0.7.1

.gitlab-ci.yml

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-    # install missing and outdated packages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

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.7.0
-Date: 2019-06-03
+Version: 0.7.1
+Date: 2019-06-23
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(

NAMESPACE

@@ -142,6 +142,7 @@ export(mo_family)
 export(mo_fullname)
 export(mo_genus)
 export(mo_gramstain)
+export(mo_info)
 export(mo_kingdom)
 export(mo_name)
 export(mo_order)
@@ -153,6 +154,7 @@ export(mo_renamed)
 export(mo_shortname)
 export(mo_species)
 export(mo_subspecies)
+export(mo_synonyms)
 export(mo_taxonomy)
 export(mo_type)
 export(mo_uncertainties)
@@ -171,8 +173,11 @@ export(ratio)
 export(read.4D)
 export(resistance_predict)
 export(right_join_microorganisms)
+export(rsi_df)
 export(rsi_predict)
 export(scale_rsi_colours)
+export(scale_type.ab)
+export(scale_type.mo)
 export(scale_y_percent)
 export(semi_join_microorganisms)
 export(set_mo_source)
@@ -217,6 +222,8 @@ exportMethods(print.rsi)
 exportMethods(pull.ab)
 exportMethods(pull.atc)
 exportMethods(pull.mo)
+exportMethods(scale_type.ab)
+exportMethods(scale_type.mo)
 exportMethods(select.freq)
 exportMethods(skewness)
 exportMethods(skewness.data.frame)
@@ -241,6 +248,7 @@ importFrom(crayon,strip_style)
 importFrom(crayon,underline)
 importFrom(crayon,white)
 importFrom(crayon,yellow)
+importFrom(data.table,address)
 importFrom(data.table,as.data.table)
 importFrom(data.table,data.table)
 importFrom(data.table,setkey)
@@ -293,6 +301,7 @@ importFrom(graphics,axis)
 importFrom(graphics,barplot)
 importFrom(graphics,boxplot)
 importFrom(graphics,hist)
+importFrom(graphics,par)
 importFrom(graphics,plot)
 importFrom(graphics,points)
 importFrom(graphics,text)
@@ -302,6 +311,7 @@ importFrom(microbenchmark,microbenchmark)
 importFrom(rlang,as_label)
 importFrom(rlang,enquos)
 importFrom(rlang,eval_tidy)
+importFrom(scales,percent)
 importFrom(stats,complete.cases)
 importFrom(stats,fivenum)
 importFrom(stats,glm)

NEWS.md

@@ -1,3 +1,64 @@
+# AMR 0.7.1
+
+#### New
+* Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:
+  ```r
+  septic_patients %>%
+    select(AMX, CIP) %>%
+    rsi_df()
+  #      antibiotic  interpretation      value  isolates
+  # 1   Amoxicillin              SI  0.4442636       546
+  # 2   Amoxicillin               R  0.5557364       683
+  # 3 Ciprofloxacin              SI  0.8381831      1181
+  # 4 Ciprofloxacin               R  0.1618169       228
+  ```
+* Support for all scientifically published pathotypes of *E. coli* to date (that we could find). Supported are: 
+
+  * AIEC (Adherent-Invasive *E. coli*) 
+  * ATEC (Atypical Entero-pathogenic *E. coli*) 
+  * DAEC (Diffusely Adhering *E. coli*) 
+  * EAEC (Entero-Aggresive *E. coli*) 
+  * EHEC (Entero-Haemorrhagic *E. coli*) 
+  * EIEC (Entero-Invasive *E. coli*) 
+  * EPEC (Entero-Pathogenic *E. coli*) 
+  * ETEC (Entero-Toxigenic *E. coli*) 
+  * NMEC (Neonatal Meningitis‐causing *E. coli*) 
+  * STEC (Shiga-toxin producing *E. coli*) 
+  * UPEC (Uropathogenic *E. coli*)
+  
+  All these lead to the microbial ID of *E. coli*:
+  ```r
+  as.mo("UPEC")
+  # B_ESCHR_COL
+  mo_name("UPEC")
+  # "Escherichia coli"
+  mo_gramstain("EHEC")
+  # "Gram-negative"
+  ```
+* Function `mo_info()` as an analogy to `ab_info()`. The `mo_info()` prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism
+* Function `mo_synonyms()` to get all previously accepted taxonomic names of a microorganism
+
+#### Changed
+* Column names of output `count_df()` and `portion_df()` are now lowercase
+* Fixed bug in translation of microorganism names
+* Fixed bug in determining taxonomic kingdoms
+* Algorithm improvements for `as.ab()` and `as.mo()` to understand even more severely misspelled input
+* Function `as.ab()` now allows spaces for coercing antibiotics names
+* Added `ggplot2` methods for automatically determining the scale type of classes `mo` and `ab`
+* Added names of object in the header in frequency tables, even when using pipes
+* Prevented `"bacteria"` from getting coerced by `as.ab()` because Bacterial is a brand name of trimethoprim (TMP)
+* Fixed a bug where setting an antibiotic would not work for `eucast_rules()` and `mdro()`
+* Fixed a EUCAST rule for Staphylococci, where amikacin resistance would not be inferred from tobramycin
+* Removed `latest_annual_release` from the `catalogue_of_life_version()` function
+* Removed antibiotic code `PVM1` from the `antibiotics` data set as this was a duplicate of `PME`
+* Fixed bug where not all old taxonomic names would be printed, when using a vector as input for `as.mo()`
+* Manually added *Trichomonas vaginalis* from the kingdom of Protozoa, which is missing from the Catalogue of Life
+* Small improvements to `plot()` and `barplot()` for MIC and RSI classes
+* Allow Catalogue of Life IDs to be coerced by `as.mo()`
+
+#### Other
+* Fixed a note thrown by CRAN tests
+
 # AMR 0.7.0
 
 #### New

R/ab.R

@@ -70,15 +70,15 @@ as.ab <- function(x) {
 
   x_bak <- x
   # remove suffices
-  x_bak_clean <- gsub("_(mic|rsi|disk|disc)$", "", x, ignore.case = TRUE)
+  x_bak_clean <- gsub("_(mic|rsi|dis[ck])$", "", x, ignore.case = TRUE)
   # remove disk concentrations, like LVX_NM -> LVX
   x_bak_clean <- gsub("_[A-Z]{2}[0-9_]{0,3}$", "", x_bak_clean, ignore.case = TRUE)
-  # clean rest of it
-  x_bak_clean <- gsub("[^A-Z0-9/-]", "", x_bak_clean, ignore.case = TRUE)
-  # keep only a-z when it's not an ATC code or only numbers
-  x_bak_clean[!x_bak_clean %like% "^([A-Z][0-9]{2}[A-Z]{2}[0-9]{2}|[0-9]+)$"] <- gsub("[^a-zA-Z]+",
-                                                                                      "",
-                                                                                      x_bak_clean[!x_bak_clean %like% "^([A-Z][0-9]{2}[A-Z]{2}[0-9]{2}|[0-9]+)$"])
+  # remove part between brackets if that's followed by another string
+  x_bak_clean <- gsub("(.*)+ [(].*[)]", "\\1", x_bak_clean)
+  # keep only a-Z, 0-9, space, slash and dash
+  x_bak_clean <- gsub("[^A-Z0-9 /-]", "", x_bak_clean, ignore.case = TRUE)
+  # keep only max 1 space
+  x_bak_clean <- trimws(gsub(" +", " ", x_bak_clean, ignore.case = TRUE))
   x <- unique(x_bak_clean)
   x_new <- rep(NA_character_, length(x))
   x_unknown <- character(0)
@@ -91,6 +91,11 @@ as.ab <- function(x) {
       x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
       next
     }
+    # prevent "bacteria" from coercing to TMP, since Bacterial is a brand name of it
+    if (identical(tolower(x[i]), "bacteria")) {
+      x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
+      next
+    }
 
     # exact AB code
     found <- AMR::antibiotics[which(AMR::antibiotics$ab == toupper(x[i])),]$ab
@@ -162,23 +167,20 @@ as.ab <- function(x) {
     }
     x_spelling <- tolower(x[i])
     x_spelling <- gsub("[iy]+", "[iy]+", x_spelling)
-    x_spelling <- gsub("[sz]+", "[sz]+", x_spelling)
-    x_spelling <- gsub("(c|k|q|qu)+", "(c|k|q|qu)+", x_spelling)
+    x_spelling <- gsub("(c|k|q|qu|s|z|x|ks)+", "(c|k|q|qu|s|z|x|ks)+", x_spelling)
     x_spelling <- gsub("(ph|f|v)+", "(ph|f|v)+", x_spelling)
     x_spelling <- gsub("(th|t)+", "(th|t)+", x_spelling)
-    x_spelling <- gsub("(x|ks)+", "(x|ks)+", x_spelling)
     x_spelling <- gsub("a+", "a+", x_spelling)
     x_spelling <- gsub("e+", "e+", x_spelling)
     x_spelling <- gsub("o+", "o+", x_spelling)
-    # allow start with C/S/Z
-    x_spelling <- gsub("^(\\(c\\|k\\|q\\|qu\\)|\\[sz\\])", "(c|k|q|qu|s|z)", x_spelling)
-    x_spelling <- gsub("(c|k|q|qu)+[sz]", "(c|k|q|qu|s|x|z)", x_spelling, fixed = TRUE)
     # allow any ending of -in/-ine and -im/-ime
     x_spelling <- gsub("(\\[iy\\]\\+(n|m)|\\[iy\\]\\+(n|m)e\\+)$", "[iy]+(n|m)e*", x_spelling)
     # allow any ending of -ol/-ole
     x_spelling <- gsub("(o\\+l|o\\+le\\+)$", "o+le*", x_spelling)
     # allow any ending of -on/-one
     x_spelling <- gsub("(o\\+n|o\\+ne\\+)$", "o+ne*", x_spelling)
+    # replace multiple same characters to single one with '+', like "ll" -> "l+"
+    x_spelling <- gsub("(.)\\1+", "\\1+", x_spelling)
     # try if name starts with it
     found <- AMR::antibiotics[which(AMR::antibiotics$name %like% paste0("^", x_spelling)),]$ab
     if (length(found) > 0) {
@@ -198,10 +200,38 @@ as.ab <- function(x) {
       next
     }
 
+    # try by removing all spaces
+    if (x[i] %like% " ") {
+      found <- suppressWarnings(as.ab(gsub(" +", "", x[i])))
+      if (length(found) > 0 & !is.na(found)) {
+        x_new[i] <- found[1L]
+        next
+      }
+    }
+
+    # try by removing all spaces and numbers
+    if (x[i] %like% " " | x[i] %like% "[0-9]") {
+      found <- suppressWarnings(as.ab(gsub("[ 0-9]", "", x[i])))
+      if (length(found) > 0 & !is.na(found)) {
+        x_new[i] <- found[1L]
+        next
+      }
+    }
+
     # not found
     x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
   }
 
+  # take failed ATC codes apart from rest
+  x_unknown_ATCs <- x_unknown[x_unknown %like% "[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]"]
+  x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
+  if (length(x_unknown_ATCs) > 0) {
+    warning("These ATC codes are not (yet) in the antibiotics data set: ",
+            paste('"', sort(unique(x_unknown_ATCs)), '"', sep = "", collapse = ', '),
+            ".",
+            call. = FALSE)
+  }
+
   if (length(x_unknown) > 0) {
     warning("These values could not be coerced to a valid antibiotic ID: ",
             paste('"', sort(unique(x_unknown)), '"', sep = "", collapse = ', '),

R/ab_property.R

@@ -73,14 +73,13 @@
 #' ab_name(21319)       # "Flucloxacillin" (using CID)
 #' ab_name("J01CF05")   # "Flucloxacillin" (using ATC)
 ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
-  x <- ab_validate(x = x, property = "name", ...)
-  res <- t(x, language = language)
+  x <- translate_AMR(ab_validate(x = x, property = "name", ...), language = language)
   if (tolower == TRUE) {
     # use perl to only transform the first character
     # as we want "polymyxin B", not "polymyxin b"
-    res <- gsub("^([A-Z])", "\\L\\1", res, perl = TRUE)
+    x <- gsub("^([A-Z])", "\\L\\1", x, perl = TRUE)
   }
-  res
+  x
 }
 
 #' @rdname ab_property
@@ -116,19 +115,19 @@ ab_tradenames <- function(x, ...) {
 #' @rdname ab_property
 #' @export
 ab_group <- function(x, language = get_locale(), ...) {
-  t(ab_validate(x = x, property = "group", ...), language = language)
+  translate_AMR(ab_validate(x = x, property = "group", ...), language = language)
 }
 
 #' @rdname ab_property
 #' @export
 ab_atc_group1 <- function(x, language = get_locale(), ...) {
-  t(ab_validate(x = x, property = "atc_group1", ...), language = language)
+  translate_AMR(ab_validate(x = x, property = "atc_group1", ...), language = language)
 }
 
 #' @rdname ab_property
 #' @export
 ab_atc_group2 <- function(x, language = get_locale(), ...) {
-  t(ab_validate(x = x, property = "atc_group2", ...), language = language)
+  translate_AMR(ab_validate(x = x, property = "atc_group2", ...), language = language)
 }
 
 #' @rdname ab_property
@@ -150,8 +149,8 @@ ab_ddd <- function(x, administration = "oral", units = FALSE, ...) {
 #' @export
 ab_info <- function(x, language = get_locale(), ...) {
   x <- AMR::as.ab(x, ...)
-  base::list(ab = x,
-             atc = ab_atc(x),
+  base::list(ab = as.character(x),
+             atc = as.character(ab_atc(x)),
              cid = ab_cid(x),
              name = ab_name(x, language = language),
              group = ab_group(x, language = language),
@@ -174,7 +173,7 @@ ab_property <- function(x, property = 'name', language = get_locale(), ...) {
     stop("invalid property: '", property, "' - use a column name of the `antibiotics` data set")
   }
 
-  t(ab_validate(x = x, property = property, ...), language = language)
+  translate_AMR(ab_validate(x = x, property = property, ...), language = language)
 }
 
 ab_validate <- function(x, property, ...) {

R/age.R

@@ -136,6 +136,9 @@ age <- function(x, reference = Sys.Date(), exact = FALSE) {
 #'   select(age_group, CIP) %>%
 #'   ggplot_rsi(x = "age_group")
 age_groups <- function(x, split_at = c(12, 25, 55, 75)) {
+  if (!is.numeric(x)) {
+    stop("`x` and must be numeric, not a ", paste0(class(x), collapse = "/"), ".")
+  }
   if (is.character(split_at)) {
     split_at <- split_at[1L]
     if (split_at %like% "^(child|kid|junior)") {
@@ -148,11 +151,7 @@ age_groups <- function(x, split_at = c(12, 25, 55, 75)) {
       split_at <- 1:10 * 10
     }
   }
-  split_at <- as.integer(split_at)
-  if (!is.numeric(x) | !is.numeric(split_at)) {
-    stop("`x` and `split_at` must both be numeric.")
-  }
-  split_at <- sort(unique(split_at))
+  split_at <- sort(unique(as.integer(split_at)))
   if (!split_at[1] == 0) {
     # add base number 0
     split_at <- c(0, split_at)

R/amr.R

@@ -67,4 +67,5 @@
 #' @rdname AMR
 #  # prevent NOTE on R >= 3.6
 #' @importFrom microbenchmark microbenchmark
+#' @importFrom scales percent
 NULL

R/catalogue_of_life.R

@@ -71,19 +71,17 @@
 #' # [1] "Castellani et al., 1919"
 #'
 #' # Do not get mistaken - the package only includes microorganisms
-#' mo_phylum("C. elegans")
-#' # [1] "Cyanobacteria"                   # Bacteria?!
-#' mo_fullname("C. elegans")
+#' mo_kingdom("C. elegans")
+#' # [1] "Bacteria"                        # Bacteria?!
+#' mo_name("C. elegans")
 #' # [1] "Chroococcus limneticus elegans"  # Because a microorganism was found
 NULL
 
 #' Version info of included Catalogue of Life
 #'
-#' This function returns information about the included data from the Catalogue of Life. It also shows if the included version is their latest annual release. The Catalogue of Life releases their annual release in March each year.
+#' This function returns information about the included data from the Catalogue of Life.
 #' @seealso \code{\link{microorganisms}}
-#' @details The list item \code{...$catalogue_of_life$is_latest_annual_release} is based on the system date.
-#'
-#' For DSMZ, see \code{?microorganisms}.
+#' @details For DSMZ, see \code{?microorganisms}.
 #' @return a \code{list}, which prints in pretty format
 #' @inheritSection catalogue_of_life Catalogue of Life
 #' @inheritSection AMR Read more on our website!
@@ -99,8 +97,6 @@ catalogue_of_life_version <- function() {
   lst <- list(catalogue_of_life =
                 list(version = gsub("{year}", catalogue_of_life$year, catalogue_of_life$version, fixed = TRUE),
                      url = gsub("{year}", catalogue_of_life$year, catalogue_of_life$url_CoL, fixed = TRUE),
-                     # annual release always somewhere in May, so before June is TRUE, FALSE otherwise
-                     is_latest_annual_release = Sys.Date() < as.Date(paste0(catalogue_of_life$year + 1, "-06-01")),
                      n = nrow(filter(AMR::microorganisms, source == "CoL"))),
               deutsche_sammlung_von_mikroorganismen_und_zellkulturen =
                 list(version = "Prokaryotic Nomenclature Up-to-Date from DSMZ",
@@ -125,7 +121,6 @@ print.catalogue_of_life_version <- function(x, ...) {
              underline(lst$catalogue_of_life$version), "\n",
              "  Available at: ", lst$catalogue_of_life$url, "\n",
              "  Number of included species: ", format(lst$catalogue_of_life$n, big.mark = ","), "\n",
-             "  (based on your system time, this is most likely ", ifelse(lst$catalogue_of_life$is_latest_annual_release, "", "not "), "the latest annual release)\n\n",
              underline(paste0(lst$deutsche_sammlung_von_mikroorganismen_und_zellkulturen$version, " (",
                               lst$deutsche_sammlung_von_mikroorganismen_und_zellkulturen$yearmonth, ")")), "\n",
              "  Available at: ", lst$deutsche_sammlung_von_mikroorganismen_und_zellkulturen$url, "\n",

R/count.R

@@ -29,9 +29,11 @@
 #' @inheritSection as.rsi Interpretation of S, I and R
 #' @details These functions are meant to count isolates. Use the \code{\link{portion}_*} functions to calculate microbial resistance.
 #'
-#' \code{n_rsi} is an alias of \code{count_all}. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to \code{\link{n_distinct}}. Their function is equal to \code{count_S(...) + count_IR(...)}.
+#' The function \code{n_rsi} is an alias of \code{count_all}. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to \code{\link{n_distinct}}. Their function is equal to \code{count_S(...) + count_IR(...)}.
 #'
-#' \code{count_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and counts the amounts of R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.
+#' The function \code{count_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and counts the amounts of S, I and R. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.
+#'
+#' The function \code{rsi_df} works exactly like \code{count_df}, but adds the percentage of S, I and R.
 #' @source Wickham H. \strong{Tidy Data.} The Journal of Statistical Software, vol. 59, 2014. \url{http://vita.had.co.nz/papers/tidy-data.html}
 #' @seealso \code{\link{portion}_*} to calculate microbial resistance and susceptibility.
 #' @keywords resistance susceptibility rsi antibiotics isolate isolates

R/data.R

@@ -22,7 +22,7 @@
 #' Data set with ~450 antibiotics
 #'
 #' A data set containing all antibiotics. Use \code{\link{as.ab}} or one of the \code{\link{ab_property}} functions to retrieve values from this data set. Three identifiers are included in this data set: an antibiotic ID (\code{ab}, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (\code{atc}) as defined by the WHO, and a Compound ID (\code{cid}) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
-#' @format A \code{\link{data.frame}} with 454 observations and 13 variables:
+#' @format A \code{\link{data.frame}} with 453 observations and 13 variables:
 #' \describe{
 #'   \item{\code{ab}}{Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available}
 #'   \item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}}
@@ -55,7 +55,7 @@
 #'
 #' A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using \code{\link{as.mo}}.
 #' @inheritSection catalogue_of_life Catalogue of Life
-#' @format A \code{\link{data.frame}} with 67,903 observations and 16 variables:
+#' @format A \code{\link{data.frame}} with 67,906 observations and 16 variables:
 #' \describe{
 #'   \item{\code{mo}}{ID of microorganism as used by this package}
 #'   \item{\code{col_id}}{Catalogue of Life ID}
@@ -69,9 +69,10 @@
 #' }
 #' @details Manually added were:
 #' \itemize{
-#'   \item{9 species of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
-#'   \item{2 species of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
-#'   \item{3 other undefined (unknown, unknown Gram negatives and unknown Gram positives)}
+#'   \item{9 entries of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
+#'   \item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
+#'   \item{3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)}
+#'   \item{3 other 'undefined' entries (unknown, unknown Gram negatives and unknown Gram positives)}
 #'   \item{8,830 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life}
 #' }
 #' @section About the records from DSMZ (see source):

R/eucast_rules.R

@@ -209,6 +209,12 @@ eucast_rules <- function(x,
     stop("`col_mo` must be set")
   }
 
+  decimal.mark <- getOption("OutDec")
+  big.mark <- ifelse(decimal.mark != ",", ",", ".")
+  formatnr <- function(x) {
+    trimws(format(x, big.mark = big.mark, decimal.mark = decimal.mark))
+  }
+
   warned <- FALSE
 
   txt_error <- function() { cat("", bgRed(white(" ERROR ")), "\n") }
@@ -219,7 +225,7 @@ eucast_rules <- function(x,
         if (no_of_changes == 1) {
           cat(blue(" (1 new change)\n"))
         } else {
-          cat(blue(paste0(" (", no_of_changes, " new changes)\n")))
+          cat(blue(paste0(" (", formatnr(no_of_changes), " new changes)\n")))
         }
       } else {
         cat(green(" (no new changes)\n"))
@@ -664,12 +670,6 @@ eucast_rules <- function(x,
     verbose_info <- verbose_info %>%
       arrange(row, rule_group, rule_name, col)
 
-    decimal.mark <- getOption("OutDec")
-    big.mark <- ifelse(decimal.mark != ",", ",", ".")
-    formatnr <- function(x) {
-      trimws(format(x, big.mark = big.mark, decimal.mark = decimal.mark))
-    }
-
     cat(paste0("\n", silver(strrep("-", options()$width - 1)), "\n"))
     cat(bold(paste('EUCAST rules', paste0(wouldve, 'affected'),
                    formatnr(n_distinct(verbose_info$row)),

R/extended.R

@@ -0,0 +1,48 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+#                                                                      #
+# This R package was created for academic research and was publicly    #
+# released in the hope that it will be useful, but it comes WITHOUT    #
+# ANY WARRANTY OR LIABILITY.                                           #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
+#' Extended functions
+#'
+#' These functions are extensions of functions in other packages.
+#' @inheritSection AMR Read more on our website!
+#' @export
+#' @keywords internal
+#' @name extended-functions
+#' @rdname extended-functions
+#' @exportMethod scale_type.mo
+#' @export
+scale_type.mo <- function(x) {
+  # fix for:
+  # "Don't know how to automatically pick scale for object of type mo. Defaulting to continuous."
+  # "Error: Discrete value supplied to continuous scale"
+  "discrete"
+}
+
+#' @rdname extended-functions
+#' @exportMethod scale_type.ab
+#' @export
+scale_type.ab <- function(x) {
+  # fix for:
+  # "Don't know how to automatically pick scale for object of type mo. Defaulting to continuous."
+  # "Error: Discrete value supplied to continuous scale"
+  "discrete"
+}
+

R/first_isolate.R

@@ -414,15 +414,15 @@ first_isolate <- function(x,
     if (length(x) == 1) {
       return(TRUE)
     }
-    indices = integer(0)
-    start = x[1]
-    ind = 1
-    indices[ind] = ind
+    indices <- integer(0)
+    start <- x[1]
+    ind <- 1
+    indices[ind] <- ind
     for (i in 2:length(x)) {
-      if (as.numeric(x[i] - start >= episode_days)) {
-        ind = ind + 1
-        indices[ind] = i
-        start = x[i]
+      if (isTRUE(as.numeric(x[i] - start) >= episode_days)) {
+        ind <- ind + 1
+        indices[ind] <- i
+        start <- x[i]
       }
     }
     result <- rep(FALSE, length(x))

