First (Weighted) Isolates — first_isolate" />
-<meta property="og:description" content="Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler et al. in 2007 (doi: 10.1086/511864
+<meta property="og:title" content="Determine First Isolates — first_isolate" />
+<meta property="og:description" content="Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler et al. in 2007 (doi: 10.1086/511864
 ). To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
 <meta name="twitter:card" content="summary_large_image" />
@ -94,7 +94,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
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@ -224,13 +224,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
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-  </a>
 </li>
      </ul>
      
@ -245,13 +238,13 @@
 <div class="row">
  <div class="col-md-9 contents">
    <div class="page-header">
-    <h1>Determine First (Weighted) Isolates</h1>
+    <h1>Determine First Isolates</h1>
    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/first_isolate.R'><code>R/first_isolate.R</code></a></small>
    <div class="hidden name"><code>first_isolate.Rd</code></div>
    </div>

    <div class="ref-description">
-    <p>Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler <em>et al.</em> in 2007 (doi: <a href='https://doi.org/10.1086/511864'>10.1086/511864</a>
+    <p>Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler <em>et al.</em> in 2007 (doi: <a href='https://doi.org/10.1086/511864'>10.1086/511864</a>
 ). To determine patient episodes not necessarily based on microorganisms, use <code><a href='get_episode.html'>is_new_episode()</a></code> that also supports grouping with the <code>dplyr</code> package.</p>
    </div>

@ -321,7 +314,7 @@
    </tr>
    <tr>
      <th>col_keyantimicrobials</th>
-      <td><p>(only useful when <code>method = "phenotype-based"</code>) column name of the key antimicrobials to determine first (weighted) isolates, see <code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code>. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use <code>col_keyantimicrobials = FALSE</code> to prevent this. Can also be the output of <code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code>.</p></td>
+      <td><p>(only useful when <code>method = "phenotype-based"</code>) column name of the key antimicrobials to determine first isolates, see <code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code>. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use <code>col_keyantimicrobials = FALSE</code> to prevent this. Can also be the output of <code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code>.</p></td>
    </tr>
    <tr>
      <th>episode_days</th>
@ -436,8 +429,8 @@


 <p>This is a more reliable method, since it also <em>weighs</em> the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:</p><ol>
-<li><p>Using <code>type = "points"</code> and argument <code>points_threshold</code></p>
-<p>This method weighs <em>all</em> antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as 0.5 points, a difference from S to R (or vice versa) counts as 1 point. When the sum of points exceeds <code>points_threshold</code>, which defaults to <code>2</code>, an isolate will be selected as a first weighted isolate.</p>
+<li><p>Using <code>type = "points"</code> and argument <code>points_threshold</code> (default)</p>
+<p>This method weighs <em>all</em> antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as <code>0.5</code> points, a difference from S to R (or vice versa) counts as <code>1</code> point. When the sum of points exceeds <code>points_threshold</code>, which defaults to <code>2</code>, an isolate will be selected as a first weighted isolate.</p>
 <p>All antimicrobials are internally selected using the <code><a href='key_antimicrobials.html'>all_antimicrobials()</a></code> function. The output of this function does not need to be passed to the <code>first_isolate()</code> function.</p></li>
 <li><p>Using <code>type = "keyantimicrobials"</code> and argument <code>ignore_I</code></p>
 <p>This method only weighs specific antimicrobial agents, called <em>key antimicrobials</em>. Any difference from S to R (or vice versa) in these key antimicrobials will select an isolate as a first weighted isolate. With <code>ignore_I = FALSE</code>, also differences from I to S or R (or vice versa) will lead to this.</p>
--- a/docs/reference/g.test.html
+++ b/docs/reference/g.test.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/get_episode.html
+++ b/docs/reference/get_episode.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/ggplot_pca.html
+++ b/docs/reference/ggplot_pca.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/ggplot_rsi.html
+++ b/docs/reference/ggplot_rsi.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/guess_ab_col.html
+++ b/docs/reference/guess_ab_col.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@ -92,7 +92,7 @@
      </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">1.7.1.9026</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
      </span>
    </div>

@ -393,7 +393,7 @@
        <td>
          <p><code><a href="first_isolate.html">first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_isolate()</a></code> </p>
        </td>
-        <td><p>Determine First (Weighted) Isolates</p></td>
+        <td><p>Determine First Isolates</p></td>
      </tr><tr>
        
