(v1.2.0.9035) as.mo() speed improvement

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.2.0.9034
+Version: 1.2.0.9035
-Date: 2020-07-13
+Date: 2020-07-22
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 1.2.0.9034
+# AMR 1.2.0.9035
-## <small>Last updated: 13-Jul-2020</small>
+## <small>Last updated: 22 July 2020</small>
 
 ### New
 * Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
@@ -19,8 +19,11 @@
 * Added Monuril as trade name for fosfomycin
 
 ### Changed
+* Big speed improvement for using any function on microorganism codes from earlier package versions (prior to `AMR` v1.2.0), such as `as.mo()`, `mo_name()`, `first_isolate()`, `eucast_rules()`, `mdro()`, etc.
+
+  As a consequence, very old microbial codes (from `AMR` v0.5.0 and lower) **are not supported anymore**. Use `as.mo()` on your microorganism names or codes to transform them to current abbreviations used in this package.
 * Improvements for `susceptibility()` and `resistance()` and all `count_*()`, `proportion_*()` functions:
-  * 95% speed improvement (!) by using other base R functions for calculation
+  * 95% speed improvement by using other base R functions for calculation
   * Using unexisting columns wil now return an error instead of dropping them silently
   * Using variables for column names (as well as selectors like `dplyr::all_of()`) now works again
 * Improvements for `as.ab()`:
@@ -33,7 +36,7 @@
 * Fixed a bug for using grouped versions of `rsi_df()`, `proportion_df()` and `count_df()`, and fixed a bug where not all different antimicrobial results were added as rows
 * Improved auto-determination for columns of types `<mo>` and `<Date>`
 * Fixed a bug in `bug_drug_combinations()` for when only one antibiotic was in the input data
-* Changed the summary for class `<mo>`, to highlight the %SI vs. %R
+* Changed the summary for class `<rsi>`, to highlight the %SI vs. %R
 * Improved error handling, giving more useful info when functions return an error
 * Any progress bar will now only show in interactive mode (i.e. not in R Markdown)
 * Speed improvement for `mdro()` and `filter_ab_class()`

R/data.R

@@ -94,6 +94,7 @@
 #' - 11 entries of *Streptococcus* (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
 #' - 2 entries of *Staphylococcus* (coagulase-negative (CoNS) and coagulase-positive (CoPS))
 #' - 3 entries of *Trichomonas* (*Trichomonas vaginalis*, and its family and genus)
+#' - 1 entry of *Candida* (*Candida krusei*), that is not (yet) in the Catalogue of Life
 #' - 1 entry of *Blastocystis* (*Blastocystis hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993)
 #' - 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
 #' - 6 families under the Enterobacterales order, according to Adeolu *et al.* (2016, PMID 27620848), that are not (yet) in the Catalogue of Life
@@ -109,13 +110,14 @@
 #' * <https://github.com/msberends/AMR/raw/master/data/microorganisms.rda>
 #' @section About the records from DSMZ (see source):
 #' Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
+#' *(from <https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date/complete-list-readme>)*
 #' 
-#' From: <https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date/complete-list-readme>
+#' In February 2020, the DSMZ records were merged with the List of Prokaryotic names with Standing in Nomenclature (LPSN).
 #' @source Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]).
 #' 
 #' Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
 #'
-#' Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date> (check included version with [catalogue_of_life_version()]).
+#' Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date> and <https://lpsn.dsmz.de> (check included version with [catalogue_of_life_version()]).
 #' @inheritSection AMR Read more on our website!
 #' @seealso [as.mo()], [mo_property()], [microorganisms.codes]
 "microorganisms"
@@ -231,6 +233,6 @@ catalogue_of_life <- list(
 #' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S"
 #' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
 #' - `uti`\cr A logical value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
-#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
+#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically.
 #' @inheritSection AMR Read more on our website!
 "rsi_translation"

R/first_isolate.R

@@ -174,10 +174,6 @@ first_isolate <- function(x,
     col_date <- search_type_in_df(x = x, type = "date")
     stop_if(is.null(col_date), "`col_date` must be set")
   }
-  # convert to Date
-  dates <- as.Date(x[, col_date, drop = TRUE])
-  dates[is.na(dates)] <- as.Date("1970-01-01")
-  x[, col_date] <- dates
   
   # -- patient id
   if (is.null(col_patient_id)) {
@@ -223,12 +219,17 @@ first_isolate <- function(x,
   check_columns_existance(col_icu)
   check_columns_existance(col_keyantibiotics)
   