R/freq.R

@@ -238,7 +238,13 @@ freq <- function(x,
       x.name <- x.name %>% strsplit("%>%", fixed = TRUE) %>% unlist() %>% .[1] %>% trimws()
     }
     if (x.name == ".") {
+      # passed on with pipe
+      x.name <- get_data_source_name(x)
+      if (!is.null(x.name)) {
+        x.name <- paste0("`", x.name, "`")
+      } else {
         x.name <- "a data.frame"
+      }
     } else {
       x.name <- paste0("`", x.name, "`")
     }
@@ -1230,3 +1236,21 @@ format.freq <- function(x, digits = 1, ...) {
   x$cum_percent <- percent(x$cum_percent, round = digits, force_zero = TRUE)
   base::format.data.frame(x, ...)
 }
+
+#' @importFrom data.table address
+get_data_source_name <- function(x, else_txt = NULL) {
+  obj_addr <- address(x)
+  # try global environment
+  addrs <- unlist(lapply(ls(".GlobalEnv"), function(x) address(get(x))))
+  res <- ls(".GlobalEnv")[addrs == obj_addr]
+  if (length(res) == 0) {
+    # check AMR package - some users might use our data sets for testing
+    addrs <- unlist(lapply(ls("package:AMR"), function(x) address(get(x))))
+    res <- ls("package:AMR")[addrs == obj_addr]
+  }
+  if (length(res) == 0) {
+    else_txt
+  } else {
+    res
+  }
+}

R/ggplot_rsi.R

@@ -24,11 +24,11 @@
 #' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}2} functions.
 #' @param data a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})
 #' @param position position adjustment of bars, either \code{"fill"} (default when \code{fun} is \code{\link{count_df}}), \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"}
-#' @param x variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
-#' @param fill variable to categorise using the plots legend, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
+#' @param x variable to show on x axis, either \code{"antibiotic"} (default) or \code{"interpretation"} or a grouping variable
+#' @param fill variable to categorise using the plots legend, either \code{"antibiotic"} (default) or \code{"interpretation"} or a grouping variable
 #' @param breaks numeric vector of positions
 #' @param limits numeric vector of length two providing limits of the scale, use \code{NA} to refer to the existing minimum or maximum
-#' @param facet variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"} or a grouping variable
+#' @param facet variable to split plots by, either \code{"interpretation"} (default) or \code{"antibiotic"} or a grouping variable
 #' @param fun function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}
 #' @inheritParams portion
 #' @param nrow (when using \code{facet}) number of rows
@@ -129,7 +129,7 @@
 #'   select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>%
 #'   group_by(hospital_id) %>%
 #'   ggplot_rsi(x = "hospital_id",
-#'              facet = "Antibiotic",
+#'              facet = "antibiotic",
 #'              nrow = 1,
 #'              title = "AMR of Anti-UTI Drugs Per Hospital",
 #'              x.title = "Hospital",
@@ -150,7 +150,7 @@
 #'   # group by MO
 #'   group_by(bug) %>%
 #'   # plot the thing, putting MOs on the facet
-#'   ggplot_rsi(x = "Antibiotic",
+#'   ggplot_rsi(x = "antibiotic",
 #'              facet = "bug",
 #'              translate_ab = FALSE,
 #'              nrow = 1,
@@ -161,8 +161,8 @@
 #' }
 ggplot_rsi <- function(data,
                        position = NULL,
-                       x = "Antibiotic",
-                       fill = "Interpretation",
+                       x = "antibiotic",
+                       fill = "interpretation",
                        # params = list(),
                        facet = NULL,
                        breaks = seq(0, 1, 0.1),
@@ -226,7 +226,7 @@ ggplot_rsi <- function(data,
              fun = fun, combine_SI = combine_SI, combine_IR = combine_IR, ...) +
     theme_rsi()
 
-  if (fill == "Interpretation") {
+  if (fill == "interpretation") {
     # set RSI colours
     if (isFALSE(colours) & missing(datalabels.colour)) {
       # set datalabel colour to middle gray
@@ -267,8 +267,8 @@ ggplot_rsi <- function(data,
 #' @rdname ggplot_rsi
 #' @export
 geom_rsi <- function(position = NULL,
-                     x = c("Antibiotic", "Interpretation"),
-                     fill = "Interpretation",
+                     x = c("antibiotic", "interpretation"),
+                     fill = "interpretation",
                      translate_ab = "name",
                      language = get_locale(),
                      combine_SI = TRUE,
@@ -286,7 +286,7 @@ geom_rsi <- function(position = NULL,
   if (!fun_name %in% c("portion_df", "count_df", "fun")) {
     stop("`fun` must be portion_df or count_df")
   }
-  y <- "Value"
+  y <- "value"
   if (identical(fun, count_df)) {
     if (missing(position) | is.null(position)) {
       position <- "fill"
@@ -312,10 +312,10 @@ geom_rsi <- function(position = NULL,
     x <- substr(x, 2, nchar(x) - 1)
   }
 
-  if (tolower(x) %in% tolower(c('ab', 'antibiotic', 'abx', 'antibiotics'))) {
-    x <- "Antibiotic"
-  } else if (tolower(x) %in% tolower(c('SIR', 'RSI', 'interpretation', 'interpretations', 'result'))) {
-    x <- "Interpretation"
+  if (tolower(x) %in% tolower(c('ab', 'abx', 'antibiotics'))) {
+    x <- "antibiotic"
+  } else if (tolower(x) %in% tolower(c('SIR', 'RSI', 'interpretations', 'result'))) {
+    x <- "interpretation"
   }
 
   ggplot2::layer(geom = "bar", stat = "identity", position = position,
@@ -332,7 +332,7 @@ geom_rsi <- function(position = NULL,
 
 #' @rdname ggplot_rsi
 #' @export
-facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
+facet_rsi <- function(facet = c("interpretation", "antibiotic"), nrow = NULL) {
 
   stopifnot_installed_package("ggplot2")
 
@@ -347,10 +347,10 @@ facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
     facet <- substr(facet, 2, nchar(facet) - 1)
   }
 
-  if (tolower(facet) %in% tolower(c('SIR', 'RSI', 'interpretation', 'interpretations', 'result'))) {
-    facet <- "Interpretation"
-  } else if (tolower(facet) %in% tolower(c('ab', 'antibiotic', 'abx', 'antibiotics'))) {
-    facet <- "Antibiotic"
+  if (tolower(facet) %in% tolower(c('SIR', 'RSI', 'interpretations', 'result'))) {
+    facet <- "interpretation"
+  } else if (tolower(facet) %in% tolower(c('ab', 'abx', 'antibiotics'))) {
+    facet <- "antibiotic"
   }
 
   ggplot2::facet_wrap(facets = facet, scales = "free_x", nrow = nrow)
@@ -408,7 +408,7 @@ theme_rsi <- function() {
 #' @importFrom dplyr mutate %>% group_by_at
 #' @export
 labels_rsi_count <- function(position = NULL,
-                             x = "Antibiotic",
+                             x = "antibiotic",
                              translate_ab = "name",
                              combine_SI = TRUE,
                              combine_IR = FALSE,
@@ -424,7 +424,7 @@ labels_rsi_count <- function(position = NULL,
   x_name <- x
   ggplot2::geom_text(mapping = ggplot2::aes_string(label = "lbl",
                                                    x = x,
-                                                   y = "Value"),
+                                                   y = "value"),
                      position = position,
                      inherit.aes = FALSE,
                      size = datalabels.size,
@@ -438,7 +438,7 @@ labels_rsi_count <- function(position = NULL,
                                 combine_SI = combine_SI,
                                 combine_IR = combine_IR) %>%
                          group_by_at(x_name) %>%
-                         mutate(lbl = paste0(percent(Value / sum(Value, na.rm = TRUE), force_zero = TRUE),
-                                             "\n(n=", Value, ")"))
+                         mutate(lbl = paste0(percent(value / sum(value, na.rm = TRUE), force_zero = TRUE),
+                                             "\n(n=", value, ")"))
                      })
 }

R/globals.R

@@ -54,6 +54,7 @@ globalVariables(c(".",
                   "index",
                   "input",
                   "Interpretation",
+                  "interpretation",
                   "item",
                   "key_ab",
                   "key_ab_lag",
@@ -89,6 +90,7 @@ globalVariables(c(".",
                   "package_v",
                   "Pasted",
                   "patient_id",
+                  "pattern",
                   "phylum",
                   "plural",
                   "prevalence",

R/key_antibiotics.R

@@ -26,17 +26,17 @@
 #' @param y,z characters to compare
 #' @inheritParams first_isolate
 #' @param universal_1,universal_2,universal_3,universal_4,universal_5,universal_6 column names of \strong{broad-spectrum} antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.
-#' @param GramPos_1,GramPos_2,GramPos_3,GramPos_4,GramPos_5,GramPos_6 column names of antibiotics for \strong{Gram positives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.
-#' @param GramNeg_1,GramNeg_2,GramNeg_3,GramNeg_4,GramNeg_5,GramNeg_6 column names of antibiotics for \strong{Gram negatives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.
+#' @param GramPos_1,GramPos_2,GramPos_3,GramPos_4,GramPos_5,GramPos_6 column names of antibiotics for \strong{Gram-positives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.
+#' @param GramNeg_1,GramNeg_2,GramNeg_3,GramNeg_4,GramNeg_5,GramNeg_6 column names of antibiotics for \strong{Gram-negatives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.
 #' @param warnings give warning about missing antibiotic columns, they will anyway be ignored
 #' @param ... other parameters passed on to function
 #' @details The function \code{key_antibiotics} returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using \code{key_antibiotics_equal}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}). The \code{\link{first_isolate}} function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible \emph{S. aureus} (MSSA) found within the same episode (see \code{episode} parameter of \code{\link{first_isolate}}). Without key antibiotic comparison it would not.
 #'
-#'   At default, the antibiotics that are used for \strong{Gram positive bacteria} are (colum names): \cr
-#'   \code{"amox"}, \code{"amcl"}, \code{"cfur"}, \code{"pita"}, \code{"cipr"}, \code{"trsu"} (until here is universal), \code{"vanc"}, \code{"teic"}, \code{"tetr"}, \code{"eryt"}, \code{"oxac"}, \code{"rifa"}.
+#'   At default, the antibiotics that are used for \strong{Gram-positive bacteria} are: \cr
+#'   amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampin.
 #'
-#'   At default, the antibiotics that are used for \strong{Gram negative bacteria} are (colum names): \cr
-#'   \code{"amox"}, \code{"amcl"}, \code{"cfur"}, \code{"pita"}, \code{"cipr"}, \code{"trsu"} (until here is universal), \code{"gent"}, \code{"tobr"}, \code{"coli"}, \code{"cfot"}, \code{"cfta"}, \code{"mero"}.
+#'   At default, the antibiotics that are used for \strong{Gram-negative bacteria} are: \cr
+#'   amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem.
 #'
 #'
 #'   The function \code{key_antibiotics_equal} checks the characters returned by \code{key_antibiotics} for equality, and returns a logical vector.
@@ -50,7 +50,7 @@
 #' @examples
 #' # septic_patients is a dataset available in the AMR package
 #' ?septic_patients
-
+#'
 #' library(dplyr)
 #' # set key antibiotics to a new variable
 #' my_patients <- septic_patients %>%
@@ -78,24 +78,24 @@
 #' # FALSE, because I is not ignored and so the 4th value differs
 key_antibiotics <- function(x,
                             col_mo = NULL,
-                            universal_1 = guess_ab_col(x, "AMX"),
-                            universal_2 = guess_ab_col(x, "AMC"),
-                            universal_3 = guess_ab_col(x, "CXM"),
-                            universal_4 = guess_ab_col(x, "TZP"),
-                            universal_5 = guess_ab_col(x, "CIP"),
-                            universal_6 = guess_ab_col(x, "SXT"),
-                            GramPos_1 = guess_ab_col(x, "VAN"),
-                            GramPos_2 = guess_ab_col(x, "TEC"),
-                            GramPos_3 = guess_ab_col(x, "TCY"),
-                            GramPos_4 = guess_ab_col(x, "ERY"),
-                            GramPos_5 = guess_ab_col(x, "OXA"),
-                            GramPos_6 = guess_ab_col(x, "RIF"),
-                            GramNeg_1 = guess_ab_col(x, "GEN"),
-                            GramNeg_2 = guess_ab_col(x, "TOB"),
-                            GramNeg_3 = guess_ab_col(x, "COL"),
-                            GramNeg_4 = guess_ab_col(x, "CTX"),
-                            GramNeg_5 = guess_ab_col(x, "CAZ"),
-                            GramNeg_6 = guess_ab_col(x, "MEM"),
+                            universal_1 = guess_ab_col(x, "amoxicillin"),
+                            universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"),
+                            universal_3 = guess_ab_col(x, "cefuroxime"),
+                            universal_4 = guess_ab_col(x, "piperacillin/tazobactam"),
+                            universal_5 = guess_ab_col(x, "ciprofloxacin"),
+                            universal_6 = guess_ab_col(x, "trimethoprim/sulfamethoxazole"),
+                            GramPos_1 = guess_ab_col(x, "vancomycin"),
+                            GramPos_2 = guess_ab_col(x, "teicoplanin"),
+                            GramPos_3 = guess_ab_col(x, "tetracycline"),
+                            GramPos_4 = guess_ab_col(x, "erythromycin"),
+                            GramPos_5 = guess_ab_col(x, "oxacillin"),
+                            GramPos_6 = guess_ab_col(x, "rifampin"),
+                            GramNeg_1 = guess_ab_col(x, "gentamicin"),
+                            GramNeg_2 = guess_ab_col(x, "tobramycin"),
+                            GramNeg_3 = guess_ab_col(x, "colistin"),
+                            GramNeg_4 = guess_ab_col(x, "cefotaxime"),
+                            GramNeg_5 = guess_ab_col(x, "ceftazidime"),
+                            GramNeg_6 = guess_ab_col(x, "meropenem"),
                             warnings = TRUE,
                             ...) {
 
@@ -170,7 +170,7 @@ key_antibiotics <- function(x,
   gram_positive <- gram_positive[!is.null(gram_positive)]
   gram_positive <- gram_positive[!is.na(gram_positive)]
   if (length(gram_positive) < 12) {
-    warning("only using ", length(gram_positive), " different antibiotics as key antibiotics for Gram positives. See ?key_antibiotics.", call. = FALSE)
+    warning("only using ", length(gram_positive), " different antibiotics as key antibiotics for Gram-positives. See ?key_antibiotics.", call. = FALSE)
   }
 
   gram_negative = c(universal,
@@ -179,7 +179,7 @@ key_antibiotics <- function(x,
   gram_negative <- gram_negative[!is.null(gram_negative)]
   gram_negative <- gram_negative[!is.na(gram_negative)]
   if (length(gram_negative) < 12) {
-    warning("only using ", length(gram_negative), " different antibiotics as key antibiotics for Gram negatives. See ?key_antibiotics.", call. = FALSE)
+    warning("only using ", length(gram_negative), " different antibiotics as key antibiotics for Gram-negatives. See ?key_antibiotics.", call. = FALSE)
   }
 
   # join to microorganisms data set
@@ -191,7 +191,7 @@ key_antibiotics <- function(x,
 
   # Gram +
   x <- x %>% mutate(key_ab =
-                      if_else(gramstain == "Gram positive",
+                      if_else(gramstain == "Gram-positive",
                               apply(X = x[, gram_positive],
                                     MARGIN = 1,
                                     FUN = function(x) paste(x, collapse = "")),
@@ -199,7 +199,7 @@ key_antibiotics <- function(x,
 
   # Gram -
   x <- x %>% mutate(key_ab =
-                      if_else(gramstain == "Gram negative",
+                      if_else(gramstain == "Gram-negative",
                               apply(X = x[, gram_negative],
                                     MARGIN = 1,
                                     FUN = function(x) paste(x, collapse = "")),
@@ -209,7 +209,8 @@ key_antibiotics <- function(x,
   key_abs <- x %>%
     pull(key_ab) %>%
     gsub('(NA|NULL)', '.', .) %>%
-    gsub('[^SIR]', '.', ., ignore.case = TRUE)
+    gsub('[^SIR]', '.', ., ignore.case = TRUE) %>%
+    toupper()
 
   key_abs
 
@@ -295,7 +296,7 @@ key_antibiotics_equal <- function(y,
         result[i] <- points >= points_threshold
 
       } else {
-        stop('`', type, '` is not a valid value for type, must be "points" or "keyantibiotics". See ?first_isolate.')
+        stop('`', type, '` is not a valid value for type, must be "points" or "keyantibiotics". See ?key_antibiotics')
       }
     }
   }

R/mic.R

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

R/misc.R

@@ -172,16 +172,19 @@ get_column_abx <- function(x,
   # get_column_abx(septic_patients %>% rename(thisone = AMX), amox = "thisone")
   dots <- list(...)
   if (length(dots) > 0) {
-    dots <- unlist(dots)
     newnames <- suppressWarnings(as.ab(names(dots)))
     if (any(is.na(newnames))) {
       warning("Invalid antibiotic reference(s): ", toString(names(dots)[is.na(newnames)]),
               call. = FALSE, immediate. = TRUE)
     }
+    # turn all NULLs to NAs
+    dots <- unlist(lapply(dots, function(x) if (is.null(x)) NA else x))
     names(dots) <- newnames
     dots <- dots[!is.na(names(dots))]
     # merge, but overwrite automatically determined ones by 'dots'
     x <- c(x[!x %in% dots & !names(x) %in% names(dots)], dots)
+    # delete NAs, this will make eucast_rules(... TMP = NULL) work to prevent TMP from being used
+    x <- x[!is.na(x)]
   }
 
   # sort on name
@@ -250,7 +253,7 @@ stopifnot_installed_package <- function(package) {
 
 # translate strings based on inst/translations.tsv
 #' @importFrom dplyr %>% filter
-t <- function(from, language = get_locale()) {
+translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
   # if (getOption("AMR_locale", "en") != language) {
   #   language <- getOption("AMR_locale", "en")
   # }
@@ -271,6 +274,9 @@ t <- function(from, language = get_locale()) {
   }
 
   df_trans <- df_trans %>% filter(lang == language)
+  if (only_unknown == TRUE) {
+    df_trans <- df_trans %>% filter(pattern %like% "unknown")
+  }
 
   # default case sensitive if value if 'ignore.case' is missing:
   df_trans$ignore.case[is.na(df_trans$ignore.case)] <- FALSE
@@ -301,5 +307,14 @@ t <- function(from, language = get_locale()) {
 }
 
 "%or%" <- function(x, y) {
-  ifelse(!is.na(x), x, ifelse(!is.na(y), y, NA))
+  if (is.null(x) | is.null(y)) {
+    if (is.null(x)) {
+      return(y)
+    } else {
+      return(x)
+    }
+  }
+  ifelse(!is.na(x),
+         x,
+         ifelse(!is.na(y), y, NA))
 }

R/mo.R

@@ -151,6 +151,7 @@
 #' as.mo("MRSA")   # Methicillin Resistant S. aureus
 #' as.mo("VISA")   # Vancomycin Intermediate S. aureus
 #' as.mo("VRSA")   # Vancomycin Resistant S. aureus
+#' as.mo(22242419) # Catalogue of Life ID
 #'
 #' # Dyslexia is no problem - these all work:
 #' as.mo("Ureaplasma urealyticum")
@@ -485,18 +486,21 @@ exec_as.mo <- function(x,
     # remove genus as first word
     x <- gsub("^Genus ", "", x)
     # allow characters that resemble others
-    x <- gsub("[iy]+", "[iy]+", x, ignore.case = TRUE)
-    x <- gsub("[sz]+", "[sz]+", x, ignore.case = TRUE)
-    x <- gsub("(c|k|q|qu)+", "(c|k|q|qu)+", x, ignore.case = TRUE)
-    x <- gsub("(ph|f|v)+", "(ph|f|v)+", x, ignore.case = TRUE)
-    x <- gsub("(th|t)+", "(th|t)+", x, ignore.case = TRUE)
-    x <- gsub("a+", "a+", x, ignore.case = TRUE)
+    if (initial_search == FALSE) {
+      x <- tolower(x)
+      x <- gsub("[iy]+", "[iy]+", x)
+      x <- gsub("(c|k|q|qu|s|z|x|ks)+", "(c|k|q|qu|s|z|x|ks)+", x)
+      x <- gsub("(ph|f|v)+", "(ph|f|v)+", x)
+      x <- gsub("(th|t)+", "(th|t)+", x)
+      x <- gsub("a+", "a+", x)
+      x <- gsub("u+", "u+", x)
       # allow any ending of -um, -us, -ium, -ius and -a (needs perl for the negative backward lookup):
       x <- gsub("(um|u\\[sz\\]\\+|\\[iy\\]\\+um|\\[iy\\]\\+u\\[sz\\]\\+|a\\+)(?![a-z[])",
                 "(um|us|ium|ius|a)", x, ignore.case = TRUE, perl = TRUE)
       x <- gsub("e+", "e+", x, ignore.case = TRUE)
       x <- gsub("o+", "o+", x, ignore.case = TRUE)
-
+      x <- gsub("(.)\\1+", "\\1+", x)
+    }
     x <- strip_whitespace(x)
 
     x_trimmed <- x
@@ -561,6 +565,17 @@ exec_as.mo <- function(x,
         next
       }
 
+      found <- microorganismsDT[col_id == x_backup[i], ..property][[1]]
+      # is a valid Catalogue of Life ID
+      if (NROW(found) > 0) {
+        x[i] <- found[1L]
+        if (initial_search == TRUE) {
+          set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
+        }
+        next
+      }
+
+
       # WHONET: xxx = no growth
       if (tolower(as.character(paste0(x_backup_without_spp[i], ""))) %in% c("", "xxx", "na", "nan")) {
         x[i] <- NA_character_
@@ -639,7 +654,19 @@ exec_as.mo <- function(x,
           }
           next
         }
-        if (toupper(x_backup_without_spp[i]) %in% c("EHEC", "EPEC", "EIEC", "STEC", "ATEC")
+        # support for:
+        # - AIEC (Adherent-Invasive E. coli)
+        # - ATEC (Atypical Entero-pathogenic E. coli)
+        # - DAEC (Diffusely Adhering E. coli)
+        # - EAEC (Entero-Aggresive E. coli)
+        # - EHEC (Entero-Haemorrhagic E. coli)
+        # - EIEC (Entero-Invasive E. coli)
+        # - EPEC (Entero-Pathogenic E. coli)
+        # - ETEC (Entero-Toxigenic E. coli)
+        # - NMEC (Neonatal Meningitis‐causing E. coli)
+        # - STEC (Shiga-toxin producing E. coli)
+        # - UPEC (Uropathogenic E. coli)
+        if (toupper(x_backup_without_spp[i]) %in% c("AIEC", "ATEC", "DAEC", "EAEC", "EHEC", "EIEC", "EPEC", "ETEC", "NMEC", "STEC", "UPEC")
             | x_backup_without_spp[i] %like% "O?(26|103|104|104|111|121|145|157)") {
           x[i] <- microorganismsDT[mo == 'B_ESCHR_COL', ..property][[1]][1L]
           if (initial_search == TRUE) {
@@ -745,7 +772,7 @@ exec_as.mo <- function(x,
               set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
             }
             options(mo_renamed = c(getOption("mo_renamed"),
-                                   magenta(paste0("Note: ",
+                                   magenta(paste0("NOTE: ",
                                                   italic("Salmonella"), " ", trimws(gsub("Salmonella", "", x_backup_without_spp[i])),
                                                   " was considered ",
                                                   italic("Salmonella species"),
@@ -757,7 +784,7 @@ exec_as.mo <- function(x,
               set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
             }
             options(mo_renamed = c(getOption("mo_renamed"),
-                                   magenta(paste0("Note: ",
+                                   magenta(paste0("NOTE: ",
                                                   italic("Salmonella"), " ", trimws(gsub("Salmonella", "", x_backup_without_spp[i])),
                                                   " was considered a subspecies of ",
                                                   italic("Salmonella enterica"),
@@ -767,7 +794,7 @@ exec_as.mo <- function(x,
         }
       }
 