        <td>
--- a/docs/reference/intrinsic_resistant.html
+++ b/docs/reference/intrinsic_resistant.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/italicise_taxonomy.html
+++ b/docs/reference/italicise_taxonomy.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/join.html
+++ b/docs/reference/join.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/key_antimicrobials.html
+++ b/docs/reference/key_antimicrobials.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/kurtosis.html
+++ b/docs/reference/kurtosis.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/lifecycle.html
+++ b/docs/reference/lifecycle.html
@ -95,7 +95,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -225,13 +225,6 @@ This page contains a section for every lifecycle (with text borrowed from the af
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/like.html
+++ b/docs/reference/like.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/mdro.html
+++ b/docs/reference/mdro.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/microorganisms.codes.html
+++ b/docs/reference/microorganisms.codes.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/microorganisms.html
+++ b/docs/reference/microorganisms.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/microorganisms.old.html
+++ b/docs/reference/microorganisms.old.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/mo_matching_score.html
+++ b/docs/reference/mo_matching_score.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/mo_property.html
+++ b/docs/reference/mo_property.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/mo_source.html
+++ b/docs/reference/mo_source.html
@ -94,7 +94,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -224,13 +224,6 @@ This is the fastest way to have your organisation (or analysis) specific codes p
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/pca.html
+++ b/docs/reference/pca.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/plot.html
+++ b/docs/reference/plot.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
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@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
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--- a/docs/reference/proportion.html
+++ b/docs/reference/proportion.html
@ -94,7 +94,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
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@ -224,13 +224,6 @@ resistance() should be used to calculate resistance, susceptibility() should be
     
    Source Code
  </a>
-</li>
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-     
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-  </a>
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--- a/docs/reference/random.html
+++ b/docs/reference/random.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
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-     
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-  </a>
 </li>
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--- a/docs/reference/resistance_predict.html
+++ b/docs/reference/resistance_predict.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/rsi_translation.html
+++ b/docs/reference/rsi_translation.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/skewness.html
+++ b/docs/reference/skewness.html
@ -94,7 +94,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -224,13 +224,6 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/reference/translate.html
+++ b/docs/reference/translate.html
@ -93,7 +93,7 @@
      </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">1.7.1.9024</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
      </span>
    </div>

@ -223,13 +223,6 @@
     
    Source Code
  </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
      </ul>
      
--- a/docs/survey.html
+++ b/docs/survey.html
@ -92,7 +92,7 @@
      </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">1.7.1.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
      </span>
    </div>

--- a/index.md
+++ b/index.md
@ -1,8 +1,8 @@
 # `AMR` (for R) <img src="./logo.png" align="right" height="120px" />

-### What is `AMR` (for R)?
+> This package formed the basis of two PhD theses, of which the first was published and defended on 25 August 2021. Click here to read it: [DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131).

-*(To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html).)*
+### What is `AMR` (for R)?

 `AMR` is a free, open-source and independent [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.

--- a/inst/CITATION
+++ b/inst/CITATION
@ -1,4 +1,4 @@
-citHeader("To cite our AMR package in publications, please use (for now):")
+citHeader("To cite our AMR package in publications, please use below preprint. This preprint was accepted for publication in the Journal of Statistical Software, but we are awaiting the actual publication. Many thanks for using our open-source method to work with microbial and antimicrobial data!")

 citEntry(
  entry        = "Article",
@ -10,7 +10,16 @@ citEntry(
  year         = 2021,
  url          = "https://www.biorxiv.org/content/10.1101/810622v4",
  textVersion  = "Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2021). AMR - An R Package for Working with
-Antimicrobial Resistance Data. Journal of Statistical Software (accepted for publication), https://www.biorxiv.org/content/10.1101/810622v4"
-)
+Antimicrobial Resistance Data. Journal of Statistical Software (accepted for publication), https://www.biorxiv.org/content/10.1101/810622v4.")

-citFooter("This preprint was accepted for publication in the Journal of Statistical Software, but we are awaiting the actual publication. Many thanks for using our open-source method to work with microbial and antimicrobial data!")
+citEntry(
+  entry        = "PhdThesis",
+  title        = "A New Instrument for Microbial Epidemiology: Empowering Antimicrobial Resistance Data Analysis",
+  author       = "M S Berends",
+  publisher    = "University of Groningen",
+  school       = "University of Groningen",
+  doi          = "10.33612/diss.177417131",
+  pages        = 288,
+  year         = 2021,
+  textVersion = "Berends, MS (2021). A New Instrument for Microbial Epidemiology: Empowering Antimicrobial Resistance Data Analysis (PhD thesis). University of Groningen, doi: 10.33612/diss.177417131."
+)
--- a/man/first_isolate.Rd
+++ b/man/first_isolate.Rd
@ -3,7 +3,7 @@
 \name{first_isolate}
 \alias{first_isolate}
 \alias{filter_first_isolate}
-\title{Determine First (Weighted) Isolates}
+\title{Determine First Isolates}
 \source{
 Methodology of this function is strictly based on:
 \itemize{
@ -60,7 +60,7 @@ filter_first_isolate(

 \item{col_icu}{column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)}

-\item{col_keyantimicrobials}{(only useful when \code{method = "phenotype-based"}) column name of the key antimicrobials to determine first (weighted) isolates, see \code{\link[=key_antimicrobials]{key_antimicrobials()}}. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use \code{col_keyantimicrobials = FALSE} to prevent this. Can also be the output of \code{\link[=key_antimicrobials]{key_antimicrobials()}}.}
+\item{col_keyantimicrobials}{(only useful when \code{method = "phenotype-based"}) column name of the key antimicrobials to determine first isolates, see \code{\link[=key_antimicrobials]{key_antimicrobials()}}. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use \code{col_keyantimicrobials = FALSE} to prevent this. Can also be the output of \code{\link[=key_antimicrobials]{key_antimicrobials()}}.}