+  # convert dates to Date
+  dates <- as.Date(x[, col_date, drop = TRUE])
+  dates[is.na(dates)] <- as.Date("1970-01-01")
+  x[, col_date] <- dates
+  
   # create original row index
   x$newvar_row_index <- seq_len(nrow(x))
-  x$newvar_mo <- x %>% pull(col_mo) %>% as.mo()
+  x$newvar_mo <- x[, col_mo, drop = TRUE]
   x$newvar_genus_species <- paste(mo_genus(x$newvar_mo), mo_species(x$newvar_mo))
-  x$newvar_date <- x %>% pull(col_date)
+  x$newvar_date <- x[, col_date, drop = TRUE]
-  x$newvar_patient_id <- x %>% pull(col_patient_id)
+  x$newvar_patient_id <- x[, col_patient_id, drop = TRUE]
   
   if (is.null(col_testcode)) {
     testcodes_exclude <- NULL
@@ -317,7 +318,7 @@ first_isolate <- function(x,
   }
   
   # Analysis of first isolate ----
-  x$other_pat_or_mo <- if_else(x$newvar_patient_id == lag(x$newvar_patient_id) &
+  x$other_pat_or_mo <- ifelse(x$newvar_patient_id == lag(x$newvar_patient_id) &
                                 x$newvar_genus_species == lag(x$newvar_genus_species),
                               FALSE,
                               TRUE)

R/globals.R

@@ -19,100 +19,47 @@
 # Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
-globalVariables(c(".",
+globalVariables(c("ab",
-                  "..property",
-                  "ab",
                   "ab_txt",
-                  "abbreviations",
                   "angle",
-                  "antibiotic",
                   "antibiotics",
                   "atc_group1",
                   "atc_group2",
-                  "CNS_CPS",
                   "code",
-                  "col_id",
-                  "count",
-                  "count.x",
                   "data",
-                  "date_lab",
-                  "diff.percent",
-                  "First name",
-                  "first_isolate_row_index",
                   "fullname",
                   "fullname_lower",
                   "g_species",
                   "genus",
                   "gr",
-                  "gramstain",
                   "group",
                   "hjust",
-                  "index",
                   "input",
-                  "interpretation",
                   "isolates",
-                  "item",
-                  "key_ab",
-                  "key_ab_lag",
-                  "key_ab_other",
-                  "kingdom",
-                  "kingdom_index",
                   "lang",
-                  "Last name",
                   "lookup",
-                  "mdr",
-                  "MDRO",
-                  "median",
                   "microorganisms",
                   "microorganisms.codes",
                   "microorganisms.old",
-                  "missing_names",
                   "mo",
-                  "mo_new",
-                  "mo_old",
-                  "mono_count",
-                  "more_than_episode_ago",
                   "name",
                   "new",
-                  "newvar_date",
-                  "newvar_genus_species",
-                  "newvar_mo",
-                  "newvar_patient_id",
-                  "newvar_row_index",
-                  "newvar_row_index_sorted",
                   "observations",
-                  "observed",
                   "old",
                   "old_name",
-                  "other_pat_or_mo",
-                  "package_version",
-                  "patient_id",
                   "pattern",
-                  "plural",
-                  "prevalence",
                   "R",
-                  "real_first_isolate",
-                  "ref",
                   "rsi_translation",
                   "rule_group",
                   "rule_name",
-                  "S",
                   "se_max",
                   "se_min",
-                  "second",
-                  "Sex",
                   "species",
                   "species_id",
-                  "subspecies",
-                  "synonyms",
                   "total",
                   "txt",
-                  "uncertainty_level",
                   "value",
                   "varname",
-                  "x",
-                  "xdr",
                   "xvar",
-                  "y",
                   "year",
                   "yvar"))

R/guess_ab_col.R

@@ -40,7 +40,7 @@
 #' # [1] "tetr"
 #'
 #' guess_ab_col(df, "J01AA07", verbose = TRUE)
-#' # Note: Using column `tetr` as input for "J01AA07".
+#' # NOTE: Using column `tetr` as input for `J01AA07` (tetracycline).
 #' # [1] "tetr"
 #'
 #' # WHONET codes

R/mdro.R

@@ -968,12 +968,12 @@ mdro <- function(x,
     }
     
     x$mono_count <- 0
-    x[drug_is_R(INH), "mono_count"] <- x[drug_is_R(INH), "mono_count"] + 1
+    x[drug_is_R(INH), "mono_count"] <- x[drug_is_R(INH), "mono_count", drop = TRUE] + 1
-    x[drug_is_R(RIF), "mono_count"] <- x[drug_is_R(RIF), "mono_count"] + 1
+    x[drug_is_R(RIF), "mono_count"] <- x[drug_is_R(RIF), "mono_count", drop = TRUE] + 1
-    x[drug_is_R(ETH), "mono_count"] <- x[drug_is_R(ETH), "mono_count"] + 1
+    x[drug_is_R(ETH), "mono_count"] <- x[drug_is_R(ETH), "mono_count", drop = TRUE] + 1
-    x[drug_is_R(PZA), "mono_count"] <- x[drug_is_R(PZA), "mono_count"] + 1
+    x[drug_is_R(PZA), "mono_count"] <- x[drug_is_R(PZA), "mono_count", drop = TRUE] + 1
-    x[drug_is_R(RIB), "mono_count"] <- x[drug_is_R(RIB), "mono_count"] + 1
+    x[drug_is_R(RIB), "mono_count"] <- x[drug_is_R(RIB), "mono_count", drop = TRUE] + 1
-    x[drug_is_R(RFP), "mono_count"] <- x[drug_is_R(RFP), "mono_count"] + 1
+    x[drug_is_R(RFP), "mono_count"] <- x[drug_is_R(RFP), "mono_count", drop = TRUE] + 1
     
     x$mono <- x$mono_count > 0
     x$poly <- x$mono_count > 1 & drug_is_not_R(RIF) & drug_is_not_R(INH)