-      # FIRST TRY FULLNAMES AND CODES
+      # FIRST TRY FULLNAMES AND CODES ----
       # if only genus is available, return only genus
       if (all(!c(x[i], x_trimmed[i]) %like% " ")) {
         found <- microorganismsDT[fullname_lower %in% tolower(c(x_species[i], x_trimmed_species[i])), ..property][[1]]
@@ -1190,11 +1217,11 @@ exec_as.mo <- function(x,
   if (NROW(uncertainties) > 0 & initial_search == TRUE) {
     options(mo_uncertainties = as.list(distinct(uncertainties, input, .keep_all = TRUE)))
 
-    plural <- c("value", "it")
+    plural <- c("", "it")
     if (NROW(uncertainties) > 1) {
-      plural <- c("values", "them")
+      plural <- c("s", "them")
     }
-    msg <- paste0("\nResults of ", nr2char(NROW(uncertainties)), " ", plural[1],
+    msg <- paste0("\nResult", plural[1], " of ", nr2char(NROW(uncertainties)), " value", plural[1],
                   " was guessed with uncertainty. Use mo_uncertainties() to review ", plural[2], ".")
     warning(red(msg),
             call. = FALSE,
@@ -1230,7 +1257,7 @@ exec_as.mo <- function(x,
     post_Becker <- c("argensis", "caeli", "cornubiensis", "edaphicus")
     if (any(x %in% MOs_staph[species %in% post_Becker, ..property][[1]])) {
 
-      warning("Becker ", italic("et al."), " (2014) does not contain species named after their publication: ",
+      warning("Becker ", italic("et al."), " (2014, 2019) does not contain species named after their publication: ",
               italic(paste("S.",
                            sort(mo_species(unique(x[x %in% MOs_staph[species %in% post_Becker, ..property][[1]]]))),
                            collapse = ", ")),
@@ -1303,7 +1330,7 @@ exec_as.mo <- function(x,
     }
     notes <- sort(notes)
     for (i in 1:length(notes)) {
-      base::message(blue(paste("Note:", notes[i])))
+      base::message(blue(paste("NOTE:", notes[i])))
     }
   }
 
@@ -1333,7 +1360,7 @@ was_renamed <- function(name_old, name_new, ref_old = "", ref_new = "", mo = "")
   }
   msg <- paste0(italic(name_old), ref_old, " was renamed ", italic(name_new), ref_new, mo)
   msg <- gsub("et al.", italic("et al."), msg)
-  options(mo_renamed = sort(msg))
+  options(mo_renamed = c(getOption("mo_renamed"), sort(msg)))
 }
 
 #' @exportMethod print.mo
@@ -1462,6 +1489,9 @@ unregex <- function(x) {
 }
 
 get_mo_code <- function(x, property) {
+  # don't use right now
+  return(NULL)
+
   if (property == "mo") {
     unique(x)
   } else {

R/mo_property.R

@@ -69,10 +69,11 @@
 #' mo_shortname("E. coli")       # "E. coli"
 #'
 #' ## other properties
-#' mo_gramstain("E. coli")       # "Gram negative"
-#' mo_type("E. coli")            # "Bacteria" (equal to kingdom)
+#' mo_gramstain("E. coli")       # "Gram-negative"
+#' mo_type("E. coli")            # "Bacteria" (equal to kingdom, but may be translated)
 #' mo_rank("E. coli")            # "species"
 #' mo_url("E. coli")             # get the direct url to the online database entry
+#' mo_synonyms("E. coli")        # get previously accepted taxonomic names
 #'
 #' ## scientific reference
 #' mo_ref("E. coli")             # "Castellani et al., 1919"
@@ -84,7 +85,7 @@
 #' mo_genus("MRSA")              # "Staphylococcus"
 #' mo_species("MRSA")            # "aureus"
 #' mo_shortname("MRSA")          # "S. aureus"
-#' mo_gramstain("MRSA")          # "Gram positive"
+#' mo_gramstain("MRSA")          # "Gram-positive"
 #'
 #' mo_genus("VISA")              # "Staphylococcus"
 #' mo_species("VISA")            # "aureus"
@@ -133,15 +134,15 @@
 #'
 #' # get a list with the complete taxonomy (from kingdom to subspecies)
 #' mo_taxonomy("E. coli")
+#' # get a list with the taxonomy, the authors and the URL to the online database
+#' mo_info("E. coli")
 mo_name <- function(x, language = get_locale(), ...) {
-  mo_fullname(x = x, language = language, ... = ...)
+  translate_AMR(mo_validate(x = x, property = "fullname", ...), language = language, only_unknown = FALSE)
 }
 
 #' @rdname mo_property
 #' @export
-mo_fullname <- function(x, language = get_locale(), ...) {
-  t(mo_validate(x = x, property = "fullname", ...), language = language)
-}
+mo_fullname <- mo_name
 
 #' @rdname mo_property
 #' @importFrom dplyr %>% mutate pull
@@ -184,69 +185,61 @@ mo_shortname <- function(x, language = get_locale(), ...) {
   res1[res1 != res2] <- res2_fullname
   result <- as.character(res1)
 
-  t(result, language = language)
+  translate_AMR(result, language = language, only_unknown = FALSE)
 }
 
 #' @rdname mo_property
 #' @export
 mo_subspecies <- function(x, language = get_locale(), ...) {
-  t(mo_validate(x = x, property = "subspecies", ...), language = language)
+  translate_AMR(mo_validate(x = x, property = "subspecies", ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
 #' @export
 mo_species <- function(x, language = get_locale(), ...) {
-  t(mo_validate(x = x, property = "species", ...), language = language)
+  translate_AMR(mo_validate(x = x, property = "species", ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
 #' @export
 mo_genus <- function(x, language = get_locale(), ...) {
-  t(mo_validate(x = x, property = "genus", ...), language = language)
+  translate_AMR(mo_validate(x = x, property = "genus", ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
 #' @export
 mo_family <- function(x, language = get_locale(), ...) {
-  t(mo_validate(x = x, property = "family", ...), language = language)
+  translate_AMR(mo_validate(x = x, property = "family", ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
 #' @export
 mo_order <- function(x, language = get_locale(), ...) {
-  t(mo_validate(x = x, property = "order", ...), language = language)
+  translate_AMR(mo_validate(x = x, property = "order", ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
 #' @export
 mo_class <- function(x, language = get_locale(), ...) {
-  t(mo_validate(x = x, property = "class", ...), language = language)
+  translate_AMR(mo_validate(x = x, property = "class", ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
 #' @export
 mo_phylum <- function(x, language = get_locale(), ...) {
-  t(mo_validate(x = x, property = "phylum", ...), language = language)
+  translate_AMR(mo_validate(x = x, property = "phylum", ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
 #' @export
 mo_kingdom <- function(x, language = get_locale(), ...) {
-  if (all(x %in% AMR::microorganisms$kingdom)) {
-    return(x)
-  }
-  x <- as.mo(x, ...)
-  kngdm <- mo_validate(x = x, property = "kingdom", ...)
-  if (language != "en") {
-    kngdm[x == "UNKNOWN"] <- t(kngdm[x == "UNKNOWN"], language = language)
-  }
-  kngdm
+  translate_AMR(mo_validate(x = x, property = "kingdom", ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
 #' @export
 mo_type <- function(x, language = get_locale(), ...) {
-  t(mo_validate(x = x, property = "kingdom", ...), language = language)
+  translate_AMR(mo_validate(x = x, property = "kingdom", ...), language = language, only_unknown = FALSE)
 }
 
 #' @rdname mo_property
@@ -254,16 +247,26 @@ mo_type <- function(x, language = get_locale(), ...) {
 mo_gramstain <- function(x, language = get_locale(), ...) {
   x.mo <- as.mo(x, ...)
   x.phylum <- mo_phylum(x.mo, language = "en")
+  # DETERMINE GRAM STAIN FOR BACTERIA
+  # Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097
+  # It says this:
+  # Kingdom Bacteria (Cavalier-Smith, 2002)
+  #    Subkingdom Posibacteria (Cavalier-Smith, 2002)
+  #   Direct Children:
+  #       Phylum  Actinobacteria (Cavalier-Smith, 2002)
+  #       Phylum  Chloroflexi (Garrity and Holt, 2002)
+  #       Phylum  Firmicutes (corrig. Gibbons and Murray, 1978)
+  #       Phylum  Tenericutes (Murray, 1984)
+  x <- NA_character_
+  # make all bacteria Gram negative
+  x[mo_kingdom(x.mo, language = "en") == "Bacteria"] <- "Gram-negative"
+  # overwrite these phyla with Gram positive
   x[x.phylum %in% c("Actinobacteria",
                     "Chloroflexi",
                     "Firmicutes",
-                    "Tenericutes")] <- "Gram positive"
-  x[x != "Gram positive"] <- "Gram negative"
-  x[mo_kingdom(x.mo, language = "en") != "Bacteria"] <- NA_character_
-  x[x.mo == "B_GRAMP"] <- "Gram positive"
-  x[x.mo == "B_GRAMN"] <- "Gram negative"
-
-  t(x, language = language)
+                    "Tenericutes")
+    | x.mo == "B_GRAMP"] <- "Gram-positive"
+  translate_AMR(x, language = language, only_unknown = FALSE)
 }
 
 #' @rdname mo_property
@@ -276,7 +279,7 @@ mo_ref <- function(x, ...) {
 #' @export
 mo_authors <- function(x, ...) {
   x <- mo_validate(x = x, property = "ref", ...)
-  # remove last 4 digits and presumably the comma and space that preceeds them
+  # remove last 4 digits and presumably the comma and space that preceed them
   x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)])
   suppressWarnings(x)
 }
@@ -300,14 +303,52 @@ mo_rank <- function(x, ...) {
 #' @export
 mo_taxonomy <- function(x, language = get_locale(),  ...) {
   x <- AMR::as.mo(x, ...)
-  base::list(kingdom = mo_kingdom(x, language = language),
-             phylum = mo_phylum(x, language = language),
-             class = mo_class(x, language = language),
-             order = mo_order(x, language = language),
-             family = mo_family(x, language = language),
-             genus = mo_genus(x, language = language),
-             species = mo_species(x, language = language),
-             subspecies = mo_subspecies(x, language = language))
+  base::list(kingdom = AMR::mo_kingdom(x, language = language),
+             phylum = AMR::mo_phylum(x, language = language),
+             class = AMR::mo_class(x, language = language),
+             order = AMR::mo_order(x, language = language),
+             family = AMR::mo_family(x, language = language),
+             genus = AMR::mo_genus(x, language = language),
+             species = AMR::mo_species(x, language = language),
+             subspecies = AMR::mo_subspecies(x, language = language))
+}
+
+#' @rdname mo_property
+#' @export
+mo_synonyms <- function(x, ...) {
+  x <- as.mo(x, ...)
+  IDs <- AMR::mo_property(x = x, property = "col_id", language = NULL)
+  syns <- lapply(IDs, function(col_id) {
+    res <- sort(AMR::microorganisms.old[which(AMR::microorganisms.old$col_id_new == col_id), "fullname"])
+    if (length(res) == 0) {
+      NULL
+    } else {
+      res
+    }
+  })
+  if (length(syns) > 1) {
+    names(syns) <- mo_fullname(x)
+    syns
+  } else {
+    unlist(syns)
+  }
+}
+
+#' @rdname mo_property
+#' @export
+mo_info <- function(x, language = get_locale(),  ...) {
+  x <- AMR::as.mo(x, ...)
+  info <- lapply(x, function(y)
+    c(mo_taxonomy(y, language = language),
+      list(synonyms = mo_synonyms(y),
+           url = unname(mo_url(y, open = FALSE)),
+           ref = mo_ref(y))))
+  if (length(info) > 1) {
+    names(info) <- mo_fullname(x)
+    info
+  } else {
+    info[[1L]]
+  }
 }
 
 #' @rdname mo_property
@@ -326,7 +367,7 @@ mo_url <- function(x, open = FALSE, ...) {
                              NA_character_))
 
   u <- df$url
-  names(u) <- mo_fullname(mo)
+  names(u) <- AMR::mo_fullname(mo)
   if (open == TRUE) {
     if (length(u) > 1) {
       warning("only the first URL will be opened, as `browseURL()` only suports one string.")
@@ -348,7 +389,7 @@ mo_property <- function(x, property = 'fullname', language = get_locale(), ...)
     stop("invalid property: '", property, "' - use a column name of the `microorganisms` data set")
   }
 
-  t(mo_validate(x = x, property = property, ...), language = language)
+  translate_AMR(mo_validate(x = x, property = property, ...), language = language, only_unknown = TRUE)
 }
 
 mo_validate <- function(x, property, ...) {
@@ -376,12 +417,15 @@ mo_validate <- function(x, property, ...) {
   if (!all(x %in% pull(AMR::microorganisms, property))
       | Becker %in% c(TRUE, "all")
       | Lancefield %in% c(TRUE, "all")) {
-    exec_as.mo(x, property = property, ...)
-  } else {
+    x <- exec_as.mo(x, property = property, ...)
+  }
+
   if (property == "mo") {
     return(structure(x, class = "mo"))
+  } else if (property == "col_id") {
+    return(as.integer(x))
   } else {
     return(x)
   }
-  }
+
 }

R/portion.R

@@ -38,7 +38,9 @@
 #'
 #' These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the \code{\link[AMR]{count}} functions to count isolates. \emph{Low counts can infuence the outcome - these \code{portion} functions may camouflage this, since they only return the portion albeit being dependent on the \code{minimum} parameter.}
 #'
-#' \code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.
+#' The function \code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each group and each variable with class \code{"rsi"}.
+#'
+#' The function \code{rsi_df} works exactly like \code{portion_df}, but adds the number of isolates.
 #' \if{html}{
 #    (created with https://www.latex4technics.com/)
 #'   \cr\cr

R/rsi.R

@@ -387,9 +387,14 @@ summary.rsi <- function(object, ...) {
 #' @importFrom dplyr %>% group_by summarise filter mutate if_else n_distinct
 #' @importFrom graphics plot text
 #' @noRd
-plot.rsi <- function(x, ...) {
-  x_name <- deparse(substitute(x))
-
+plot.rsi <- function(x,
+                     lwd = 2,
+                     ylim = NULL,
+                     ylab = 'Percentage',
+                     xlab = 'Antimicrobial Interpretation',
+                     main = paste('Susceptibility Analysis of', deparse(substitute(x))),
+                     axes = FALSE,
+                     ...) {
   suppressWarnings(
     data <- data.frame(x = x,
                        y = 1,
@@ -415,13 +420,12 @@ plot.rsi <- function(x, ...) {
 
   plot(x = data$x,
        y = data$s,
-       lwd = 2,
-       col = c('green', 'orange', 'red'),
+       lwd = lwd,
        ylim = c(0, ymax),
-       ylab = 'Percentage',
-       xlab = 'Antimicrobial Interpretation',
-       main = paste('Susceptibility Analysis of', x_name),
-       axes = FALSE,
+       ylab = ylab,
+       xlab = xlab,
+       main = main,
+       axes = axes,
        ...)
   # x axis
   axis(side = 1, at = 1:n_distinct(data$x), labels = levels(data$x), lwd = 0)
@@ -437,26 +441,34 @@ plot.rsi <- function(x, ...) {
 #' @exportMethod barplot.rsi
 #' @export
 #' @importFrom dplyr %>% group_by summarise
-#' @importFrom graphics barplot axis
+#' @importFrom graphics barplot axis par
 #' @noRd
-barplot.rsi <- function(height, ...) {
-  x <- height
-  x_name <- deparse(substitute(height))
-
-  suppressWarnings(
-    data <- data.frame(rsi = x, cnt = 1) %>%
-      group_by(rsi) %>%
-      summarise(cnt = sum(cnt)) %>%
-      droplevels()
-  )
-
-  barplot(table(x),
+barplot.rsi <- function(height,
                         col = c('green3', 'orange2', 'red3'),
-          xlab = 'Antimicrobial Interpretation',
-          main = paste('Susceptibility Analysis of', x_name),
+                        xlab = ifelse(beside, 'Antimicrobial Interpretation', ''),
+                        main = paste('Susceptibility Analysis of', deparse(substitute(height))),
                         ylab = 'Frequency',
+                        beside = TRUE,
+                        axes = beside,
+                        ...) {
+
+  if (axes == TRUE) {
+    par(mar =  c(5, 4, 4, 2) + 0.1)
+  } else {
+    par(mar =  c(2, 4, 4, 2) + 0.1)
+  }
+
+  barplot(as.matrix(table(height)),
+          col = col,
+          xlab = xlab,
+          main = main,
+          ylab = ylab,
+          beside = beside,
           axes = FALSE,
           ...)
   # y axis, 0-100%
-  axis(side = 2, at = seq(0, max(data$cnt) + max(data$cnt) * 1.1, by = 25))
+  axis(side = 2, at = seq(0, max(table(height)) + max(table(height)) * 1.1, by = 25))
+  if (axes == TRUE && beside == TRUE) {
+    axis(side = 1, labels = levels(height), at = c(1, 2, 3) + 0.5, lwd = 0)
+  }
 }

R/rsi_calc.R

@@ -151,6 +151,7 @@ rsi_calc <- function(...,
   }
 }
 
+#' @importFrom dplyr %>% summarise_if mutate select everything bind_rows
 rsi_calc_df <- function(type, # "portion" or "count"
                         data,
                         translate_ab = "name",
@@ -196,8 +197,8 @@ rsi_calc_df <- function(type, # "portion" or "count"
                            .funs = int_fn)
     }
     summ %>%
-      mutate(Interpretation = int) %>%
-      select(Interpretation, everything())
+      mutate(interpretation = int) %>%
+      select(interpretation, everything())
   }
 
   resS <- get_summaryfunction("S")
@@ -209,28 +210,29 @@ rsi_calc_df <- function(type, # "portion" or "count"
 
   if (isFALSE(combine_SI) & isFALSE(combine_IR)) {
     res <- bind_rows(resS, resI, resR) %>%
-      mutate(Interpretation = factor(Interpretation,
+      mutate(interpretation = factor(interpretation,
                                      levels = c("S", "I", "R"),
                                      ordered = TRUE))
 
   } else if (isTRUE(combine_IR)) {
     res <- bind_rows(resS, resIR) %>%
-      mutate(Interpretation = factor(Interpretation,
+      mutate(interpretation = factor(interpretation,
                                      levels = c("S", "IR"),
                                      ordered = TRUE))
 
   } else if (isTRUE(combine_SI)) {
     res <- bind_rows(resSI, resR) %>%
-      mutate(Interpretation = factor(Interpretation,
+      mutate(interpretation = factor(interpretation,
                                      levels = c("SI", "R"),
                                      ordered = TRUE))
   }
 
   res <- res %>%
-    tidyr::gather(Antibiotic, Value, -Interpretation, -data.groups)
+    tidyr::gather(antibiotic, value, -interpretation, -data.groups) %>%
+    select(antibiotic, everything())
 
   if (!translate_ab == FALSE) {
-    res <- res %>% mutate(Antibiotic = ab_property(Antibiotic, property = translate_ab, language = language))
+    res <- res %>% mutate(antibiotic = ab_property(antibiotic, property = translate_ab, language = language))
   }
 
   res

R/rsi_df.R

@@ -0,0 +1,58 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+#                                                                      #
+# This R package was created for academic research and was publicly    #
+# released in the hope that it will be useful, but it comes WITHOUT    #
+# ANY WARRANTY OR LIABILITY.                                           #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
+#' @rdname portion
+#' @rdname count
+#' @importFrom dplyr %>% select_if bind_rows summarise_if mutate group_vars select everything
+#' @export
+rsi_df <- function(data,
+                   translate_ab = "name",
+                   language = get_locale(),
+                   minimum = 30,
+                   as_percent = FALSE,
+                   combine_SI = TRUE,
+                   combine_IR = FALSE) {
+
+  portions <- rsi_calc_df(type = "portion",
+                          data = data,
+                          translate_ab = translate_ab,
+                          language = language,
+                          minimum = minimum,
+                          as_percent = as_percent,
+                          combine_SI = combine_SI,
+                          combine_IR = combine_IR,
+                          combine_SI_missing = missing(combine_SI))
+
+  counts <- rsi_calc_df(type = "count",
+                        data = data,
+                        translate_ab = FALSE,
+                        language = "en",
+                        minimum = minimum,
+                        as_percent = as_percent,
+                        combine_SI = combine_SI,
+                        combine_IR = combine_IR,
+                        combine_SI_missing = missing(combine_SI))
+
+  data.frame(portions,
+             isolates = counts$value,
+             stringsAsFactors = FALSE)
+
+}

R/zzz.R

@@ -51,6 +51,33 @@
 
 }
 
+
+.onAttach <- function(...) {
+  if (interactive() & !isFALSE(getOption("AMR_survey"))) {
+    options(AMR_survey = FALSE)
+    console_width <- options()$width - 1
+    url <- "https://www.surveymonkey.com/r/AMR_for_R"
+    txt <- paste0("Thanks for using the AMR package! ",
+                 "As researchers, we are interested in how and why you use this package and if there are things you're missing from it. ",
+                 "Please fill in our 2-minute survey at: ", url, ". ",
+                 "This message can be turned off with: options(AMR_survey = FALSE)")
+
+    # make it honour new lines bases on console width:
+    txt <- unlist(strsplit(txt, " "))
+    txt_new <- ""
+    total_chars <- 0
+    for (i in 1:length(txt)) {
+      total_chars <- total_chars + nchar(txt[i]) + 1
+      if (total_chars > console_width) {
+        txt_new <- paste0(txt_new, "\n")
+        total_chars <- 0
+      }
+      txt_new <- paste0(txt_new, txt[i], " ")
+    }
+    # packageStartupMessage(txt_new)
+  }
+}
+
 #' @importFrom data.table as.data.table setkey
 make_DT <- function() {
   microorganismsDT <- as.data.table(AMR::microorganisms)
@@ -253,9 +280,10 @@ make_trans_tbl <- function() {
     B_GRDNR = "B_GRLLA", B_SGMNS = "B_SNGMNS", B_TCLLS = "B_THBCL",
     F_CCCCS = "F_CRYPT",
     # renamings of old genus + species
-    F_CANDD_GLB = "F_CANDD_GLA", F_CANDD_KRU = "F_ISSTC_ORI",
-    F_CANDD_GUI = "F_MYRZY_GUI",
-    F_CANDD_LUS = "F_CLVSP_LUS", B_STRPT_TUS = "B_STRPT",
+    # putting full names here will throw notes with new taxonomic names
+    F_CANDD_GLB = "F_CANDD_GLA", F_CANDD_KRU = "Candida krusei",
+    F_CANDD_GUI = "Candida guilliermondii", F_HNSNL_ANO = "Hansenula anomala",
+    F_CANDD_LUS = "Candida lusitaniae", B_STRPT_TUS = "B_STRPT",
     B_PRVTL_OLA = "B_PRVTL_OULO", B_FSBCT_RUM = "B_FSBCT",
     B_CRYNB_EYI = "B_CRYNB_FRE", B_OLGLL_LIS = "B_OLGLL_URE")
 }