 \item{episode_days}{episode in days after which a genus/species combination will be determined as 'first isolate' again. The default of 365 days is based on the guideline by CLSI, see \emph{Source}.}

@ -90,7 +90,7 @@ filter_first_isolate(
 A \code{\link{logical}} vector
 }
 \description{
-Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler \emph{et al.} in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use \code{\link[=is_new_episode]{is_new_episode()}} that also supports grouping with the \code{dplyr} package.
+Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler \emph{et al.} in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use \code{\link[=is_new_episode]{is_new_episode()}} that also supports grouping with the \code{dplyr} package.
 }
 \details{
 To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below.
@ -147,9 +147,9 @@ This is the most common method to correct for duplicate isolates. Patients are c

 This is a more reliable method, since it also \emph{weighs} the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:
 \enumerate{
-\item Using \code{type = "points"} and argument \code{points_threshold}
+\item Using \code{type = "points"} and argument \code{points_threshold} (default)

-This method weighs \emph{all} antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as 0.5 points, a difference from S to R (or vice versa) counts as 1 point. When the sum of points exceeds \code{points_threshold}, which defaults to \code{2}, an isolate will be selected as a first weighted isolate.
+This method weighs \emph{all} antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as \code{0.5} points, a difference from S to R (or vice versa) counts as \code{1} point. When the sum of points exceeds \code{points_threshold}, which defaults to \code{2}, an isolate will be selected as a first weighted isolate.

 All antimicrobials are internally selected using the \code{\link[=all_antimicrobials]{all_antimicrobials()}} function. The output of this function does not need to be passed to the \code{\link[=first_isolate]{first_isolate()}} function.
 \item Using \code{type = "keyantimicrobials"} and argument \code{ignore_I}
--- a/pkgdown/extra.js
+++ b/pkgdown/extra.js
@ -98,9 +98,10 @@ $(document).ready(function() {
      x = x.replace(/Author, maintainer/g, "Main developer");
      x = x.replace(/Author, contributor/g, "Main contributor");
      x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
-      x = x.replace("Alex", "Prof. Dr. Alex");
-      x = x.replace("Bhanu", "Prof. Dr. Bhanu");
-      x = x.replace("Casper", "Prof. Dr. Casper");
+      x = x.replace("Matthijs", "Dr. Matthijs");
+      x = x.replace("Alex", "Prof. Alex");
+      x = x.replace("Bhanu", "Prof. Bhanu");
+      x = x.replace("Casper", "Prof. Casper");
      x = x.replace("Corinna", "Dr. Corinna");
      // others
      x = x.replace("Bart", "Dr. Bart");
--- a/tests/tinytest.R
+++ b/tests/tinytest.R
@ -29,13 +29,18 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
  .libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths()))
  if (AMR:::pkg_is_available("tinytest")) {
    library(AMR)
-    out <- test_package("AMR", 
+    out <- test_package("AMR",
                        testdir = ifelse(AMR:::dir.exists("inst/tinytest"),
                                         "inst/tinytest",
                                         "tinytest"),
-                        verbose = FALSE)
-    cat(attributes(out)$duration, "\n")
+                        verbose = 99,
+                        pattern = "first.*\\.[rR]$",
+                        color = FALSE)
+    cat("SUMMARY:\n")
    print(summary(out))
+    cat("WARNINGS:\n")
    print(warnings())
+    cat(attributes(out)$duration, "\n")
+    
  }
 }
Author	SHA1	Message	Date
dr. M.S. (Matthijs) Berends	81a1a432bd	(v1.7.1.9038) dplyr grouping fix on windows?	2021-09-01 16:52:55 +02:00
dr. M.S. (Matthijs) Berends	bcab74fb6d	(v1.7.1.9037) dplyr grouping fix on windows?	2021-08-31 17:06:44 +02:00
dr. M.S. (Matthijs) Berends	953dfac9e5	(v1.7.1.9036) dplyr grouping fix on windows?	2021-08-30 16:49:46 +02:00
dr. M.S. (Matthijs) Berends	986bd826ee	(v1.7.1.9035) dplyr grouping fix on windows?	2021-08-30 15:43:12 +02:00
dr. M.S. (Matthijs) Berends	af23f91e5c	website update	2021-08-30 15:07:18 +02:00
dr. M.S. (Matthijs) Berends	1daa117e9f	(v1.7.1.9033) dplyr grouping fix on windows?	2021-08-30 15:01:32 +02:00
dr. M.S. (Matthijs) Berends	6ca6a3f6df	(v1.7.1.9032) dplyr grouping fix on windows?	2021-08-30 14:17:27 +02:00
dr. M.S. (Matthijs) Berends	e6ce25162e	(v1.7.1.9031) dplyr grouping fix on windows?	2021-08-30 14:07:46 +02:00
dr. M.S. (Matthijs) Berends	d6a916d70b	(v1.7.1.9030) unit test	2021-08-29 23:50:45 +02:00
dr. M.S. (Matthijs) Berends	f0a4d29fe0	(v1.7.1.9029) unit test fix	2021-08-21 10:20:05 +02:00