_pkgdown.yml

@@ -19,152 +19,160 @@
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
-title: 'AMR (for R)'
-url: 'https://msberends.gitlab.io/AMR'
+title: "AMR (for R)"
+url: "https://msberends.gitlab.io/AMR"
+
 development:
-  mode: release # improves indexing by search engines
+  mode: "release" # improves indexing by search engines
+  version_tooltip: "Latest development version"
+
 news:
   one_page: true
 
 navbar:
-  title: 'AMR (for R)'
+  title: "AMR (for R)"
   left:
-    - text: 'Home'
-      icon: 'fa-home'
-      href: 'index.html'
-    - text: 'How to'
-      icon: 'fa-question-circle'
+    - text: "Home"
+      icon: "fa-home"
+      href: "index.html"
+    - text: "How to"
+      icon: "fa-question-circle"
       menu:
-      - text: 'Conduct AMR analysis'
-        icon: 'fa-directions'
-        href: 'articles/AMR.html'
-      - text: 'Predict antimicrobial resistance'
-        icon: 'fa-dice'
-        href: 'articles/resistance_predict.html'
-      - text: 'Determine multi-drug resistance (MDR)'
-        icon: 'fa-skull-crossbones'
-        href: 'articles/MDR.html'
-      - text: 'Work with WHONET data'
-        icon: 'fa-globe-americas'
-        href: 'articles/WHONET.html'
-      - text: 'Import data from SPSS/SAS/Stata'
-        icon: 'fa-file-upload'
-        href: 'articles/SPSS.html'
-      - text: 'Apply EUCAST rules'
-        icon: 'fa-exchange-alt'
-        href: 'articles/EUCAST.html'
-      - text: 'Get properties of a microorganism'
-        icon: 'fa-bug'
-        href: 'reference/mo_property.html' # reference instead of article
-      - text: 'Get properties of an antibiotic'
-        icon: 'fa-capsules'
-        href: 'reference/ab_property.html' # reference instead of article
-      - text: 'Create frequency tables'
-        icon: 'fa-sort-amount-down'
-        href: 'articles/freq.html'
-      - text: 'Use the G-test'
-        icon: 'fa-clipboard-check'
-        href: 'reference/g.test.html' # reference instead of article
-      - text: 'Other: benchmarks'
-        icon: 'fa-shipping-fast'
-        href: 'articles/benchmarks.html'
-    - text: 'Manual'
-      icon: 'fa-book-open'
-      href: 'reference/'
-    - text: 'Authors'
-      icon: 'fa-users'
-      href: 'authors.html'
-    - text: 'Changelog'
-      icon: 'far fa-newspaper'
-      href: 'news/'
+      - text: "Conduct AMR analysis"
+        icon: "fa-directions"
+        href: "articles/AMR.html"
+      - text: "Predict antimicrobial resistance"
+        icon: "fa-dice"
+        href: "articles/resistance_predict.html"
+      - text: "Determine multi-drug resistance (MDR)"
+        icon: "fa-skull-crossbones"
+        href: "articles/MDR.html"
+      - text: "Work with WHONET data"
+        icon: "fa-globe-americas"
+        href: "articles/WHONET.html"
+      - text: "Import data from SPSS/SAS/Stata"
+        icon: "fa-file-upload"
+        href: "articles/SPSS.html"
+      - text: "Apply EUCAST rules"
+        icon: "fa-exchange-alt"
+        href: "articles/EUCAST.html"
+      - text: "Get properties of a microorganism"
+        icon: "fa-bug"
+        href: "reference/mo_property.html" # reference instead of article
+      - text: "Get properties of an antibiotic"
+        icon: "fa-capsules"
+        href: "reference/ab_property.html" # reference instead of article
+      - text: "Create frequency tables"
+        icon: "fa-sort-amount-down"
+        href: "articles/freq.html"
+#       - text: "Use the G-test"
+#         icon: "fa-clipboard-check"
+#         href: "reference/g.test.html" # reference instead of article
+      - text: "Other: benchmarks"
+        icon: "fa-shipping-fast"
+        href: "articles/benchmarks.html"
+    - text: "Manual"
+      icon: "fa-book-open"
+      href: "reference/"
+    - text: "Authors"
+      icon: "fa-users"
+      href: "authors.html"
+    - text: "Changelog"
+      icon: "far fa-newspaper"
+      href: "news/"
   right:
-    - text: 'Source Code'
-      icon: 'fab fa-gitlab'
-      href: 'https://gitlab.com/msberends/AMR'
-    - text: 'Licence'
-      icon: 'fa-book'
-      href: 'LICENSE-text.html'
+    - text: "Source Code"
+      icon: "fab fa-gitlab"
+      href: "https://gitlab.com/msberends/AMR"
+    - text: "Licence"
+      icon: "fa-book"
+      href: "LICENSE-text.html"
 
 reference:
-  - title: 'Background information'
+  - title: "Background information"
     desc: >
       Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
       for more information about how to work with functions in this package.
     contents:
-    - '`AMR`'
-    - '`catalogue_of_life`'
-    - '`catalogue_of_life_version`'
-    - '`WHOCC`'
-  - title: 'Cleaning your data'
+    - "`AMR`"
+    - "`catalogue_of_life`"
+    - "`catalogue_of_life_version`"
+    - "`WHOCC`"
+  - title: "Cleaning your data"
     desc: >
       Functions for cleaning and optimising your data, to be able to add
       variables later on (like taxonomic properties) or to fix and extend
       antibiotic interpretations by applying [EUCAST rules](http://www.eucast.org/expert_rules_and_intrinsic_resistance/).
     contents:
     - starts_with("as.")
-    - '`mo_source`'
-    - '`eucast_rules`'
-    - '`rsi_translation`'
-    - '`guess_ab_col`'
-    - '`read.4D`'
-  - title: 'Adding variables to your data'
+    - "`mo_source`"
+    - "`eucast_rules`"
+    - "`rsi_translation`"
+    - "`guess_ab_col`"
+    - "`read.4D`"
+  - title: "Adding variables to your data"
     desc: >
       Functions to add new data to existing data, like the determination
       of first isolates, multi-drug resistant microorganisms (MDRO), getting
       properties of microorganisms or antibiotics and determining the age of
       patients or divide ages into age groups.
     contents:
-    - '`first_isolate`'
-    - '`mdro`'
-    - '`key_antibiotics`'
-    - '`mo_property`'
-    - '`ab_property`'
-    - '`age`'
-    - '`age_groups`'
-    - '`p.symbol`'
-    - '`join`'
-    - '`atc_online_property`'
-  - title: 'Analysing your data'
+    - "`first_isolate`"
+    - "`mdro`"
+    - "`key_antibiotics`"
+    - "`mo_property`"
+    - "`ab_property`"
+    - "`age`"
+    - "`age_groups`"
+    - "`p.symbol`"
+    - "`join`"
+    - "`atc_online_property`"
+  - title: "Analysing your data"
     desc: >
       Functions for conducting AMR analysis, like counting isolates, calculating
       resistance or susceptibility, creating frequency tables or make plots.
     contents:
-    - '`availability`'
-    - '`count`'
-    - '`portion`'
-    - '`filter_ab_class`'
-    - '`freq`'
-    - '`g.test`'
-    - '`ggplot_rsi`'
-    - '`kurtosis`'
-    - '`resistance_predict`'
-    - '`skewness`'
-  - title: 'Included data sets'
+    - "`availability`"
+    - "`count`"
+    - "`portion`"
+    - "`filter_ab_class`"
+    - "`freq`"
+    - "`g.test`"
+    - "`ggplot_rsi`"
+    - "`kurtosis`"
+    - "`resistance_predict`"
+    - "`skewness`"
+  - title: "Included data sets"
     desc: >
       References for microorganisms and antibiotics, and even a
       genuine data set with isolates from septic patients.
     contents:
-    - '`antibiotics`'
-    - '`microorganisms`'
-    - '`septic_patients`'
-    - '`WHONET`'
-    - '`microorganisms.codes`'
-    - '`microorganisms.old`'
+    - "`antibiotics`"
+    - "`microorganisms`"
+    - "`septic_patients`"
+    - "`WHONET`"
+    - "`microorganisms.codes`"
+    - "`microorganisms.old`"
   - title: Other functions
     desc: >
       These functions are mostly for internal use, but some of
       them may also be suitable for your analysis. Especially the
       'like' function can be useful: `if (x %like% y) {...}`.
     contents:
-    - '`get_locale`'
-    - '`like`'
-  - title: Deprecated functions
+    - "`get_locale`"
+    - "`like`"
+  - title: Extended functions
+    desc: >
+      These functions are extensions of functions in other packages.
+    contents:
+    - "`extended-functions`"
+  - title:  functions
     desc: >
       These functions are deprecated, meaning that they still
       work but show a warning with every use and will be removed
       in a future version.
     contents:
-    - '`AMR-deprecated`'
+    - "`AMR-deprecated`"
 
 authors:
   Matthijs S. Berends:
@@ -179,11 +187,11 @@ authors:
     href: https://www.rug.nl/staff/b.sinha/
 
 template:
-  assets: pkgdown/logos # use logos in this folder
+  assets: "pkgdown/logos" # use logos in this folder
   params:
     noindex: false
-    bootswatch: flatly
+    bootswatch: "flatly"
     docsearch:
       # using algolia.com
-      api_key: 'f737050abfd4d726c63938e18f8c496e'
-      index_name: 'amr'
+      api_key: "f737050abfd4d726c63938e18f8c496e"
+      index_name: "amr"

data-raw/eucast_rules.tsv

@@ -59,12 +59,12 @@ genus_species	is	Moraxella catarrhalis	ERY	S	AZM, CLR, RXT	S	Moraxella catarrhal
 genus_species	is	Moraxella catarrhalis	ERY	I	AZM, CLR, RXT	I	Moraxella catarrhalis	Breakpoints
 genus_species	is	Moraxella catarrhalis	ERY	R	AZM, CLR, RXT	R	Moraxella catarrhalis	Breakpoints
 genus_species	is	Moraxella catarrhalis	TCY	S	DOX, MNO	S	Moraxella catarrhalis	Breakpoints
-genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	S	AMP, AMX, PIP, TZP, TIC	S	Anaerobic Gram positives	Breakpoints
-genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	I	AMP, AMX, PIP, TZP, TIC	I	Anaerobic Gram positives	Breakpoints
-genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	R	AMP, AMX, PIP, TZP, TIC	R	Anaerobic Gram positives	Breakpoints
-genus	one_of	Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella	PEN	S	AMP, AMX, PIP, TZP, TIC	S	Anaerobic Gram negatives	Breakpoints
-genus	one_of	Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella	PEN	I	AMP, AMX, PIP, TZP, TIC	I	Anaerobic Gram negatives	Breakpoints
-genus	one_of	Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella	PEN	R	AMP, AMX, PIP, TZP, TIC	R	Anaerobic Gram negatives	Breakpoints
+genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	S	AMP, AMX, PIP, TZP, TIC	S	Anaerobic Gram-positives	Breakpoints
+genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	I	AMP, AMX, PIP, TZP, TIC	I	Anaerobic Gram-positives	Breakpoints
+genus	one_of	Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium	PEN	R	AMP, AMX, PIP, TZP, TIC	R	Anaerobic Gram-positives	Breakpoints
+genus	one_of	Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella	PEN	S	AMP, AMX, PIP, TZP, TIC	S	Anaerobic Gram-negatives	Breakpoints
+genus	one_of	Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella	PEN	I	AMP, AMX, PIP, TZP, TIC	I	Anaerobic Gram-negatives	Breakpoints
+genus	one_of	Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella	PEN	R	AMP, AMX, PIP, TZP, TIC	R	Anaerobic Gram-negatives	Breakpoints
 genus_species	is	Pasteurella multocida	PEN	S	AMP, AMX	S	Pasteurella multocida	Breakpoints
 genus_species	is	Pasteurella multocida	PEN	I	AMP, AMX	I	Pasteurella multocida	Breakpoints
 genus_species	is	Pasteurella multocida	PEN	R	AMP, AMX	R	Pasteurella multocida	Breakpoints
@@ -135,7 +135,7 @@ genus	is	Neisseria			TMP	R	Table 03: Intrinsic resistance in other Gram-negative
 genus_species	is	Campylobacter fetus			FUS, streptogramins, TMP, NAL	R	Table 03: Intrinsic resistance in other Gram-negative bacteria	Expert Rules
 genus_species	is	Campylobacter jejuni			FUS, streptogramins, TMP	R	Table 03: Intrinsic resistance in other Gram-negative bacteria	Expert Rules
 genus_species	is	Campylobacter coli			FUS, streptogramins, TMP	R	Table 03: Intrinsic resistance in other Gram-negative bacteria	Expert Rules
-gramstain	is	Gram positive			ATM, polymyxins, NAL	R	Table 04: Intrinsic resistance in Gram-positive bacteria	Expert Rules
+gramstain	is	Gram-positive			ATM, polymyxins, NAL	R	Table 04: Intrinsic resistance in Gram-positive bacteria	Expert Rules
 genus_species	is	Staphylococcus saprophyticus			FUS, CAZ, FOS, NOV	R	Table 04: Intrinsic resistance in Gram-positive bacteria	Expert Rules
 genus_species	is	Staphylococcus cohnii			CAZ, NOV	R	Table 04: Intrinsic resistance in Gram-positive bacteria	Expert Rules
 genus_species	is	Staphylococcus xylosus			CAZ, NOV	R	Table 04: Intrinsic resistance in Gram-positive bacteria	Expert Rules
@@ -165,7 +165,7 @@ family	is	Enterobacteriaceae	TIC, PIP	R, S	PIP	R	Table 09: Interpretive rules fo
 genus	is	.*	ERY	S	AZM, CLR	S	Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins	Expert Rules
 genus	is	.*	ERY	I	AZM, CLR	I	Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins	Expert Rules
 genus	is	.*	ERY	R	AZM, CLR	R	Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins	Expert Rules
-genus	is	Staphylococcus	TOB	R	KAN, amik	R	Table 12: Interpretive rules for aminoglycosides	Expert Rules
+genus	is	Staphylococcus	TOB	R	KAN, AMK	R	Table 12: Interpretive rules for aminoglycosides	Expert Rules
 genus	is	Staphylococcus	GEN	R	aminoglycosides	R	Table 12: Interpretive rules for aminoglycosides	Expert Rules
 family	is	Enterobacteriaceae	GEN, TOB	I, S	GEN	R	Table 12: Interpretive rules for aminoglycosides	Expert Rules
 family	is	Enterobacteriaceae	GEN, TOB	R, I	TOB	R	Table 12: Interpretive rules for aminoglycosides	Expert Rules

data-raw/internals.R

@@ -5,8 +5,8 @@
 # "minopenicillins", "ureidopenicillins", "fluoroquinolones", "all_betalactams",
 # and all separate EARS-Net letter codes like "AMC". They can be separated by comma: "AMC, fluoroquinolones".
 # The mo_property can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
-# This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in:
-# LiPuma JJ, 2015 (PMID 16217180).
+# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in:
+# LiPuma JJ, Curr Opin Pulm Med. 2005 Nov;11(6):528-33. (PMID 16217180).
 eucast_rules_file <- dplyr::arrange(
   .data = utils::read.delim(file = "data-raw/eucast_rules.tsv",
                             sep = "\t",
@@ -18,7 +18,7 @@ eucast_rules_file <- dplyr::arrange(
   reference.rule)
 
 # Translations -----
-translations_file <- utils::read.table(file = "data-raw/translations.tsv",
+translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
                                        sep = "\t",
                                        stringsAsFactors = FALSE,
                                        header = TRUE,
@@ -27,7 +27,9 @@ translations_file <- utils::read.table(file = "data-raw/translations.tsv",
                                        strip.white = TRUE,
                                        encoding = "UTF-8",
                                        fileEncoding = "UTF-8",
-                                       na.strings = c(NA, "", NULL))
+                                       na.strings = c(NA, "", NULL),
+                                       allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
+                                       quote = "")
 
 # Export to package as internal data ----
 usethis::use_data(eucast_rules_file, translations_file,

data-raw/reproduction_of_antibiotics.R

@@ -289,6 +289,9 @@ antibiotics <- filter(antibiotics, ab != "MOX")
 antibiotics <- filter(antibiotics, ab != "RFP")
 antibiotics[which(antibiotics$ab == "RFP1"), "ab"] <- "RFP"
 antibiotics[which(antibiotics$ab == "RFP"), "abbreviations"][[1]] <- list(c("rifp"))
+# PME and PVM1 (the J0 one) both mean 'Pivmecillinam', so:
+antibiotics <- filter(antibiotics, ab != "PME")
+antibiotics[which(antibiotics$ab == "PVM1"), "ab"] <- "PME"
 # ESBL E-test codes:
 antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]] <- list(c("xtzl"))
 antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "xtz", "cefta"))

data-raw/reproduction_of_microorganisms.R

@@ -318,13 +318,13 @@ MOs <- MOs %>%
                stringsAsFactors = FALSE),
     data.frame(mo = "B_GRAMN",
                col_id = NA_integer_,
-               fullname = "(unknown Gram negatives)",
+               fullname = "(unknown Gram-negatives)",
                kingdom = "Bacteria",
                phylum = "(unknown phylum)",
                class = "(unknown class)",
                order = "(unknown order)",
                family = "(unknown family)",
-               genus = "(unknown Gram negatives)",
+               genus = "(unknown Gram-negatives)",
                species = "(unknown species)",
                subspecies = "(unknown subspecies)",
                rank = "species",
@@ -334,13 +334,13 @@ MOs <- MOs %>%
                stringsAsFactors = FALSE),
     data.frame(mo = "B_GRAMP",
                col_id = NA_integer_,
-               fullname = "(unknown Gram positives)",
+               fullname = "(unknown Gram-positives)",
                kingdom = "Bacteria",
                phylum = "(unknown phylum)",
                class = "(unknown class)",
                order = "(unknown order)",
                family = "(unknown family)",
-               genus = "(unknown Gram positives)",
+               genus = "(unknown Gram-positives)",
                species = "(unknown species)",
                subspecies = "(unknown subspecies)",
                rank = "species",
@@ -444,7 +444,43 @@ MOs <- MOs %>%
              fullname = "Beta-haemolytic Streptococcus",
              ref = NA_character_,
              species_id = "",
-             source = "manually added")
+             source = "manually added"),
+    # Trichomonas vaginalis is missing, same order as Dientamoeba
+    MOs %>%
+      filter(fullname == "Dientamoeba") %>%
+      mutate(mo = gsub("DNTMB", "THMNS", mo),
+             col_id = NA,
+             fullname = "Trichomonas",
+             family = "Trichomonadidae",
+             genus = "Trichomonas",
+             source = "manually added",
+             ref = "Donne, 1836",
+             species_id = ""),
+    MOs %>%
+      filter(fullname == "Dientamoeba fragilis") %>%
+      mutate(mo = gsub("DNTMB", "THMNS", mo),
+             mo = gsub("FRA", "VAG", mo),
+             col_id = NA,
+             fullname = "Trichomonas vaginalis",
+             family = "Trichomonadidae",
+             genus = "Trichomonas",
+             species = "vaginalis",
+             source = "manually added",
+             ref = "Donne, 1836",
+             species_id = ""),
+    MOs %>% # add family as such too
+      filter(fullname == "Monocercomonadidae") %>%
+      mutate(mo = gsub("MNCRCMND", "TRCHMNDD", mo),
+             col_id = NA,
+             fullname = "Trichomonadidae",
+             family = "Trichomonadidae",
+             rank = "family",
+             genus = "",
+             species = "",
+             source = "manually added",
+             ref = "",
+             species_id = ""),
+
   )
 
 
@@ -457,7 +493,7 @@ MOs <- MOs %>%
   mutate(prevalence = case_when(
     class == "Gammaproteobacteria"
     | genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
-    | mo == "UNKNOWN"
+    | mo %in% c("UNKNOWN", "B_GRAMN", "B_GRAMP")
     ~ 1,
     phylum %in% c("Proteobacteria",
                   "Firmicutes",
@@ -485,17 +521,25 @@ MOs <- MOs %>%
     TRUE ~ 3
   ))
 
-# save it
-MOs <- as.data.frame(MOs %>% arrange(fullname), stringsAsFactors = FALSE)
+# arrange
+MOs <- MOs %>% arrange(fullname)
+MOs.old <- MOs.old %>% arrange(fullname)
+
+# transform
+MOs <- as.data.frame(MOs, stringsAsFactors = FALSE)
 MOs.old <- as.data.frame(MOs.old, stringsAsFactors = FALSE)
 class(MOs$mo) <- "mo"
+MOs$col_id <- as.integer(MOs$col_id)
+MOs.old$col_id <- as.integer(MOs.old$col_id)
+MOs.old$col_id_new <- as.integer(MOs.old$col_id_new)
 
+# save
 saveRDS(MOs, "microorganisms.rds")
 saveRDS(MOs.old, "microorganisms.old.rds")
 
-# on the server:
-usethis::use_data(microorganisms, overwrite = TRUE)
-usethis::use_data(microorganisms.old, overwrite = TRUE)
+# on the server, do:
+usethis::use_data(microorganisms, overwrite = TRUE, version = 2)
+usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2)
 rm(microorganisms)
 rm(microorganisms.old)
 # and update the year in R/data.R

data-raw/translations.tsv

@@ -2,8 +2,8 @@ lang	pattern	replacement	fixed	ignore.case
 de	Coagulase-negative Staphylococcus	Koagulase-negative Staphylococcus	FALSE	FALSE
 de	Coagulase-positive Staphylococcus	Koagulase-positive Staphylococcus	FALSE	FALSE
 de	Beta-haemolytic Streptococcus	Beta-hämolytischer Streptococcus	FALSE	FALSE
-de	unknown Gram negatives	unbekannte Gramnegativen	FALSE	FALSE
-de	unknown Gram positives	unbekannte Grampositiven	FALSE	FALSE
+de	unknown Gram-negatives	unbekannte Gramnegativen	FALSE	FALSE
+de	unknown Gram-positives	unbekannte Grampositiven	FALSE	FALSE
 de	unknown name	unbekannte Name	FALSE	FALSE
 de	unknown kingdom	unbekanntes Reich	FALSE	FALSE
 de	unknown phylum	unbekannter Stamm	FALSE	FALSE
@@ -16,8 +16,8 @@ de	unknown subspecies	unbekannte Unterart	FALSE	FALSE
 de	unknown rank	unbekannter Rang	FALSE	FALSE
 de	(CoNS)	(KNS)	TRUE	FALSE
 de	(CoPS)	(KPS)	TRUE	FALSE
-de	Gram negative	Gramnegativ	FALSE	FALSE
-de	Gram positive	Grampositiv	FALSE	FALSE
+de	Gram-negative	Gramnegativ	FALSE	FALSE
+de	Gram-positive	Grampositiv	FALSE	FALSE
 de	Bacteria	Bakterien	FALSE	FALSE
 de	Fungi	Hefen/Pilze	FALSE	FALSE
 de	Protozoa	Protozoen	FALSE	FALSE
@@ -29,8 +29,8 @@ de	([([ ]*?)Group	\\1Gruppe	FALSE	FALSE
 nl	Coagulase-negative Staphylococcus	Coagulase-negatieve Staphylococcus	FALSE	FALSE
 nl	Coagulase-positive Staphylococcus	Coagulase-positieve Staphylococcus	FALSE	FALSE
 nl	Beta-haemolytic Streptococcus	Beta-hemolytische Streptococcus	FALSE	FALSE
-nl	unknown Gram negatives	onbekende Gram-negatieven	FALSE	FALSE
-nl	unknown Gram positives	onbekende Gram-positieven	FALSE	FALSE
+nl	unknown Gram-negatives	onbekende Gram-negatieven	FALSE	FALSE
+nl	unknown Gram-positives	onbekende Gram-positieven	FALSE	FALSE
 nl	unknown name	onbekende naam	FALSE	FALSE
 nl	unknown kingdom	onbekend koninkrijk	FALSE	FALSE
 nl	unknown phylum	onbekend fylum	FALSE	FALSE
@@ -43,8 +43,8 @@ nl	unknown subspecies	onbekende ondersoort	FALSE	FALSE
 nl	unknown rank	onbekende rang	FALSE	FALSE
 nl	(CoNS)	(CNS)	TRUE	FALSE
 nl	(CoPS)	(CPS)	TRUE	FALSE
-nl	Gram negative	Gram-negatief	FALSE	FALSE
-nl	Gram positive	Gram-positief	FALSE	FALSE
+nl	Gram-negative	Gram-negatief	FALSE	FALSE
+nl	Gram-positive	Gram-positief	FALSE	FALSE
 nl	Bacteria	Bacteriën	FALSE	FALSE
 nl	Fungi	Schimmels/gisten	FALSE	FALSE
 nl	Protozoa	protozoën	FALSE	FALSE
@@ -55,8 +55,8 @@ nl	([([ ]*?)Group	\\1Groep	FALSE	FALSE
 es	Coagulase-negative Staphylococcus	Staphylococcus coagulasa negativo	FALSE	FALSE
 es	Coagulase-positive Staphylococcus	Staphylococcus coagulasa positivo	FALSE	FALSE
 es	Beta-haemolytic Streptococcus	Streptococcus Beta-hemolítico	FALSE	FALSE
-es	unknown Gram negatives	Gram negativos desconocidos	FALSE	FALSE
-es	unknown Gram positives	Gram positivos desconocidos	FALSE	FALSE
+es	unknown Gram-negatives	Gram negativos desconocidos	FALSE	FALSE
+es	unknown Gram-positives	Gram positivos desconocidos	FALSE	FALSE
 es	unknown name	nombre desconocido	FALSE	FALSE
 es	unknown kingdom	reino desconocido	FALSE	FALSE
 es	unknown phylum	filo desconocido	FALSE	FALSE
@@ -69,8 +69,8 @@ es	unknown subspecies	subespecie desconocida	FALSE	FALSE
 es	unknown rank	rango desconocido	FALSE	FALSE
 es	(CoNS)	(SCN)	TRUE	FALSE
 es	(CoPS)	(SCP)	TRUE	FALSE
-es	Gram negative	Gram negativo	FALSE	FALSE
-es	Gram positive	Gram positivo	FALSE	FALSE
+es	Gram-negative	Gram negativo	FALSE	FALSE
+es	Gram-positive	Gram positivo	FALSE	FALSE
 es	Bacteria	Bacterias	FALSE	FALSE
 es	Fungi	Hongos	FALSE	FALSE
 es	Protozoa	Protozoarios	FALSE	FALSE
@@ -82,8 +82,8 @@ es	([([ ]*?)Group	\\1Grupo	FALSE	FALSE
 it	Coagulase-negative Staphylococcus	Staphylococcus negativo coagulasi	FALSE	FALSE
 it	Coagulase-positive Staphylococcus	Staphylococcus positivo coagulasi	FALSE	FALSE
 it	Beta-haemolytic Streptococcus	Streptococcus Beta-emolitico	FALSE	FALSE
-it	unknown Gram negatives	Gram negativi sconosciuti	FALSE	FALSE
-it	unknown Gram positives	Gram positivi sconosciuti	FALSE	FALSE
+it	unknown Gram-negatives	Gram negativi sconosciuti	FALSE	FALSE
+it	unknown Gram-positives	Gram positivi sconosciuti	FALSE	FALSE
 it	unknown name	nome sconosciuto	FALSE	FALSE
 it	unknown kingdom	regno sconosciuto	FALSE	FALSE
 it	unknown phylum	phylum sconosciuto	FALSE	FALSE
@@ -94,8 +94,8 @@ it	unknown genus	genere sconosciuto	FALSE	FALSE
 it	unknown species	specie sconosciute	FALSE	FALSE
 it	unknown subspecies	sottospecie sconosciute	FALSE	FALSE
 it	unknown rank	grado sconosciuto	FALSE	FALSE
-it	Gram negative	Gram negativo	FALSE	FALSE
-it	Gram positive	Gram positivo	FALSE	FALSE
+it	Gram-negative	Gram negativo	FALSE	FALSE
+it	Gram-positive	Gram positivo	FALSE	FALSE
 it	Bacteria	Batteri	FALSE	FALSE
 it	Fungi	Fungo	FALSE	FALSE
 it	Protozoa	Protozoi	FALSE	FALSE
@@ -107,8 +107,8 @@ it	([([ ]*?)Group	\\1Gruppo	FALSE	FALSE
 fr	Coagulase-negative Staphylococcus	Staphylococcus à coagulase négative	FALSE	FALSE
 fr	Coagulase-positive Staphylococcus	Staphylococcus à coagulase positif	FALSE	FALSE
 fr	Beta-haemolytic Streptococcus	Streptococcus Bêta-hémolytique	FALSE	FALSE
-fr	unknown Gram negatives	Gram négatifs inconnus	FALSE	FALSE
-fr	unknown Gram positives	Gram positifs inconnus	FALSE	FALSE
+fr	unknown Gram-negatives	Gram négatifs inconnus	FALSE	FALSE
+fr	unknown Gram-positives	Gram positifs inconnus	FALSE	FALSE
 fr	unknown name	nom inconnu	FALSE	FALSE
 fr	unknown kingdom	règme inconnu	FALSE	FALSE
 fr	unknown phylum	embranchement inconnu	FALSE	FALSE
@@ -119,8 +119,8 @@ fr	unknown genus	genre inconnu	FALSE	FALSE
 fr	unknown species	espèce inconnue	FALSE	FALSE
 fr	unknown subspecies	sous-espèce inconnue	FALSE	FALSE
 fr	unknown rank	rang inconnu	FALSE	FALSE
-fr	Gram negative	Gram négatif	FALSE	FALSE
-fr	Gram positive	Gram positif	FALSE	FALSE
+fr	Gram-negative	Gram négatif	FALSE	FALSE
+fr	Gram-positive	Gram positif	FALSE	FALSE
 fr	Bacteria	Bactéries	FALSE	FALSE
 fr	Fungi	Champignons	FALSE	FALSE
 fr	Protozoa	Protozoaires	FALSE	FALSE
@@ -131,8 +131,8 @@ fr	([([ ]*?)Group	\\1Groupe	FALSE	FALSE
 pt	Coagulase-negative Staphylococcus	Staphylococcus coagulase negativo	FALSE	FALSE
 pt	Coagulase-positive Staphylococcus	Staphylococcus coagulase positivo	FALSE	FALSE
 pt	Beta-haemolytic Streptococcus	Streptococcus Beta-hemolítico	FALSE	FALSE
-pt	unknown Gram negatives	Gram negativos desconhecidos	FALSE	FALSE
-pt	unknown Gram positives	Gram positivos desconhecidos	FALSE	FALSE
+pt	unknown Gram-negatives	Gram negativos desconhecidos	FALSE	FALSE
+pt	unknown Gram-positives	Gram positivos desconhecidos	FALSE	FALSE
 pt	unknown name	nome desconhecido	FALSE	FALSE
 pt	unknown kingdom	reino desconhecido	FALSE	FALSE
 pt	unknown phylum	filo desconhecido	FALSE	FALSE
@@ -143,8 +143,8 @@ pt	unknown genus	gênero desconhecido	FALSE	FALSE
 pt	unknown species	espécies desconhecida	FALSE	FALSE
 pt	unknown subspecies	subespécies desconhecida	FALSE	FALSE
 pt	unknown rank	classificação desconhecido	FALSE	FALSE
-pt	Gram negative	Gram negativo	FALSE	FALSE
-pt	Gram positive	Gram positivo	FALSE	FALSE
+pt	Gram-negative	Gram negativo	FALSE	FALSE
+pt	Gram-positive	Gram positivo	FALSE	FALSE
 pt	Bacteria	Bactérias	FALSE	FALSE
 pt	Fungi	Fungos	FALSE	FALSE
 pt	Protozoa	Protozoários	FALSE	FALSE
@@ -154,6 +154,8 @@ pt	vegetative	vegetativo	FALSE	FALSE
 pt	([([ ]*?)group	\\1grupo	FALSE	FALSE
 pt	([([ ]*?)Group	\\1Grupo	FALSE	FALSE
 
+de	clavulanic acid	Clavulansäure	FALSE	TRUE
+
 nl	4-aminosalicylic acid	4-aminosalicylzuur
 nl	Adefovir dipivoxil	Adefovir
 nl	Aldesulfone sodium	Aldesulfon
@@ -348,8 +350,10 @@ nl	Thiamphenicol	Thiamfenicol
 nl	Thioacetazone/isoniazid	Thioacetazon/isoniazide
 nl	Ticarcillin	Ticarcilline
 nl	Ticarcillin/beta-lactamase inhibitor	Ticarcilline/enzymremmer
+nl	Ticarcillin/clavulanic acid	Ticarcilline/clavulaanzuur
 nl	Tinidazole	Tinidazol
 nl	Tobramycin	Tobramycine
+nl	Trimethoprim/sulfamethoxazole	Trimethoprim/sulfamethoxazol
 nl	Troleandomycin	Troleandomycine
 nl	Trovafloxacin	Trovafloxacine
 nl	Vancomycin	Vancomycine

docs/LICENSE-text.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
       </span>
     </div>
 
@@ -163,13 +163,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/articles/EUCAST.html

@@ -40,7 +40,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -125,13 +125,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -199,7 +192,7 @@
       <h1>How to apply EUCAST rules</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">03 June 2019</h4>
+            <h4 class="date">22 June 2019</h4>
       
       
       <div class="hidden name"><code>EUCAST.Rmd</code></div>

docs/articles/MDR.html

@@ -40,7 +40,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -125,13 +125,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -199,7 +192,7 @@
       <h1>How to determine multi-drug resistance (MDR)</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">03 June 2019</h4>
+            <h4 class="date">22 June 2019</h4>
       
       
       <div class="hidden name"><code>MDR.Rmd</code></div>
@@ -242,19 +235,19 @@
 <p>The data set looks like this now:</p>
 <div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(my_TB_data)</a>
 <a class="sourceLine" id="cb3-2" title="2"><span class="co">#   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
-<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1          S         S            S          R            I            S</span></a>
-<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2          R         R            R          I            R            S</span></a>
-<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3          R         S            S          S            S            I</span></a>
-<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4          S         R            S          R            S            S</span></a>
-<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5          R         S            S          S            S            R</span></a>
-<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6          R         S            S          S            R            R</span></a>
+<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1          S         S            R          S            R            I</span></a>
+<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2          S         S            R          S            R            S</span></a>
+<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3          R         R            S          S            S            S</span></a>
+<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4          S         I            S          I            S            S</span></a>
+<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5          S         S            I          I            R            R</span></a>
+<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6          R         R            R          R            R            R</span></a>
 <a class="sourceLine" id="cb3-9" title="9"><span class="co">#   kanamycin</span></a>
 <a class="sourceLine" id="cb3-10" title="10"><span class="co"># 1         R</span></a>
-<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2         R</span></a>
-<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3         S</span></a>
-<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4         S</span></a>
+<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2         I</span></a>
+<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3         R</span></a>
+<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4         I</span></a>
 <a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5         R</span></a>
-<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6         S</span></a></code></pre></div>
+<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6         I</span></a></code></pre></div>
 <p>We can now add the interpretation of MDR-TB to our data set:</p>
 <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">my_TB_data<span class="op">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
 <a class="sourceLine" id="cb4-2" title="2"><span class="co"># </span><span class="al">NOTE</span><span class="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></a>
@@ -263,8 +256,7 @@
 <a class="sourceLine" id="cb4-5" title="5"><span class="co"># Version:   WHO/HTM/TB/2014.11</span></a>
 <a class="sourceLine" id="cb4-6" title="6"><span class="co"># Author:    WHO (World Health Organization)</span></a>
 <a class="sourceLine" id="cb4-7" title="7"><span class="co"># Source:    https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></a>
-<a class="sourceLine" id="cb4-8" title="8"><span class="co"># Warning: Reliability might be improved if these antimicrobial results would</span></a>
-<a class="sourceLine" id="cb4-9" title="9"><span class="co"># be available too: CAP (capreomycin), RIB (rifabutin), RFP (rifapentine)</span></a></code></pre></div>
+<a class="sourceLine" id="cb4-8" title="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Reliability might be improved if these antimicrobial results would be available too: CAP (capreomycin), RIB (rifabutin), RFP (rifapentine)</span></a></code></pre></div>
 <p>And review the result with a frequency table:</p>
 <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a></code></pre></div>
 <p><strong>Frequency table of <code>mdr</code> from <code>my_TB_data</code> (5,000 x 8)</strong></p>
@@ -285,32 +277,32 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistance</td>
-<td align="right">3,238</td>
-<td align="right">64.8%</td>
-<td align="right">3,238</td>
-<td align="right">64.8%</td>
+<td align="right">3,284</td>
+<td align="right">65.7%</td>
+<td align="right">3,284</td>
+<td align="right">65.7%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">662</td>
-<td align="right">13.2%</td>
-<td align="right">3,900</td>
-<td align="right">78.0%</td>
+<td align="right">675</td>
+<td align="right">13.5%</td>
+<td align="right">3,959</td>
+<td align="right">79.2%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multidrug resistance</td>
-<td align="right">613</td>
-<td align="right">12.3%</td>
-<td align="right">4,513</td>
-<td align="right">90.3%</td>
+<td align="right">570</td>
+<td align="right">11.4%</td>
+<td align="right">4,529</td>
+<td align="right">90.6%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistance</td>
-<td align="right">279</td>
-<td align="right">5.6%</td>
+<td align="right">263</td>
+<td align="right">5.3%</td>
 <td align="right">4,792</td>
 <td align="right">95.8%</td>
 </tr>

docs/articles/SPSS.html

@@ -40,7 +40,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -125,13 +125,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -199,7 +192,7 @@
       <h1>How to import data from SPSS / SAS / Stata</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">03 June 2019</h4>
+            <h4 class="date">22 June 2019</h4>
       
       
       <div class="hidden name"><code>SPSS.Rmd</code></div>
@@ -259,7 +252,7 @@
 <a class="sourceLine" id="cb1-8" title="8"></a>
 <a class="sourceLine" id="cb1-9" title="9"><span class="co"># the Gram stain is avaiable for all bacteria:</span></a>
 <a class="sourceLine" id="cb1-10" title="10"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
-<a class="sourceLine" id="cb1-11" title="11"><span class="co"># [1] "Gram negative"</span></a>
+<a class="sourceLine" id="cb1-11" title="11"><span class="co"># [1] "Gram-negative"</span></a>
 <a class="sourceLine" id="cb1-12" title="12"></a>
 <a class="sourceLine" id="cb1-13" title="13"><span class="co"># Klebsiella is intrinsic resistant to amoxicllin, according to EUCAST:</span></a>
 <a class="sourceLine" id="cb1-14" title="14">klebsiella_test &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(<span class="dt">mo =</span> <span class="st">"klebsiella"</span>, </a>

docs/articles/WHONET.html

@@ -40,7 +40,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -125,13 +125,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -199,7 +192,7 @@
       <h1>How to work with WHONET data</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">03 June 2019</h4>
+            <h4 class="date">22 June 2019</h4>
       
       
       <div class="hidden name"><code>WHONET.Rmd</code></div>
@@ -238,7 +231,7 @@
 <p>No errors or warnings, so all values are transformed succesfully. Let’s check it though, with a couple of frequency tables:</p>
 <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="co"># our newly created `mo` variable</span></a>
 <a class="sourceLine" id="cb4-2" title="2">data <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(mo, <span class="dt">nmax =</span> <span class="dv">10</span>)</a></code></pre></div>
-<p><strong>Frequency table of <code>mo</code> from a <code>data.frame</code> (500 x 54)</strong></p>
+<p><strong>Frequency table of <code>mo</code> from <code>data</code> (500 x 54)</strong></p>
 <p>Class: mo (character)<br>
 Length: 500 (of which NA: 0 = 0.00%)<br>
 Unique: 39</p>
@@ -342,7 +335,7 @@ Species: 38</p>
 <a class="sourceLine" id="cb5-2" title="2"><span class="co"># our transformed antibiotic columns</span></a>
 <a class="sourceLine" id="cb5-3" title="3"><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></a>
 <a class="sourceLine" id="cb5-4" title="4">data <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(AMC_ND2)</a></code></pre></div>
-<p><strong>Frequency table of <code>AMC_ND2</code> from a <code>data.frame</code> (500 x 54)</strong></p>
+<p><strong>Frequency table of <code>AMC_ND2</code> from <code>data</code> (500 x 54)</strong></p>
 <p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
 Length: 500 (of which NA: 19 = 3.80%)<br>
 Levels: 3: S &lt; I &lt; R<br>

docs/articles/ab_property.html

@@ -40,7 +40,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -125,13 +125,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -199,7 +192,7 @@
       <h1>How to get properties of an antibiotic</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">03 June 2019</h4>
+            <h4 class="date">22 June 2019</h4>
       
       
       <div class="hidden name"><code>ab_property.Rmd</code></div>

docs/articles/benchmarks.html

@@ -40,7 +40,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -125,13 +125,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -199,7 +192,7 @@
       <h1>Benchmarks</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">03 June 2019</h4>
+            <h4 class="date">22 June 2019</h4>
       
       
       <div class="hidden name"><code>benchmarks.Rmd</code></div>
@@ -225,13 +218,13 @@
 <a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
 <a class="sourceLine" id="cb2-10" title="10"><span class="co"># Unit: milliseconds</span></a>
 <a class="sourceLine" id="cb2-11" title="11"><span class="co">#                            expr  min   lq mean median   uq max neval</span></a>
-<a class="sourceLine" id="cb2-12" title="12"><span class="co">#                    as.mo("sau")  18 18 22.0   18.0 18.0  62    10</span></a>
-<a class="sourceLine" id="cb2-13" title="13"><span class="co">#                   as.mo("stau")  48 48 53.0   48.0 48.0  93    10</span></a>
-<a class="sourceLine" id="cb2-14" title="14"><span class="co">#                 as.mo("staaur")  17 18 22.0   18.0 18.0  62    10</span></a>
-<a class="sourceLine" id="cb2-15" title="15"><span class="co">#                 as.mo("STAAUR")  18 18 22.0   18.0 18.0  62    10</span></a>
-<a class="sourceLine" id="cb2-16" title="16"><span class="co">#              as.mo("S. aureus")  28 28 29.0   28.0 29.0  29    10</span></a>
-<a class="sourceLine" id="cb2-17" title="17"><span class="co">#             as.mo("S.  aureus")  28 28 57.0   51.0 73.0 130    10</span></a>
-<a class="sourceLine" id="cb2-18" title="18"><span class="co">#  as.mo("Staphylococcus aureus")   8  8  9.3    8.1  8.3  20    10</span></a></code></pre></div>
+<a class="sourceLine" id="cb2-12" title="12"><span class="co">#                    as.mo("sau") 18.0 18.0   22   18.0 18.0  63    10</span></a>
+<a class="sourceLine" id="cb2-13" title="13"><span class="co">#                   as.mo("stau") 66.0 66.0   71   66.0 66.0 110    10</span></a>
+<a class="sourceLine" id="cb2-14" title="14"><span class="co">#                 as.mo("staaur") 18.0 18.0   18   18.0 18.0  18    10</span></a>
+<a class="sourceLine" id="cb2-15" title="15"><span class="co">#                 as.mo("STAAUR") 18.0 18.0   18   18.0 18.0  20    10</span></a>
+<a class="sourceLine" id="cb2-16" title="16"><span class="co">#              as.mo("S. aureus") 53.0 53.0   70   53.0 55.0 180    10</span></a>
+<a class="sourceLine" id="cb2-17" title="17"><span class="co">#             as.mo("S.  aureus") 52.0 53.0   73   54.0 97.0 110    10</span></a>
+<a class="sourceLine" id="cb2-18" title="18"><span class="co">#  as.mo("Staphylococcus aureus")  8.2  8.2   17    8.3  8.4  53    10</span></a></code></pre></div>
 <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 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
 <p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Thermus islandicus</em> (<code>B_THERMS_ISL</code>), a bug probably never found before in humans:</p>
 <div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">T.islandicus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a>
@@ -243,12 +236,12 @@
 <a class="sourceLine" id="cb3-7" title="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
 <a class="sourceLine" id="cb3-8" title="8"><span class="co"># Unit: milliseconds</span></a>
 <a class="sourceLine" id="cb3-9" title="9"><span class="co">#                         expr min  lq mean median  uq max neval</span></a>
-<a class="sourceLine" id="cb3-10" title="10"><span class="co">#              as.mo("theisl") 470 470  500    510 520 530    10</span></a>
-<a class="sourceLine" id="cb3-11" title="11"><span class="co">#              as.mo("THEISL") 470 470  480    470 510 520    10</span></a>
-<a class="sourceLine" id="cb3-12" title="12"><span class="co">#       as.mo("T. islandicus")  74  75   84     75  77 120    10</span></a>
-<a class="sourceLine" id="cb3-13" title="13"><span class="co">#      as.mo("T.  islandicus")  74  74   93     74 120 120    10</span></a>
-<a class="sourceLine" id="cb3-14" title="14"><span class="co">#  as.mo("Thermus islandicus")  72  73   84     74  77 120    10</span></a></code></pre></div>
-<p>That takes 8.1 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
+<a class="sourceLine" id="cb3-10" title="10"><span class="co">#              as.mo("theisl") 400 400  430    430 450 450    10</span></a>
+<a class="sourceLine" id="cb3-11" title="11"><span class="co">#              as.mo("THEISL") 390 400  420    420 450 460    10</span></a>
+<a class="sourceLine" id="cb3-12" title="12"><span class="co">#       as.mo("T. islandicus") 210 210  260    240 270 430    10</span></a>
+<a class="sourceLine" id="cb3-13" title="13"><span class="co">#      as.mo("T.  islandicus") 210 210  250    260 260 270    10</span></a>
+<a class="sourceLine" id="cb3-14" title="14"><span class="co">#  as.mo("Thermus islandicus")  74  75   94     76 120 120    10</span></a></code></pre></div>
+<p>That takes 7 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
 <p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Thermus islandicus</em> (which is very uncommon):</p>
 <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a>
 <a class="sourceLine" id="cb4-2" title="2"></a>
@@ -294,8 +287,8 @@
 <a class="sourceLine" id="cb5-24" title="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
 <a class="sourceLine" id="cb5-25" title="25"><span class="co"># Unit: milliseconds</span></a>
 <a class="sourceLine" id="cb5-26" title="26"><span class="co">#            expr  min   lq mean median   uq  max neval</span></a>
-<a class="sourceLine" id="cb5-27" title="27"><span class="co">#  mo_fullname(x) 1120 1150 1210   1190 1220 1430    10</span></a></code></pre></div>
-<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.19 seconds (1194 ms). You only lose time on your unique input values.</p>
+<a class="sourceLine" id="cb5-27" title="27"><span class="co">#  mo_fullname(x) 1090 1130 1190   1170 1230 1320    10</span></a></code></pre></div>
+<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.17 seconds (1167 ms). You only lose time on your unique input values.</p>
 </div>
 <div id="precalculated-results" class="section level3">
 <h3 class="hasAnchor">
@@ -308,9 +301,9 @@
 <a class="sourceLine" id="cb6-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
 <a class="sourceLine" id="cb6-6" title="6"><span class="co"># Unit: milliseconds</span></a>
 <a class="sourceLine" id="cb6-7" title="7"><span class="co">#  expr   min    lq  mean median    uq    max neval</span></a>
-<a class="sourceLine" id="cb6-8" title="8"><span class="co">#     A 13.20 13.4 13.80  13.70 14.20 14.40    10</span></a>
-<a class="sourceLine" id="cb6-9" title="9"><span class="co">#     B 25.50 25.9 31.00  26.20 27.60 72.30    10</span></a>
-<a class="sourceLine" id="cb6-10" title="10"><span class="co">#     C  1.78  1.8  1.89   1.84  2.03  2.06    10</span></a></code></pre></div>
+<a class="sourceLine" id="cb6-8" title="8"><span class="co">#     A 13.00 13.20 13.70  13.60 14.10  14.70    10</span></a>
+<a class="sourceLine" id="cb6-9" title="9"><span class="co">#     B 50.40 50.90 57.80  51.80 52.80 104.00    10</span></a>
+<a class="sourceLine" id="cb6-10" title="10"><span class="co">#     C  1.72  1.77  1.86   1.83  1.98   2.02    10</span></a></code></pre></div>
 <p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0018 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="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
 <a class="sourceLine" id="cb7-2" title="2">                         <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
@@ -324,14 +317,14 @@
 <a class="sourceLine" id="cb7-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
 <a class="sourceLine" id="cb7-11" title="11"><span class="co"># Unit: milliseconds</span></a>
 <a class="sourceLine" id="cb7-12" title="12"><span class="co">#  expr   min    lq  mean median    uq   max neval</span></a>
-<a class="sourceLine" id="cb7-13" title="13"><span class="co">#     A 0.526 0.606 0.652  0.639 0.721 0.771    10</span></a>
-<a class="sourceLine" id="cb7-14" title="14"><span class="co">#     B 0.575 0.582 0.665  0.658 0.689 0.898    10</span></a>
-<a class="sourceLine" id="cb7-15" title="15"><span class="co">#     C 1.820 1.870 1.940  1.950 2.020 2.070    10</span></a>
-<a class="sourceLine" id="cb7-16" title="16"><span class="co">#     D 0.547 0.596 0.702  0.665 0.850 0.891    10</span></a>
-<a class="sourceLine" id="cb7-17" title="17"><span class="co">#     E 0.521 0.560 0.624  0.625 0.655 0.843    10</span></a>
-<a class="sourceLine" id="cb7-18" title="18"><span class="co">#     F 0.487 0.518 0.596  0.559 0.720 0.754    10</span></a>
-<a class="sourceLine" id="cb7-19" title="19"><span class="co">#     G 0.483 0.573 0.621  0.605 0.667 0.762    10</span></a>
-<a class="sourceLine" id="cb7-20" title="20"><span class="co">#     H 0.196 0.270 0.304  0.314 0.348 0.418    10</span></a></code></pre></div>
+<a class="sourceLine" id="cb7-13" title="13"><span class="co">#     A 0.591 0.635 0.719  0.681 0.808 0.968    10</span></a>
+<a class="sourceLine" id="cb7-14" title="14"><span class="co">#     B 0.575 0.643 0.702  0.688 0.738 0.893    10</span></a>
+<a class="sourceLine" id="cb7-15" title="15"><span class="co">#     C 1.550 1.660 1.780  1.730 1.920 2.170    10</span></a>
+<a class="sourceLine" id="cb7-16" title="16"><span class="co">#     D 0.594 0.685 0.725  0.732 0.760 0.928    10</span></a>
+<a class="sourceLine" id="cb7-17" title="17"><span class="co">#     E 0.584 0.614 0.667  0.650 0.730 0.782    10</span></a>
+<a class="sourceLine" id="cb7-18" title="18"><span class="co">#     F 0.473 0.479 0.617  0.629 0.712 0.810    10</span></a>
+<a class="sourceLine" id="cb7-19" title="19"><span class="co">#     G 0.495 0.526 0.576  0.559 0.602 0.756    10</span></a>
+<a class="sourceLine" id="cb7-20" title="20"><span class="co">#     H 0.489 0.519 0.565  0.575 0.607 0.647    10</span></a></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> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
 </div>
 <div id="results-in-other-languages" class="section level3">
@@ -358,13 +351,13 @@
 <a class="sourceLine" id="cb8-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
 <a class="sourceLine" id="cb8-19" title="19"><span class="co"># Unit: milliseconds</span></a>
 <a class="sourceLine" id="cb8-20" title="20"><span class="co">#  expr   min    lq  mean median    uq    max neval</span></a>
-<a class="sourceLine" id="cb8-21" title="21"><span class="co">#    en 18.45 18.62 18.93  18.81 19.03 20.02    10</span></a>
-<a class="sourceLine" id="cb8-22" title="22"><span class="co">#    de 21.13 21.19 21.67  21.26 21.37 25.28    10</span></a>
-<a class="sourceLine" id="cb8-23" title="23"><span class="co">#    nl 34.19 34.39 34.74  34.55 34.93 35.99    10</span></a>
-<a class="sourceLine" id="cb8-24" title="24"><span class="co">#    es 20.92 21.03 25.70  21.26 21.47 65.90    10</span></a>
-<a class="sourceLine" id="cb8-25" title="25"><span class="co">#    it 20.79 20.94 25.96  21.23 21.88 65.69    10</span></a>
-<a class="sourceLine" id="cb8-26" title="26"><span class="co">#    fr 20.97 21.04 21.30  21.27 21.44 21.86    10</span></a>
-<a class="sourceLine" id="cb8-27" title="27"><span class="co">#    pt 20.81 20.91 25.66  21.01 21.24 66.88    10</span></a></code></pre></div>
+<a class="sourceLine" id="cb8-21" title="21"><span class="co">#    en 43.75 43.82 44.07  43.93 44.28  44.90    10</span></a>
+<a class="sourceLine" id="cb8-22" title="22"><span class="co">#    de 45.96 46.09 47.68  46.20 46.65  59.40    10</span></a>
+<a class="sourceLine" id="cb8-23" title="23"><span class="co">#    nl 59.57 59.72 64.49  59.88 60.34 104.30    10</span></a>
+<a class="sourceLine" id="cb8-24" title="24"><span class="co">#    es 45.82 45.89 50.72  46.30 46.60  90.94    10</span></a>
+<a class="sourceLine" id="cb8-25" title="25"><span class="co">#    it 45.77 45.94 55.86  46.46 48.05  96.85    10</span></a>
+<a class="sourceLine" id="cb8-26" title="26"><span class="co">#    fr 45.67 45.99 55.17  46.39 46.78  92.03    10</span></a>
+<a class="sourceLine" id="cb8-27" title="27"><span class="co">#    pt 45.84 45.92 46.27  46.04 46.36  47.24    10</span></a></code></pre></div>
 <p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
 </div>
   </div>

docs/articles/freq.html

@@ -40,7 +40,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -125,13 +125,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -199,7 +192,7 @@
       <h1>How to create frequency tables</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">03 June 2019</h4>
+            <h4 class="date">22 June 2019</h4>
       
       
       <div class="hidden name"><code>freq.Rmd</code></div>
@@ -228,7 +221,7 @@
 <a class="sourceLine" id="cb1-9" title="9"></a>
 <a class="sourceLine" id="cb1-10" title="10"><span class="co"># Probably the fastest and easiest:</span></a>
 <a class="sourceLine" id="cb1-11" title="11">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)  </a></code></pre></div>
-<p><strong>Frequency table of <code>gender</code> from a <code>data.frame</code> (2,000 x 49)</strong></p>
+<p><strong>Frequency table of <code>gender</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
 <p>Class: character<br>
 Length: 2,000 (of which NA: 0 = 0.00%)<br>
 Unique: 2</p>
@@ -285,7 +278,7 @@ Longest: 1</p>
 <p>So now the <code>genus</code> and <code>species</code> variables are available. A frequency table of these combined variables can be created like this:</p>
 <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">my_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb5-2" title="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species, <span class="dt">nmax =</span> <span class="dv">15</span>)</a></code></pre></div>
-<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (2,000 x 64)</strong></p>
+<p><strong>Frequency table of <code>genus</code> and <code>species</code> from <code>my_patients</code> (2,000 x 64)</strong></p>
 <p>Columns: 2<br>
 Length: 2,000 (of which NA: 0 = 0.00%)<br>
 Unique: 95</p>
@@ -515,7 +508,7 @@ Outliers: 15 (unique count: 12)</p>
 <p><code>sort.count</code> is <code>TRUE</code> by default. Compare this default behaviour…</p>
 <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb7-2" title="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id)</a></code></pre></div>
-<p><strong>Frequency table of <code>hospital_id</code> from a <code>data.frame</code> (2,000 x 49)</strong></p>
+<p><strong>Frequency table of <code>hospital_id</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
 <p>Class: factor (numeric)<br>
 Length: 2,000 (of which NA: 0 = 0.00%)<br>
 Levels: 4: A, B, C, D<br>
@@ -567,7 +560,7 @@ Unique: 4</p>
 <p>… to this, where items are now sorted on factor levels:</p>
 <div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb8-2" title="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">sort.count =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
-<p><strong>Frequency table of <code>hospital_id</code> from a <code>data.frame</code> (2,000 x 49)</strong></p>
+<p><strong>Frequency table of <code>hospital_id</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
 <p>Class: factor (numeric)<br>
 Length: 2,000 (of which NA: 0 = 0.00%)<br>
 Levels: 4: A, B, C, D<br>
@@ -619,7 +612,7 @@ Unique: 4</p>
 <p>All classes will be printed into the header. Variables with the new <code>rsi</code> class of this AMR package are actually ordered factors and have three classes (look at <code>Class</code> in the header):</p>
 <div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb9-2" title="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(AMX, <span class="dt">header =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
-<p><strong>Frequency table of <code>AMX</code> from a <code>data.frame</code> (2,000 x 49)</strong></p>
+<p><strong>Frequency table of <code>AMX</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
 <p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
 Length: 2,000 (of which NA: 771 = 38.55%)<br>
 Levels: 3: S &lt; I &lt; R<br>
@@ -670,7 +663,7 @@ Group: Beta-lactams/penicillins<br>
 <p>Frequencies of dates will show the oldest and newest date in the data, and the amount of days between them:</p>
 <div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb10-2" title="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(date, <span class="dt">nmax =</span> <span class="dv">5</span>, <span class="dt">header =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
-<p><strong>Frequency table of <code>date</code> from a <code>data.frame</code> (2,000 x 49)</strong></p>
+<p><strong>Frequency table of <code>date</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
 <p>Class: Date (numeric)<br>
 Length: 2,000 (of which NA: 0 = 0.00%)<br>
 Unique: 1,140</p>
@@ -752,7 +745,7 @@ Median: 31 July 2009 (47.39%)</p>
 <p>With the <code>na.rm</code> parameter you can remove <code>NA</code> values from the frequency table (defaults to <code>TRUE</code>, but the number of <code>NA</code> values will always be shown into the header):</p>
 <div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb13-2" title="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(AMX, <span class="dt">na.rm =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
-<p><strong>Frequency table of <code>AMX</code> from a <code>data.frame</code> (2,000 x 49)</strong></p>
+<p><strong>Frequency table of <code>AMX</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
 <p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
 Length: 2,000 (of which NA: 771 = 38.55%)<br>
 Levels: 3: S &lt; I &lt; R<br>
@@ -812,7 +805,7 @@ Group: Beta-lactams/penicillins<br>
 <p>A frequency table shows row indices. To remove them, use <code>row.names = FALSE</code>:</p>
 <div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb14-2" title="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">row.names =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
-<p><strong>Frequency table of <code>hospital_id</code> from a <code>data.frame</code> (2,000 x 49)</strong></p>
+<p><strong>Frequency table of <code>hospital_id</code> from <code>septic_patients</code> (2,000 x 49)</strong></p>
 <p>Class: factor (numeric)<br>
 Length: 2,000 (of which NA: 0 = 0.00%)<br>
 Levels: 4: A, B, C, D<br>
@@ -864,7 +857,7 @@ Unique: 4</p>
 <p>The <code>markdown</code> parameter is <code>TRUE</code> at default in non-interactive sessions, like in reports created with R Markdown. This will always print all rows, unless <code>nmax</code> is set. Without markdown (like in regular R), a frequency table would print like:</p>
 <div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb15-2" title="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id, <span class="dt">markdown =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb15-3" title="3"><span class="co"># Frequency table of `hospital_id` from a data.frame (2,000 x 49) </span></a>
+<a class="sourceLine" id="cb15-3" title="3"><span class="co"># Frequency table of `hospital_id` from `septic_patients` (2,000 x 49) </span></a>
 <a class="sourceLine" id="cb15-4" title="4"><span class="co"># </span></a>
 <a class="sourceLine" id="cb15-5" title="5"><span class="co"># Class:   factor (numeric)</span></a>
 <a class="sourceLine" id="cb15-6" title="6"><span class="co"># Length:  2,000 (of which NA: 0 = 0.00%)</span></a>

docs/articles/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
       </span>
     </div>
 
@@ -163,13 +163,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -248,10 +241,8 @@
         <li><a href="MDR.html">How to determine multi-drug resistance (MDR)</a></li>
         <li><a href="SPSS.html">How to import data from SPSS / SAS / Stata</a></li>
         <li><a href="WHONET.html">How to work with WHONET data</a></li>
-        <li><a href="ab_property.html">How to get properties of an antibiotic</a></li>
         <li><a href="benchmarks.html">Benchmarks</a></li>
         <li><a href="freq.html">How to create frequency tables</a></li>
-        <li><a href="mo_property.html">How to get properties of a microorganism</a></li>
         <li><a href="resistance_predict.html">How to predict antimicrobial resistance</a></li>
       </ul>
     </div>

docs/articles/mo_property.html

@@ -40,7 +40,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
       </span>
     </div>
 
@@ -199,7 +199,7 @@
       <h1>How to get properties of a microorganism</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">03 June 2019</h4>
+            <h4 class="date">07 June 2019</h4>
       
       
       <div class="hidden name"><code>mo_property.Rmd</code></div>

docs/articles/resistance_predict.html

@@ -40,7 +40,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
       </span>
     </div>
 
@@ -125,13 +125,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -199,7 +192,7 @@
       <h1>How to predict antimicrobial resistance</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">03 June 2019</h4>
+            <h4 class="date">22 June 2019</h4>
       
       
       <div class="hidden name"><code>resistance_predict.Rmd</code></div>
@@ -309,7 +302,7 @@
 <a href="#choosing-the-right-model" class="anchor"></a>Choosing the right model</h3>
 <p>Resistance is not easily predicted; if we look at vancomycin resistance in Gram positives, the spread (i.e. standard error) is enormous:</p>
 <div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
-<a class="sourceLine" id="cb8-2" title="2"><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo) <span class="op">==</span><span class="st"> "Gram positive"</span>) <span class="op">%&gt;%</span></a>
+<a class="sourceLine" id="cb8-2" title="2"><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo, <span class="dt">language =</span> <span class="ot">NULL</span>) <span class="op">==</span><span class="st"> "Gram-positive"</span>) <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb8-3" title="3"><span class="st">  </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"VAN"</span>, <span class="dt">year_min =</span> <span class="dv">2010</span>, <span class="dt">info =</span> <span class="ot">FALSE</span>) <span class="op">%&gt;%</span><span class="st"> </span></a>
 <a class="sourceLine" id="cb8-4" title="4"><span class="st">  </span><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()</a>
 <a class="sourceLine" id="cb8-5" title="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a></code></pre></div>
@@ -354,7 +347,7 @@
 </table>
 <p>For the vancomycin resistance in Gram positive bacteria, a linear model might be more appropriate since no (left half of a) binomial distribution is to be expected based on the observed years:</p>
 <div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
-<a class="sourceLine" id="cb9-2" title="2"><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo) <span class="op">==</span><span class="st"> "Gram positive"</span>) <span class="op">%&gt;%</span></a>
+<a class="sourceLine" id="cb9-2" title="2"><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo, <span class="dt">language =</span> <span class="ot">NULL</span>) <span class="op">==</span><span class="st"> "Gram-positive"</span>) <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb9-3" title="3"><span class="st">  </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"VAN"</span>, <span class="dt">year_min =</span> <span class="dv">2010</span>, <span class="dt">info =</span> <span class="ot">FALSE</span>, <span class="dt">model =</span> <span class="st">"linear"</span>) <span class="op">%&gt;%</span><span class="st"> </span></a>
 <a class="sourceLine" id="cb9-4" title="4"><span class="st">  </span><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()</a>
 <a class="sourceLine" id="cb9-5" title="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a></code></pre></div>

docs/authors.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
       </span>
     </div>
 
@@ -163,13 +163,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/extra.css

@@ -202,13 +202,3 @@ table a:not(.btn):hover, .table a:not(.btn):hover {
   color: black;
   font-weight: bold;
 }
-
-#collapseDisqus {
-  padding: 2%;
-  border: 2px #2c3e50 dashed;
-  margin-top: 1%;
-}
-#btn_collapseDisqus {
-  white-space: normal;
-}
-

docs/extra.js

@@ -23,8 +23,6 @@
 
 // Add updated Font Awesome 5.8.2 library
 $('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.8.2/css/all.css">');
-// Add Disqus
-$('head').append('<script src="https://amr-for-r.disqus.com/embed.js" data-timestamp="' + new Date()  + '"></script>');
 
 // Email template for new GitLab issues
 //https://stackoverflow.com/a/33190494/4575331
@@ -32,6 +30,13 @@ $('head').append('<script src="https://amr-for-r.disqus.com/embed.js" data-times
 
 $( document ).ready(function() {
 
+  // add SurveyMonkey
+  $('body').append('<script>(function(t,e,s,o){var n,a,c;t.SMCX=t.SMCX||[],e.getElementById(o)||(n=e.getElementsByTagName(s),a=n[n.length-1],c=e.createElement(s),c.type="text/javascript",c.async=!0,c.id=o,c.src=["https:"===location.protocol?"https://":"http://","widget.surveymonkey.com/collect/website/js/tRaiETqnLgj758hTBazgd_2BrwaGaWbg59AiLjNGdPaaJiBHKqgXKIw46VauwBvZ67.js"].join(""),a.parentNode.insertBefore(c,a))})(window,document,"script","smcx-sdk");</script>');
+
+  // add link to survey at home sidebar
+  $('.template-home #sidebar .list-unstyled:first').append('<li><strong>Please fill in our survey at</strong> <br><a href="https://www.surveymonkey.com/r/AMR_for_R" target="_blank">https://www.surveymonkey.com/r/AMR_for_R</a></li>');
+
+
   // remove version label from header
   $(".version.label").remove();
 
@@ -56,18 +61,6 @@ $( document ).ready(function() {
     '</div>');
   }
 
-  // add Disqus to all pages
-  var disqus =
-    '<button id="btn_collapseDisqus" class="btn btn-primary" type="button" data-toggle="collapse" data-target="#collapseDisqus" aria-expanded="false" aria-controls="collapseDisqus">' +
-      '  Having a question? Or knowing something we don\'t? Click here to open comments.' +
-    '</button>' +
-    '<div class="collapse" id="collapseDisqus">' +
-      '<div id="disqus_thread"></div>' +
-    '</div>';
-
-  $(disqus).insertBefore('footer');
-  $('#disqus_thread footer').remove();
-
   // edit footer
   $('footer').html(
     '<div>' +

docs/index.html

@@ -42,7 +42,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
       </span>
     </div>
 
@@ -127,13 +127,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/news/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
       </span>
     </div>
 
@@ -163,13 +163,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -239,23 +232,104 @@
       
     </div>
 
-    <div id="amr-070" class="section level1">
+    <div id="amr-0709015" class="section level1">
 <h1 class="page-header">
-<a href="#amr-070" class="anchor"></a>AMR 0.7.0<small> Unreleased </small>
+<a href="#amr-0709015" class="anchor"></a>AMR 0.7.0.9015<small> Unreleased </small>
 </h1>
 <div id="new" class="section level4">
 <h4 class="hasAnchor">
 <a href="#new" class="anchor"></a>New</h4>
 <ul>
+<li>
+<p>Function <code><a href="../reference/portion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/portion.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
+<a class="sourceLine" id="cb1-2" title="2"><span class="st">  </span><span class="kw">select</span>(AMX, CIP) <span class="op">%&gt;%</span></a>
+<a class="sourceLine" id="cb1-3" title="3"><span class="st">  </span><span class="kw"><a href="../reference/portion.html">rsi_df</a></span>()</a>
+<a class="sourceLine" id="cb1-4" title="4"><span class="co">#      antibiotic  interpretation      value  isolates</span></a>
+<a class="sourceLine" id="cb1-5" title="5"><span class="co"># 1   Amoxicillin              SI  0.4442636       546</span></a>
+<a class="sourceLine" id="cb1-6" title="6"><span class="co"># 2   Amoxicillin               R  0.5557364       683</span></a>
+<a class="sourceLine" id="cb1-7" title="7"><span class="co"># 3 Ciprofloxacin              SI  0.8381831      1181</span></a>
+<a class="sourceLine" id="cb1-8" title="8"><span class="co"># 4 Ciprofloxacin               R  0.1618169       228</span></a></code></pre></div>
+</li>
+<li>
+<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date (that we could find). Supported are:</p>
+<ul>
+<li>AIEC (Adherent-Invasive <em>E. coli</em>)</li>
+<li>ATEC (Atypical Entero-pathogenic <em>E. coli</em>)</li>
+<li>DAEC (Diffusely Adhering <em>E. coli</em>)</li>
+<li>EAEC (Entero-Aggresive <em>E. coli</em>)</li>
+<li>EHEC (Entero-Haemorrhagic <em>E. coli</em>)</li>
+<li>EIEC (Entero-Invasive <em>E. coli</em>)</li>
+<li>EPEC (Entero-Pathogenic <em>E. coli</em>)</li>
+<li>ETEC (Entero-Toxigenic <em>E. coli</em>)</li>
+<li>NMEC (Neonatal Meningitis‐causing <em>E. coli</em>)</li>
+<li>STEC (Shiga-toxin producing <em>E. coli</em>)</li>
+<li>UPEC (Uropathogenic <em>E. coli</em>)</li>
+</ul>
+<p>All these lead to the microbial ID of <em>E. coli</em>:</p>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)</a>
+<a class="sourceLine" id="cb2-2" title="2"><span class="co"># B_ESCHR_COL</span></a>
+<a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)</a>
+<a class="sourceLine" id="cb2-4" title="4"><span class="co"># "Escherichia coli"</span></a>
+<a class="sourceLine" id="cb2-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)</a>
+<a class="sourceLine" id="cb2-6" title="6"><span class="co"># "Gram-negative"</span></a></code></pre></div>
+</li>
+<li>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</li>
+<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
+</ul>
+</div>
+<div id="changed" class="section level4">
+<h4 class="hasAnchor">
+<a href="#changed" class="anchor"></a>Changed</h4>
+<ul>
+<li>Column names of output <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/portion.html">portion_df()</a></code> are now lowercase</li>
+<li>Fixed bug in translation of microorganism names</li>
+<li>Fixed bug in determining taxonomic kingdoms</li>
+<li>Algorithm improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code> and <code><a href="../reference/as.mo.html">as.mo()</a></code> to understand even more severely misspelled input</li>
+<li>Function <code><a href="../reference/as.ab.html">as.ab()</a></code> now allows spaces for coercing antibiotics names</li>
+<li>Added <code>ggplot2</code> methods for automatically determining the scale type of classes <code>mo</code> and <code>ab</code>
+</li>
+<li>Added names of object in the header in frequency tables, even when using pipes</li>
+<li>Prevented <code>"bacteria"</code> from getting coerced by <code><a href="../reference/as.ab.html">as.ab()</a></code> because Bacterial is a brand name of trimethoprim (TMP)</li>
+<li>Fixed a bug where setting an antibiotic would not work for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>
+</li>
+<li>Fixed a EUCAST rule for Staphylococci, where amikacin resistance would not be inferred from tobramycin</li>
+<li>Removed <code>latest_annual_release</code> from the <code><a href="../reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> function</li>
+<li>Removed antibiotic code <code>PVM1</code> from the <code>antibiotics</code> data set as this was a duplicate of <code>PME</code>
+</li>
+<li>Fixed bug where not all old taxonomic names would be printed, when using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code>
+</li>
+<li>Manually added <em>Trichomonas vaginalis</em> from the kingdom of Protozoa, which is missing from the Catalogue of Life</li>
+<li>Small improvements to <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> and <code><a href="https://www.rdocumentation.org/packages/graphics/topics/barplot">barplot()</a></code> for MIC and RSI classes</li>
+<li>Allow Catalogue of Life IDs to be coerced by <code><a href="../reference/as.mo.html">as.mo()</a></code>
+</li>
+</ul>
+</div>
+<div id="other" class="section level4">
+<h4 class="hasAnchor">
+<a href="#other" class="anchor"></a>Other</h4>
+<ul>
+<li>Fixed a note thrown by CRAN tests</li>
+</ul>
+</div>
+</div>
+    <div id="amr-070" class="section level1">
+<h1 class="page-header">
+<a href="#amr-070" class="anchor"></a>AMR 0.7.0<small> 2019-06-03 </small>
+</h1>
+<div id="new-1" class="section level4">
+<h4 class="hasAnchor">
+<a href="#new-1" class="anchor"></a>New</h4>
+<ul>
 <li>Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><a href="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><a href="../reference/as.disk.html">as.disk()</a></code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
 <li>Function <code><a href="../reference/mo_property.html">mo_name()</a></code> as alias of <code><a href="../reference/mo_property.html">mo_fullname()</a></code>
 </li>
 <li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code><a href="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read this tutorial <a href="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li>
 </ul>
 </div>
-<div id="changed" class="section level4">
+<div id="changed-1" class="section level4">
 <h4 class="hasAnchor">
-<a href="#changed" class="anchor"></a>Changed</h4>
+<a href="#changed-1" class="anchor"></a>Changed</h4>
 <ul>
 <li>Fixed a critical bug in <code><a href="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li>
 <li>Fixedd a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
@@ -297,14 +371,14 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Tra
 <li>when all values are unique it now shows a message instead of a warning</li>
 <li>
 <p>support for boxplots:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb1-2" title="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb1-3" title="3"><span class="st">  </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a>
-<a class="sourceLine" id="cb1-4" title="4"><span class="co"># grouped boxplots:</span></a>
-<a class="sourceLine" id="cb1-5" title="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb1-6" title="6"><span class="st">  </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb1-7" title="7"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span></a>
-<a class="sourceLine" id="cb1-8" title="8"><span class="st">  </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
+<a class="sourceLine" id="cb3-2" title="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span><span class="st"> </span></a>
+<a class="sourceLine" id="cb3-3" title="3"><span class="st">  </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a>
+<a class="sourceLine" id="cb3-4" title="4"><span class="co"># grouped boxplots:</span></a>
+<a class="sourceLine" id="cb3-5" title="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
+<a class="sourceLine" id="cb3-6" title="6"><span class="st">  </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
+<a class="sourceLine" id="cb3-7" title="7"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span></a>
+<a class="sourceLine" id="cb3-8" title="8"><span class="st">  </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a></code></pre></div>
 </li>
 </ul>
 </li>
@@ -327,9 +401,9 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=EUC
 <li><p>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> where species would not be determined correctly</p></li>
 </ul>
 </div>
-<div id="other" class="section level4">
+<div id="other-1" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other" class="anchor"></a>Other</h4>
+<a href="#other-1" class="anchor"></a>Other</h4>
 <ul>
 <li>Support for R 3.6.0 and later by providing support for <a href="https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html">staged install</a>
 </li>
@@ -340,9 +414,9 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=EUC
 <h1 class="page-header">
 <a href="#amr-061" class="anchor"></a>AMR 0.6.1<small> 2019-03-29 </small>
 </h1>
-<div id="changed-1" class="section level4">
+<div id="changed-2" class="section level4">
 <h4 class="hasAnchor">
-<a href="#changed-1" class="anchor"></a>Changed</h4>
+<a href="#changed-2" class="anchor"></a>Changed</h4>
 <ul>
 <li>Fixed a critical bug when using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> with <code>verbose = TRUE</code>
 </li>
@@ -360,9 +434,9 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=EUC
 <li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
 <li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis, import data from WHONET or SPSS and many more.</li>
 </ul>
-<div id="new-1" class="section level4">
+<div id="new-2" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-1" class="anchor"></a>New</h4>
+<a href="#new-2" class="anchor"></a>New</h4>
 <ul>
 <li>
 <strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</li>
@@ -389,32 +463,32 @@ This data is updated annually - check the included version with the new function
 </li>
 <li>
 <p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
-<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
-<a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
-<a class="sourceLine" id="cb2-4" title="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
-<a class="sourceLine" id="cb2-5" title="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
-<a class="sourceLine" id="cb2-6" title="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
-<a class="sourceLine" id="cb2-7" title="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
-<a class="sourceLine" id="cb2-8" title="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
-<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
-<a class="sourceLine" id="cb2-10" title="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
-<a class="sourceLine" id="cb2-11" title="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
+<a class="sourceLine" id="cb4-2" title="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
+<a class="sourceLine" id="cb4-3" title="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
+<a class="sourceLine" id="cb4-4" title="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
+<a class="sourceLine" id="cb4-5" title="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
+<a class="sourceLine" id="cb4-6" title="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
+<a class="sourceLine" id="cb4-7" title="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
+<a class="sourceLine" id="cb4-8" title="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
+<a class="sourceLine" id="cb4-9" title="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
+<a class="sourceLine" id="cb4-10" title="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
+<a class="sourceLine" id="cb4-11" title="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
 <p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
-<a class="sourceLine" id="cb3-2" title="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
-<a class="sourceLine" id="cb3-3" title="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
-<a class="sourceLine" id="cb3-4" title="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
+<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
+<a class="sourceLine" id="cb5-2" title="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
+<a class="sourceLine" id="cb5-3" title="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
+<a class="sourceLine" id="cb5-4" title="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
 </li>
 <li>
 <p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
-<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">ab_property -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_property</a></span>()</a>
-<a class="sourceLine" id="cb4-2" title="2">ab_name -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_name</a></span>()</a>
-<a class="sourceLine" id="cb4-3" title="3">ab_official -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_official</a></span>()</a>
-<a class="sourceLine" id="cb4-4" title="4">ab_trivial_nl -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_trivial_nl</a></span>()</a>
-<a class="sourceLine" id="cb4-5" title="5">ab_certe -&gt;<span class="st"> </span><span class="kw">atc_certe</span>()</a>
-<a class="sourceLine" id="cb4-6" title="6">ab_umcg -&gt;<span class="st"> </span><span class="kw">atc_umcg</span>()</a>
-<a class="sourceLine" id="cb4-7" title="7">ab_tradenames -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_tradenames</a></span>()</a></code></pre></div>
+<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">ab_property -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_property</a></span>()</a>
+<a class="sourceLine" id="cb6-2" title="2">ab_name -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_name</a></span>()</a>
+<a class="sourceLine" id="cb6-3" title="3">ab_official -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_official</a></span>()</a>
+<a class="sourceLine" id="cb6-4" title="4">ab_trivial_nl -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_trivial_nl</a></span>()</a>
+<a class="sourceLine" id="cb6-5" title="5">ab_certe -&gt;<span class="st"> </span><span class="kw">atc_certe</span>()</a>
+<a class="sourceLine" id="cb6-6" title="6">ab_umcg -&gt;<span class="st"> </span><span class="kw">atc_umcg</span>()</a>
+<a class="sourceLine" id="cb6-7" title="7">ab_tradenames -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_tradenames</a></span>()</a></code></pre></div>
 These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li>
 <li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
 <li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
@@ -426,29 +500,29 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
 <li>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
 <li>
 <p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">x &lt;-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
-<a class="sourceLine" id="cb5-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a>
-<a class="sourceLine" id="cb5-3" title="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
+<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">x &lt;-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
+<a class="sourceLine" id="cb7-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a>
+<a class="sourceLine" id="cb7-3" title="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
 </li>
 <li>
 <p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
-<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
-<a class="sourceLine" id="cb6-2" title="2"><span class="co"># or</span></a>
-<a class="sourceLine" id="cb6-3" title="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
+<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
+<a class="sourceLine" id="cb8-2" title="2"><span class="co"># or</span></a>
+<a class="sourceLine" id="cb8-3" title="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
 <p>is equal to:</p>
-<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
-<a class="sourceLine" id="cb7-2" title="2"><span class="st">  </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%&gt;%</span></a>
-<a class="sourceLine" id="cb7-3" title="3"><span class="st">  </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%&gt;%</span></a>
-<a class="sourceLine" id="cb7-4" title="4"><span class="st">  </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
+<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
+<a class="sourceLine" id="cb9-2" title="2"><span class="st">  </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%&gt;%</span></a>
+<a class="sourceLine" id="cb9-3" title="3"><span class="st">  </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%&gt;%</span></a>
+<a class="sourceLine" id="cb9-4" title="4"><span class="st">  </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
 </li>
 <li>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code>
 </li>
 <li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
 </ul>
 </div>
-<div id="changed-2" class="section level4">
+<div id="changed-3" class="section level4">
 <h4 class="hasAnchor">
-<a href="#changed-2" class="anchor"></a>Changed</h4>
+<a href="#changed-3" class="anchor"></a>Changed</h4>
 <ul>
 <li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
 <ul>
@@ -468,33 +542,33 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
 <ul>
 <li>
 <p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
-<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a>
-<a class="sourceLine" id="cb8-2" title="2"></a>
-<a class="sourceLine" id="cb8-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</a>
-<a class="sourceLine" id="cb8-4" title="4"><span class="co">#&gt; [1] "Staphylococcus aureus"</span></a>
-<a class="sourceLine" id="cb8-5" title="5"></a>
-<a class="sourceLine" id="cb8-6" title="6"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)</a>
-<a class="sourceLine" id="cb8-7" title="7"><span class="co">#&gt; [1] "Staphylococcus kloosii"</span></a></code></pre></div>
+<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a>
+<a class="sourceLine" id="cb10-2" title="2"></a>
+<a class="sourceLine" id="cb10-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</a>
+<a class="sourceLine" id="cb10-4" title="4"><span class="co">#&gt; [1] "Staphylococcus aureus"</span></a>
+<a class="sourceLine" id="cb10-5" title="5"></a>
+<a class="sourceLine" id="cb10-6" title="6"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)</a>
+<a class="sourceLine" id="cb10-7" title="7"><span class="co">#&gt; [1] "Staphylococcus kloosii"</span></a></code></pre></div>
 </li>
 <li>
 <p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
-<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="co"># equal:</span></a>
-<a class="sourceLine" id="cb9-2" title="2"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">TRUE</span>)</a>
-<a class="sourceLine" id="cb9-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">2</span>)</a>
-<a class="sourceLine" id="cb9-4" title="4"></a>
-<a class="sourceLine" id="cb9-5" title="5"><span class="co"># also equal:</span></a>
-<a class="sourceLine" id="cb9-6" title="6"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb9-7" title="7"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">0</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="co"># equal:</span></a>
+<a class="sourceLine" id="cb11-2" title="2"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">TRUE</span>)</a>
+<a class="sourceLine" id="cb11-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">2</span>)</a>
+<a class="sourceLine" id="cb11-4" title="4"></a>
+<a class="sourceLine" id="cb11-5" title="5"><span class="co"># also equal:</span></a>
+<a class="sourceLine" id="cb11-6" title="6"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb11-7" title="7"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">0</span>)</a></code></pre></div>
 Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></code> could lead to very unreliable results.</li>
 <li>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em>
 </li>
 <li>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</li>
 <li>
 <p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
-<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</a>
-<a class="sourceLine" id="cb10-2" title="2"><span class="co"># Warning: </span></a>
-<a class="sourceLine" id="cb10-3" title="3"><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a>
-<a class="sourceLine" id="cb10-4" title="4"><span class="co">#&gt; [1] "(género desconocido)"</span></a></code></pre></div>
+<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</a>
+<a class="sourceLine" id="cb12-2" title="2"><span class="co"># Warning: </span></a>
+<a class="sourceLine" id="cb12-3" title="3"><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a>
+<a class="sourceLine" id="cb12-4" title="4"><span class="co">#&gt; [1] "(género desconocido)"</span></a></code></pre></div>
 </li>
 <li>Fix for vector containing only empty values</li>
 <li>Finds better results when input is in other languages</li>
@@ -540,19 +614,19 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <ul>
 <li>
 <p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
-<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
-<a class="sourceLine" id="cb11-2" title="2"><span class="co"># OLD WAY</span></a>
-<a class="sourceLine" id="cb11-3" title="3">septic_patients <span class="op">%&gt;%</span></a>
-<a class="sourceLine" id="cb11-4" title="4"><span class="st">  </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%&gt;%</span></a>
-<a class="sourceLine" id="cb11-5" title="5"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus)</a>
-<a class="sourceLine" id="cb11-6" title="6"><span class="co"># NEW WAY</span></a>
-<a class="sourceLine" id="cb11-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb11-8" title="8"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
-<a class="sourceLine" id="cb11-9" title="9"></a>
-<a class="sourceLine" id="cb11-10" title="10"><span class="co"># Even supports grouping variables:</span></a>
-<a class="sourceLine" id="cb11-11" title="11">septic_patients <span class="op">%&gt;%</span></a>
-<a class="sourceLine" id="cb11-12" title="12"><span class="st">  </span><span class="kw">group_by</span>(gender) <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb11-13" title="13"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
+<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
+<a class="sourceLine" id="cb13-2" title="2"><span class="co"># OLD WAY</span></a>
+<a class="sourceLine" id="cb13-3" title="3">septic_patients <span class="op">%&gt;%</span></a>
+<a class="sourceLine" id="cb13-4" title="4"><span class="st">  </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%&gt;%</span></a>
+<a class="sourceLine" id="cb13-5" title="5"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus)</a>
+<a class="sourceLine" id="cb13-6" title="6"><span class="co"># NEW WAY</span></a>
+<a class="sourceLine" id="cb13-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
+<a class="sourceLine" id="cb13-8" title="8"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
+<a class="sourceLine" id="cb13-9" title="9"></a>
+<a class="sourceLine" id="cb13-10" title="10"><span class="co"># Even supports grouping variables:</span></a>
+<a class="sourceLine" id="cb13-11" title="11">septic_patients <span class="op">%&gt;%</span></a>
+<a class="sourceLine" id="cb13-12" title="12"><span class="st">  </span><span class="kw">group_by</span>(gender) <span class="op">%&gt;%</span><span class="st"> </span></a>
+<a class="sourceLine" id="cb13-13" title="13"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
 </li>
 <li>Header info is now available as a list, with the <code>header</code> function</li>
 <li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li>
@@ -575,9 +649,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <li>if using different lengths of pattern and x in <code>%like%</code>, it will now return the call</li>
 </ul>
 </div>
-<div id="other-1" class="section level4">
+<div id="other-2" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-1" class="anchor"></a>Other</h4>
+<a href="#other-2" class="anchor"></a>Other</h4>
 <ul>
 <li>Updated licence text to emphasise GPL 2.0 and that this is an R package.</li>
 </ul>
@@ -587,9 +661,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <h1 class="page-header">
 <a href="#amr-050" class="anchor"></a>AMR 0.5.0<small> 2018-11-30 </small>
 </h1>
-<div id="new-2" class="section level4">
+<div id="new-3" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-2" class="anchor"></a>New</h4>
+<a href="#new-3" class="anchor"></a>New</h4>
 <ul>
 <li>Repository moved to GitLab: <a href="https://gitlab.com/msberends/AMR" class="uri">https://gitlab.com/msberends/AMR</a>
 </li>
@@ -601,9 +675,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <li>Functions <code>mo_authors</code> and <code>mo_year</code> to get specific values about the scientific reference of a taxonomic entry</li>
 </ul>
 </div>
-<div id="changed-3" class="section level4">
+<div id="changed-4" class="section level4">
 <h4 class="hasAnchor">
-<a href="#changed-3" class="anchor"></a>Changed</h4>
+<a href="#changed-4" class="anchor"></a>Changed</h4>
 <ul>
 <li>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code>
 </li>
@@ -627,10 +701,10 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li>
 <li>
 <p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
-<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>)        <span class="co"># B_ESCHR</span></a>
-<a class="sourceLine" id="cb12-2" title="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>)     <span class="co"># "Escherichia species"</span></a>
-<a class="sourceLine" id="cb12-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>)            <span class="co"># B_STPHY</span></a>
-<a class="sourceLine" id="cb12-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>)  <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
+<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>)        <span class="co"># B_ESCHR</span></a>
+<a class="sourceLine" id="cb14-2" title="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>)     <span class="co"># "Escherichia species"</span></a>
+<a class="sourceLine" id="cb14-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>)            <span class="co"># B_STPHY</span></a>
+<a class="sourceLine" id="cb14-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>)  <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
 </li>
 <li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li>
 <li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
@@ -643,15 +717,15 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <ul>
 <li>
 <p>Support for grouping variables, test with:</p>
-<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb13-2" title="2"><span class="st">  </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb13-3" title="3"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
+<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
+<a class="sourceLine" id="cb15-2" title="2"><span class="st">  </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
+<a class="sourceLine" id="cb15-3" title="3"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
 </li>
 <li>
 <p>Support for (un)selecting columns:</p>
-<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb14-2" title="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb14-3" title="3"><span class="st">  </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
+<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
+<a class="sourceLine" id="cb16-2" title="2"><span class="st">  </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
+<a class="sourceLine" id="cb16-3" title="3"><span class="st">  </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
 </li>
 <li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/hms">hms::is.hms</a></code>
 </li>
@@ -700,9 +774,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <li><p>Percentages will now will rounded more logically (e.g. in <code>freq</code> function)</p></li>
 </ul>
 </div>
-<div id="other-2" class="section level4">
+<div id="other-3" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-2" class="anchor"></a>Other</h4>
+<a href="#other-3" class="anchor"></a>Other</h4>
 <ul>
 <li>New dependency on package <code>crayon</code>, to support formatted text in the console</li>
 <li>Dependency <code>tidyr</code> is now mandatory (went to <code>Import</code> field) since <code>portion_df</code> and <code>count_df</code> rely on it</li>
@@ -714,9 +788,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <h1 class="page-header">
 <a href="#amr-040" class="anchor"></a>AMR 0.4.0<small> 2018-10-01 </small>
 </h1>
-<div id="new-3" class="section level4">
+<div id="new-4" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-3" class="anchor"></a>New</h4>
+<a href="#new-4" class="anchor"></a>New</h4>
 <ul>
 <li>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <a href="https://itis.gov" class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</li>
 <li>New functions based on the existing function <code>mo_property</code>:
@@ -731,18 +805,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 </li>
 </ul>
 <p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
-<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
-<a class="sourceLine" id="cb15-2" title="2"><span class="co"># [1] "Gram negative"</span></a>
-<a class="sourceLine" id="cb15-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
-<a class="sourceLine" id="cb15-4" title="4"><span class="co"># [1] "Gramnegativ"</span></a>
-<a class="sourceLine" id="cb15-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
-<a class="sourceLine" id="cb15-6" title="6"><span class="co"># [1] "Gram negativo"</span></a>
-<a class="sourceLine" id="cb15-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
-<a class="sourceLine" id="cb15-8" title="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
+<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
+<a class="sourceLine" id="cb17-2" title="2"><span class="co"># [1] "Gram negative"</span></a>
+<a class="sourceLine" id="cb17-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
+<a class="sourceLine" id="cb17-4" title="4"><span class="co"># [1] "Gramnegativ"</span></a>
+<a class="sourceLine" id="cb17-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
+<a class="sourceLine" id="cb17-6" title="6"><span class="co"># [1] "Gram negativo"</span></a>
+<a class="sourceLine" id="cb17-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
+<a class="sourceLine" id="cb17-8" title="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
 <p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
-<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
-<a class="sourceLine" id="cb16-2" title="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
-<a class="sourceLine" id="cb16-3" title="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
+<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
+<a class="sourceLine" id="cb18-2" title="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
+<a class="sourceLine" id="cb18-3" title="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
 </li>
 <li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates
 <ul>
@@ -753,18 +827,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 </li>
 <li>
 <p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
-<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
-<a class="sourceLine" id="cb17-2" title="2"><span class="co"># [1] B_ESCHR_COL</span></a>
-<a class="sourceLine" id="cb17-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
-<a class="sourceLine" id="cb17-4" title="4"><span class="co"># [1] B_STPHY_AUR</span></a>
-<a class="sourceLine" id="cb17-5" title="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
-<a class="sourceLine" id="cb17-6" title="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
+<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
+<a class="sourceLine" id="cb19-2" title="2"><span class="co"># [1] B_ESCHR_COL</span></a>
+<a class="sourceLine" id="cb19-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
+<a class="sourceLine" id="cb19-4" title="4"><span class="co"># [1] B_STPHY_AUR</span></a>
+<a class="sourceLine" id="cb19-5" title="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
+<a class="sourceLine" id="cb19-6" title="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
 <p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
-<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1">thousands_of_E_colis &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
-<a class="sourceLine" id="cb18-2" title="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
-<a class="sourceLine" id="cb18-3" title="3"><span class="co"># Unit: seconds</span></a>
-<a class="sourceLine" id="cb18-4" title="4"><span class="co">#         min       median         max  neval</span></a>
-<a class="sourceLine" id="cb18-5" title="5"><span class="co">#  0.01817717  0.01843957  0.03878077    100</span></a></code></pre></div>
+<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1">thousands_of_E_colis &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
+<a class="sourceLine" id="cb20-2" title="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
+<a class="sourceLine" id="cb20-3" title="3"><span class="co"># Unit: seconds</span></a>
+<a class="sourceLine" id="cb20-4" title="4"><span class="co">#         min       median         max  neval</span></a>
+<a class="sourceLine" id="cb20-5" title="5"><span class="co">#  0.01817717  0.01843957  0.03878077    100</span></a></code></pre></div>
 </li>
 <li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li>
 <li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:
@@ -785,19 +859,19 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <li><p>Renamed <code>septic_patients$sex</code> to <code>septic_patients$gender</code></p></li>
 </ul>
 </div>
-<div id="changed-4" class="section level4">
+<div id="changed-5" class="section level4">
 <h4 class="hasAnchor">
-<a href="#changed-4" class="anchor"></a>Changed</h4>
+<a href="#changed-5" class="anchor"></a>Changed</h4>
 <ul>
 <li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
 <li>
 <p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
-<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_official</a></span>(<span class="st">"Bactroban"</span>)</a>
-<a class="sourceLine" id="cb19-2" title="2"><span class="co"># [1] "Mupirocin"</span></a>
-<a class="sourceLine" id="cb19-3" title="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
-<a class="sourceLine" id="cb19-4" title="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
-<a class="sourceLine" id="cb19-5" title="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
-<a class="sourceLine" id="cb19-6" title="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
+<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_official</a></span>(<span class="st">"Bactroban"</span>)</a>
+<a class="sourceLine" id="cb21-2" title="2"><span class="co"># [1] "Mupirocin"</span></a>
+<a class="sourceLine" id="cb21-3" title="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
+<a class="sourceLine" id="cb21-4" title="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
+<a class="sourceLine" id="cb21-5" title="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
+<a class="sourceLine" id="cb21-6" title="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
 </li>
 <li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
 <li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li>
@@ -808,13 +882,13 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 </li>
 <li>
 <p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
-<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
-<a class="sourceLine" id="cb20-2" title="2"><span class="co"># which is the same as:</span></a>
-<a class="sourceLine" id="cb20-3" title="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
-<a class="sourceLine" id="cb20-4" title="4"></a>
-<a class="sourceLine" id="cb20-5" title="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
-<a class="sourceLine" id="cb20-6" title="6">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
-<a class="sourceLine" id="cb20-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
+<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
+<a class="sourceLine" id="cb22-2" title="2"><span class="co"># which is the same as:</span></a>
+<a class="sourceLine" id="cb22-3" title="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
+<a class="sourceLine" id="cb22-4" title="4"></a>
+<a class="sourceLine" id="cb22-5" title="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
+<a class="sourceLine" id="cb22-6" title="6">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
+<a class="sourceLine" id="cb22-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
 </li>
 <li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li>
 <li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
@@ -828,18 +902,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 </li>
 <li>
 <p>Support for types (classes) list and matrix for <code>freq</code></p>
-<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
-<a class="sourceLine" id="cb21-2" title="2"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
+<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
+<a class="sourceLine" id="cb23-2" title="2"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
 <p>For lists, subsetting is possible:</p>
-<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
-<a class="sourceLine" id="cb22-2" title="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
-<a class="sourceLine" id="cb22-3" title="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
+<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
+<a class="sourceLine" id="cb24-2" title="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
+<a class="sourceLine" id="cb24-3" title="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
 </li>
 </ul>
 </div>
-<div id="other-3" class="section level4">
+<div id="other-4" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-3" class="anchor"></a>Other</h4>
+<a href="#other-4" class="anchor"></a>Other</h4>
 <ul>
 <li>More unit tests to ensure better integrity of functions</li>
 </ul>
@@ -849,9 +923,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <h1 class="page-header">
 <a href="#amr-030" class="anchor"></a>AMR 0.3.0<small> 2018-08-14 </small>
 </h1>
-<div id="new-4" class="section level4">
+<div id="new-5" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-4" class="anchor"></a>New</h4>
+<a href="#new-5" class="anchor"></a>New</h4>
 <ul>
 <li>
 <strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.
@@ -922,9 +996,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 </li>
 </ul>
 </div>
-<div id="changed-5" class="section level4">
+<div id="changed-6" class="section level4">
 <h4 class="hasAnchor">
-<a href="#changed-5" class="anchor"></a>Changed</h4>
+<a href="#changed-6" class="anchor"></a>Changed</h4>
 <ul>
 <li>Improvements for forecasting with <code>resistance_predict</code> and added more examples</li>
 <li>More antibiotics added as parameters for EUCAST rules</li>
@@ -966,9 +1040,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <li>Other small fixes</li>
 </ul>
 </div>
-<div id="other-4" class="section level4">
+<div id="other-5" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-4" class="anchor"></a>Other</h4>
+<a href="#other-5" class="anchor"></a>Other</h4>
 <ul>
 <li>Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher
 <ul>
@@ -986,9 +1060,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <h1 class="page-header">
 <a href="#amr-020" class="anchor"></a>AMR 0.2.0<small> 2018-05-03 </small>
 </h1>
-<div id="new-5" class="section level4">
+<div id="new-6" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-5" class="anchor"></a>New</h4>
+<a href="#new-6" class="anchor"></a>New</h4>
 <ul>
 <li>Full support for Windows, Linux and macOS</li>
 <li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
@@ -1008,9 +1082,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <li>New print format for <code>tibble</code>s and <code>data.table</code>s</li>
 </ul>
 </div>
-<div id="changed-6" class="section level4">
+<div id="changed-7" class="section level4">
 <h4 class="hasAnchor">
-<a href="#changed-6" class="anchor"></a>Changed</h4>
+<a href="#changed-7" class="anchor"></a>Changed</h4>
 <ul>
 <li>Fixed <code>rsi</code> class for vectors that contain only invalid antimicrobial interpretations</li>
 <li>Renamed dataset <code>ablist</code> to <code>antibiotics</code>
@@ -1028,9 +1102,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <li>Functions <code>as.rsi</code> and <code>as.mic</code> now add the package name and version as attributes</li>
 </ul>
 </div>
-<div id="other-5" class="section level4">
+<div id="other-6" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-5" class="anchor"></a>Other</h4>
+<a href="#other-6" class="anchor"></a>Other</h4>
 <ul>
 <li>Expanded <code>README.md</code> with more examples</li>
 <li>Added <a href="https://orcid.org">ORCID</a> of authors to DESCRIPTION file</li>
@@ -1067,6 +1141,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
     <div id="tocnav">
       <h2>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
+        <li><a href="#amr-0709015">0.7.0.9015</a></li>
         <li><a href="#amr-070">0.7.0</a></li>
         <li><a href="#amr-061">0.6.1</a></li>
         <li><a href="#amr-060">0.6.0</a></li>

docs/pkgdown.yml

@@ -7,10 +7,8 @@ articles:
   MDR: MDR.html
   SPSS: SPSS.html
   WHONET: WHONET.html
-  ab_property: ab_property.html
   benchmarks: benchmarks.html
   freq: freq.html
-  mo_property: mo_property.html
   resistance_predict: resistance_predict.html
 urls:
   reference: https://msberends.gitlab.io/AMR/reference

docs/reference/AMR-deprecated.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/AMR.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/WHOCC.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/WHONET.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/ab_property.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/age.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/age_groups.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/antibiotics.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -252,7 +245,7 @@
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 454 observations and 13 variables:</p><dl class='dl-horizontal'>
+    <p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 453 observations and 13 variables:</p><dl class='dl-horizontal'>
   <dt><code>ab</code></dt><dd><p>Antibiotic ID as used in this package (like <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></dd>
   <dt><code>atc</code></dt><dd><p>ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></dd>
   <dt><code>cid</code></dt><dd><p>Compound ID as found in PubChem</p></dd>

docs/reference/as.ab.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/as.atc.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/as.disk.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/as.mic.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/as.mo.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -395,6 +388,7 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
 <span class='fu'>as.mo</span>(<span class='st'>"MRSA"</span>)   <span class='co'># Methicillin Resistant S. aureus</span>
 <span class='fu'>as.mo</span>(<span class='st'>"VISA"</span>)   <span class='co'># Vancomycin Intermediate S. aureus</span>
 <span class='fu'>as.mo</span>(<span class='st'>"VRSA"</span>)   <span class='co'># Vancomycin Resistant S. aureus</span>
+<span class='fu'>as.mo</span>(<span class='fl'>22242419</span>) <span class='co'># Catalogue of Life ID</span>
 
 <span class='co'># Dyslexia is no problem - these all work:</span>
 <span class='fu'>as.mo</span>(<span class='st'>"Ureaplasma urealyticum"</span>)

docs/reference/as.rsi.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/atc_online.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/availability.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/catalogue_of_life.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -307,9 +300,9 @@ Function <code><a href='as.mo.html'>as.mo</a>()</code> to use the data for intel
 <span class='co'># [1] "Castellani et al., 1919"</span>
 
 <span class='co'># Do not get mistaken - the package only includes microorganisms</span>
-<span class='fu'><a href='mo_property.html'>mo_phylum</a></span>(<span class='st'>"C. elegans"</span>)
-<span class='co'># [1] "Cyanobacteria"                   # Bacteria?!</span>
-<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"C. elegans"</span>)
+<span class='fu'><a href='mo_property.html'>mo_kingdom</a></span>(<span class='st'>"C. elegans"</span>)
+<span class='co'># [1] "Bacteria"                        # Bacteria?!</span>
+<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"C. elegans"</span>)
 <span class='co'># [1] "Chroococcus limneticus elegans"  # Because a microorganism was found</span>
 <span class='co'># }</span></pre>
   </div>

docs/reference/catalogue_of_life_version.html

@@ -47,7 +47,7 @@
   <script src="../extra.js"></script>
 <meta property="og:title" content="Version info of included Catalogue of Life — catalogue_of_life_version" />
 
-<meta property="og:description" content="This function returns information about the included data from the Catalogue of Life. It also shows if the included version is their latest annual release. The Catalogue of Life releases their annual release in March each year." />
+<meta property="og:description" content="This function returns information about the included data from the Catalogue of Life." />
 
 <meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
 <meta name="twitter:card" content="summary" />
@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -244,7 +237,7 @@
 
     <div class="ref-description">
     
-    <p>This function returns information about the included data from the Catalogue of Life. It also shows if the included version is their latest annual release. The Catalogue of Life releases their annual release in March each year.</p>
+    <p>This function returns information about the included data from the Catalogue of Life.</p>
     
     </div>
 
@@ -256,8 +249,7 @@
     
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
-    <p>The list item <code>...$catalogue_of_life$is_latest_annual_release</code> is based on the system date.</p>
-<p>For DSMZ, see <code><a href='microorganisms.html'>?microorganisms</a></code>.</p>
+    <p>For DSMZ, see <code><a href='microorganisms.html'>?microorganisms</a></code>.</p>
     
     <h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
 

docs/reference/count.html

@@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -166,13 +166,6 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -311,8 +304,9 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     <p>These functions are meant to count isolates. Use the <code><a href='portion.html'>portion</a>_*</code> functions to calculate microbial resistance.</p>
-<p><code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
-<p><code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p>
+<p>The function <code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
+<p>The function <code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of S, I and R. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p>
+<p>The function <code>rsi_df</code> works exactly like <code>count_df</code>, but adds the percentage of S, I and R.</p>
     
     <h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>
 

docs/reference/eucast_rules.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/extended-functions.html

@@ -0,0 +1,297 @@
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+    <li>
+      <a href="../articles/AMR.html">
+        <span class="fa fa-directions"></span>
+         
+        Conduct AMR analysis
+      </a>
+    </li>
+    <li>
+      <a href="../articles/resistance_predict.html">
+        <span class="fa fa-dice"></span>
+         
+        Predict antimicrobial resistance
+      </a>
+    </li>
+    <li>
+      <a href="../articles/MDR.html">
+        <span class="fa fa-skull-crossbones"></span>
+         
+        Determine multi-drug resistance (MDR)
+      </a>
+    </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
+    <li>
+      <a href="../articles/SPSS.html">
+        <span class="fa fa-file-upload"></span>
+         
+        Import data from SPSS/SAS/Stata
+      </a>
+    </li>
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+      <a href="../articles/EUCAST.html">
+        <span class="fa fa-exchange-alt"></span>
+         
+        Apply EUCAST rules
+      </a>
+    </li>
+    <li>
+      <a href="../reference/mo_property.html">
+        <span class="fa fa-bug"></span>
+         
+        Get properties of a microorganism
+      </a>
+    </li>
+    <li>
+      <a href="../reference/ab_property.html">
+        <span class="fa fa-capsules"></span>
+         
+        Get properties of an antibiotic
+      </a>
+    </li>
+    <li>
+      <a href="../articles/freq.html">
+        <span class="fa fa-sort-amount-down"></span>
+         
+        Create frequency tables
+      </a>
+    </li>
+    <li>
+      <a href="../articles/benchmarks.html">
+        <span class="fa fa-shipping-fast"></span>
+         
+        Other: benchmarks
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+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Extended functions</h1>
+    
+    <div class="hidden name"><code>extended-functions.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    
+    <p>These functions are extensions of functions in other packages.</p>
+    
+    </div>
+
+    <pre class="usage"><span class='fu'>scale_type.mo</span>(<span class='no'>x</span>)
+
+<span class='fu'>scale_type.ab</span>(<span class='no'>x</span>)</pre>
+        
+    <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
+
+    
+    <p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
+    
+
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      
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+          </ul>
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+      <div class="copyright">
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docs/reference/filter_ab_class.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/first_isolate.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/freq.html

@@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -166,13 +166,6 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/g.test.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/ggplot_rsi.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -244,12 +237,12 @@
 
     <div class="ref-description">
     
-    <p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a>2</code> functions.</p>
+    <p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a>2</code> functions.</p>
     
     </div>
 
-    <pre class="usage"><span class='fu'>ggplot_rsi</span>(<span class='no'>data</span>, <span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>,
-  <span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"Interpretation"</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
+    <pre class="usage"><span class='fu'>ggplot_rsi</span>(<span class='no'>data</span>, <span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
+  <span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"interpretation"</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
   <span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>,
   <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>colours</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>S</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>SI</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>I</span> <span class='kw'>=</span>
@@ -258,12 +251,12 @@
   <span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>caption</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x.title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>y.title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='no'>...</span>)
 
-<span class='fu'>geom_rsi</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Antibiotic"</span>, <span class='st'>"Interpretation"</span>),
-  <span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"Interpretation"</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
+<span class='fu'>geom_rsi</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"antibiotic"</span>, <span class='st'>"interpretation"</span>),
+  <span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"interpretation"</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
   <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>, <span class='no'>...</span>)
 
-<span class='fu'>facet_rsi</span>(<span class='kw'>facet</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Interpretation"</span>, <span class='st'>"Antibiotic"</span>), <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
+<span class='fu'>facet_rsi</span>(<span class='kw'>facet</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"interpretation"</span>, <span class='st'>"antibiotic"</span>), <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
 
 <span class='fu'>scale_y_percent</span>(<span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>), <span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
 
@@ -272,7 +265,7 @@
 
 <span class='fu'>theme_rsi</span>()
 
-<span class='fu'>labels_rsi_count</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>,
+<span class='fu'>labels_rsi_count</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
   <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>datalabels.size</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"gray15"</span>)</pre>
     
@@ -289,15 +282,15 @@
     </tr>
     <tr>
       <th>x</th>
-      <td><p>variable to show on x axis, either <code>"Antibiotic"</code> (default) or <code>"Interpretation"</code> or a grouping variable</p></td>
+      <td><p>variable to show on x axis, either <code>"antibiotic"</code> (default) or <code>"interpretation"</code> or a grouping variable</p></td>
     </tr>
     <tr>
       <th>fill</th>
-      <td><p>variable to categorise using the plots legend, either <code>"Antibiotic"</code> (default) or <code>"Interpretation"</code> or a grouping variable</p></td>
+      <td><p>variable to categorise using the plots legend, either <code>"antibiotic"</code> (default) or <code>"interpretation"</code> or a grouping variable</p></td>
     </tr>
     <tr>
       <th>facet</th>
-      <td><p>variable to split plots by, either <code>"Interpretation"</code> (default) or <code>"Antibiotic"</code> or a grouping variable</p></td>
+      <td><p>variable to split plots by, either <code>"interpretation"</code> (default) or <code>"antibiotic"</code> or a grouping variable</p></td>
     </tr>
     <tr>
       <th>breaks</th>
@@ -378,11 +371,11 @@
     <p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name</a></code>. This can be set with the <code>translate_ab</code> parameter. See <code><a href='count.html'>count_df</a></code>.</p>
 <p><strong>The functions</strong><br />
 <code>geom_rsi</code> will take any variable from the data that has an <code>rsi</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) using <code>fun</code> (<code><a href='count.html'>count_df</a></code> at default, can also be <code><a href='portion.html'>portion_df</a></code>) and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
-<p><code>facet_rsi</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/facet_wrap'>facet_wrap</a></code>.</p>
+<p><code>facet_rsi</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://ggplot2.tidyverse.org/reference/facet_wrap.html'>facet_wrap</a></code>.</p>
 <p><code>scale_y_percent</code> transforms the y axis to a 0 to 100% range using <code>scale_continuous</code>.</p>
 <p><code>scale_rsi_colours</code> sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using <code>scale_brewer</code>.</p>
-<p><code>theme_rsi</code> is a <code>ggplot <a href='https://www.rdocumentation.org/packages/ggplot2/topics/theme'>theme</a></code> with minimal distraction.</p>
-<p><code>labels_rsi_count</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/geom_text'>geom_text</a></code></p>
+<p><code>theme_rsi</code> is a <code>ggplot <a href='https://ggplot2.tidyverse.org/reference/theme.html'>theme</a></code> with minimal distraction.</p>
+<p><code>labels_rsi_count</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://ggplot2.tidyverse.org/reference/geom_text.html'>geom_text</a></code></p>
 <p><code>ggplot_rsi</code> is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (<code>%&gt;%</code>). See Examples.</p>
     
     <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@@ -397,12 +390,12 @@
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>ggplot2</span>)
 
 <span class='co'># get antimicrobial results for drugs against a UTI:</span>
-<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>)) +
+<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>)) +
   <span class='fu'>geom_rsi</span>()
 
 <span class='co'># prettify the plot using some additional functions:</span>
 <span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>)
-<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>df</span>) +
+<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>df</span>) +
   <span class='fu'>geom_rsi</span>() +
   <span class='fu'>scale_y_percent</span>() +
   <span class='fu'>scale_rsi_colours</span>() +
@@ -446,7 +439,7 @@
 <span class='co'># for colourblind mode, use divergent colours from the viridis package:</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'>ggplot_rsi</span>() + <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/scale_viridis'>scale_fill_viridis_d</a></span>()
+  <span class='fu'>ggplot_rsi</span>() + <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_fill_viridis_d</a></span>()
 <span class='co'># a shorter version which also adjusts data label colours:</span>
 <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
@@ -458,7 +451,7 @@
   <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
   <span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"hospital_id"</span>,
-             <span class='kw'>facet</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>,
+             <span class='kw'>facet</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
              <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>,
              <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
              <span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Hospital"</span>,
@@ -479,7 +472,7 @@
   <span class='co'># group by MO</span>
   <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>bug</span>) <span class='kw'>%&gt;%</span>
   <span class='co'># plot the thing, putting MOs on the facet</span>
-  <span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>,
+  <span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
              <span class='kw'>facet</span> <span class='kw'>=</span> <span class='st'>"bug"</span>,
              <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
              <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>,

docs/reference/guess_ab_col.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
       </span>
     </div>
 
@@ -163,13 +163,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -380,7 +373,7 @@
       </tr><tr>
         
         <td>
-          <p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
+          <p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
         </td>
         <td><p>Property of a microorganism</p></td>
       </tr><tr>
@@ -442,7 +435,7 @@
       </tr><tr>
         
         <td>
-          <p><code><a href="portion.html">portion_R()</a></code> <code><a href="portion.html">portion_IR()</a></code> <code><a href="portion.html">portion_I()</a></code> <code><a href="portion.html">portion_SI()</a></code> <code><a href="portion.html">portion_S()</a></code> <code><a href="portion.html">portion_df()</a></code> </p>
+          <p><code><a href="portion.html">portion_R()</a></code> <code><a href="portion.html">portion_IR()</a></code> <code><a href="portion.html">portion_I()</a></code> <code><a href="portion.html">portion_SI()</a></code> <code><a href="portion.html">portion_S()</a></code> <code><a href="portion.html">portion_df()</a></code> <code><a href="portion.html">rsi_df()</a></code> </p>
         </td>
         <td><p>Calculate resistance of isolates</p></td>
       </tr><tr>
@@ -555,7 +548,21 @@
     </tbody><tbody>
       <tr>
         <th colspan="2">
-          <h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2>
+          <h2 id="section-extended-functions" class="hasAnchor"><a href="#section-extended-functions" class="anchor"></a>Extended functions</h2>
+          <p class="section-desc"><p>These functions are extensions of functions in other packages.</p></p>
+        </th>
+      </tr>
+      <tr>
+        
+        <td>
+          <p><code><a href="extended-functions.html">scale_type.mo()</a></code> <code><a href="extended-functions.html">scale_type.ab()</a></code> </p>
+        </td>
+        <td><p>Extended functions</p></td>
+      </tr>
+    </tbody><tbody>
+      <tr>
+        <th colspan="2">
+          <h2 id="section-functions" class="hasAnchor"><a href="#section-functions" class="anchor"></a>functions</h2>
           <p class="section-desc"><p>These functions are deprecated, meaning that they still work but show a warning with every use and will be removed in a future version.</p></p>
         </th>
       </tr>
@@ -579,7 +586,8 @@
       <li><a href="#section-analysing-your-data">Analysing your data</a></li>
       <li><a href="#section-included-data-sets">Included data sets</a></li>
       <li><a href="#section-other-functions">Other functions</a></li>
-      <li><a href="#section-deprecated-functions">Deprecated functions</a></li>
+      <li><a href="#section-extended-functions">Extended functions</a></li>
+      <li><a href="#section-functions">functions</a></li>
     </ul>
   </div>
 </div>

docs/reference/join.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/key_antibiotics.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -248,19 +241,22 @@
     
     </div>
 
-    <pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"AMX"</span>),
-  <span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"AMC"</span>), <span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
-  <span class='st'>"CXM"</span>), <span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"TZP"</span>),
-  <span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"CIP"</span>), <span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
-  <span class='st'>"SXT"</span>), <span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"VAN"</span>),
-  <span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"TEC"</span>), <span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
-  <span class='st'>"TCY"</span>), <span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"ERY"</span>),
-  <span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"OXA"</span>), <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
-  <span class='st'>"RIF"</span>), <span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"GEN"</span>),
-  <span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"TOB"</span>), <span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
-  <span class='st'>"COL"</span>), <span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"CTX"</span>),
-  <span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"CAZ"</span>), <span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
-  <span class='st'>"MEM"</span>), <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+    <pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
+  <span class='st'>"amoxicillin"</span>), <span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
+  <span class='st'>"amoxicillin/clavulanic acid"</span>), <span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
+  <span class='st'>"cefuroxime"</span>), <span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
+  <span class='st'>"piperacillin/tazobactam"</span>), <span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
+  <span class='st'>"ciprofloxacin"</span>), <span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
+  <span class='st'>"trimethoprim/sulfamethoxazole"</span>), <span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
+  <span class='st'>"vancomycin"</span>), <span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"teicoplanin"</span>),
+  <span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"tetracycline"</span>),
+  <span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"erythromycin"</span>),
+  <span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"oxacillin"</span>), <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
+  <span class='st'>"rifampin"</span>), <span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"gentamicin"</span>),
+  <span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"tobramycin"</span>),
+  <span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"colistin"</span>), <span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
+  <span class='st'>"cefotaxime"</span>), <span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"ceftazidime"</span>),
+  <span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"meropenem"</span>), <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
 
 <span class='fu'>key_antibiotics_equal</span>(<span class='no'>y</span>, <span class='no'>z</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
   <span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
@@ -282,11 +278,11 @@
     </tr>
     <tr>
       <th>GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6</th>
-      <td><p>column names of antibiotics for <strong>Gram positives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td>
+      <td><p>column names of antibiotics for <strong>Gram-positives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td>
     </tr>
     <tr>
       <th>GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6</th>
-      <td><p>column names of antibiotics for <strong>Gram negatives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td>
+      <td><p>column names of antibiotics for <strong>Gram-negatives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td>
     </tr>
     <tr>
       <th>warnings</th>
@@ -321,10 +317,10 @@
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     <p>The function <code>key_antibiotics</code> returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>). The <code><a href='first_isolate.html'>first_isolate</a></code> function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible <em>S. aureus</em> (MSSA) found within the same episode (see <code>episode</code> parameter of <code><a href='first_isolate.html'>first_isolate</a></code>). Without key antibiotic comparison it would not.</p>
-<p>At default, the antibiotics that are used for <strong>Gram positive bacteria</strong> are (colum names): <br />
-  <code>"amox"</code>, <code>"amcl"</code>, <code>"cfur"</code>, <code>"pita"</code>, <code>"cipr"</code>, <code>"trsu"</code> (until here is universal), <code>"vanc"</code>, <code>"teic"</code>, <code>"tetr"</code>, <code>"eryt"</code>, <code>"oxac"</code>, <code>"rifa"</code>.</p>
-<p>At default, the antibiotics that are used for <strong>Gram negative bacteria</strong> are (colum names): <br />
-  <code>"amox"</code>, <code>"amcl"</code>, <code>"cfur"</code>, <code>"pita"</code>, <code>"cipr"</code>, <code>"trsu"</code> (until here is universal), <code>"gent"</code>, <code>"tobr"</code>, <code>"coli"</code>, <code>"cfot"</code>, <code>"cfta"</code>, <code>"mero"</code>.</p>
+<p>At default, the antibiotics that are used for <strong>Gram-positive bacteria</strong> are: <br />
+  amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampin.</p>
+<p>At default, the antibiotics that are used for <strong>Gram-negative bacteria</strong> are: <br />
+  amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem.</p>
     <p>The function <code>key_antibiotics_equal</code> checks the characters returned by <code>key_antibiotics</code> for equality, and returns a logical vector.</p>
     
     <h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key antibiotics</h2>
@@ -350,6 +346,7 @@
     <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='co'># septic_patients is a dataset available in the AMR package</span>
 ?<span class='no'>septic_patients</span>
+
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='co'># set key antibiotics to a new variable</span>
 <span class='no'>my_patients</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>

docs/reference/kurtosis.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/like.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/mdro.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/microorganisms.codes.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/reference/microorganisms.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
       </span>
     </div>
 
@@ -165,13 +165,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -252,7 +245,7 @@
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 67,903 observations and 16 variables:</p><dl class='dl-horizontal'>
+    <p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 67,906 observations and 16 variables:</p><dl class='dl-horizontal'>
   <dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd>
   <dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
   <dt><code>fullname</code></dt><dd><p>Full name, like <code>"Escherichia coli"</code></p></dd>
@@ -272,9 +265,10 @@
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     <p>Manually added were:</p><ul>
-<li><p>9 species of <em>Streptococcus</em> (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)</p></li>
-<li><p>2 species of <em>Staphylococcus</em> (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li>
-<li><p>3 other undefined (unknown, unknown Gram negatives and unknown Gram positives)</p></li>
+<li><p>9 entries of <em>Streptococcus</em> (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)</p></li>
+<li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li>
+<li><p>3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)</p></li>
+<li><p>3 other 'undefined' entries (unknown, unknown Gram negatives and unknown Gram positives)</p></li>
 <li><p>8,830 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life</p></li>
 </ul>