R/mo.R

@@ -55,7 +55,7 @@
 #'                             C (Chromista), F (Fungi), P (Protozoa)
 #' ```
 #'
-#' Values that cannot be coered will be considered 'unknown' and will get the MO code `UNKNOWN`.
+#' Values that cannot be coerced will be considered 'unknown' and will get the MO code `UNKNOWN`.
 #'
 #' Use the [`mo_*`][mo_property()] functions to get properties based on the returned code, see Examples.
 #'
@@ -77,27 +77,27 @@
 #' - Uncertainty level 2: allow all of level 1, strip values between brackets, inverse the words of the input, strip off text elements from the end keeping at least two elements;
 #' - Uncertainty level 3: allow all of level 1 and 2, strip off text elements from the end, allow any part of a taxonomic name.
 #' 
-#' This leads to e.g.:
+#' The level of uncertainty can be set using the argument `allow_uncertain`. The default is `allow_uncertain = TRUE`, which is equal to uncertainty level 2. Using `allow_uncertain = FALSE` is equal to uncertainty level 0 and will skip all rules. You can also use e.g. `as.mo(..., allow_uncertain = 1)` to only allow up to level 1 uncertainty.
+#' 
+#' With the default setting (`allow_uncertain = TRUE`, level 2), below examples will lead to valid results:
 #' - `"Streptococcus group B (known as S. agalactiae)"`. The text between brackets will be removed and a warning will be thrown that the result *Streptococcus group B* (``r as.mo("Streptococcus group B")``) needs review.
 #' - `"S. aureus - please mind: MRSA"`. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result *Staphylococcus aureus* (``r as.mo("Staphylococcus aureus")``) needs review.
 #' - `"Fluoroquinolone-resistant Neisseria gonorrhoeae"`. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result *Neisseria gonorrhoeae* (``r as.mo("Neisseria gonorrhoeae")``) needs review.
 #' 
-#' The level of uncertainty can be set using the argument `allow_uncertain`. The default is `allow_uncertain = TRUE`, which is equal to uncertainty level 2. Using `allow_uncertain = FALSE` is equal to uncertainty level 0 and will skip all rules. You can also use e.g. `as.mo(..., allow_uncertain = 1)` to only allow up to level 1 uncertainty.
+#' There are three helper functions that can be run after using the [as.mo()] function:
-#' 
+#' - Use [mo_uncertainties()] to get a [`data.frame`] with all values that were coerced to a valid value, but with uncertainty. The output contains a score, that is calculated as \eqn{(n - 0.5 * L) / n}, where *n* is the number of characters of the full taxonomic name of the microorganism, and *L* is the [Levenshtein distance](https://en.wikipedia.org/wiki/Levenshtein_distance) between that full name and the user input.
-#' There are three helper functions that can be run after then [as.mo()] function:
+#' - Use [mo_failures()] to get a [`character`] [`vector`] with all values that could not be coerced to a valid value.
-#' - Use [mo_uncertainties()] to get a [`data.frame`] with all values that were coerced to a valid value, but with uncertainty. The output contains a score, that is calculated as \eqn{(n - 0.5 * L) / n}, where *n* is the number of characters of the returned full name of the microorganism, and *L* is the [Levenshtein distance](https://en.wikipedia.org/wiki/Levenshtein_distance) between that full name and the user input.
+#' - Use [mo_renamed()] to get a [`data.frame`] with all values that could be coerced based on old, previously accepted taxonomic names.
-#' - Use [mo_failures()] to get a [`vector`] with all values that could not be coerced to a valid value.
-#' - Use [mo_renamed()] to get a [`data.frame`] with all values that could be coerced based on an old, previously accepted taxonomic name.
 #'
 #' ## Microbial prevalence of pathogens in humans
 #' 
 #' The intelligent rules consider the prevalence of microorganisms in humans grouped into three groups, which is available as the `prevalence` columns in the [microorganisms] and [microorganisms.old] data sets. The grouping into prevalence groups is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence.
 #' 
-#' Group 1 (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is  *Enterococcus*, *Staphylococcus* or *Streptococcus*. This group consequently contains all common Gram-negative bacteria, such as *Pseudomonas* and *Legionella* and all species within the order Enterobacteriales. 
+#' Group 1 (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is  *Enterococcus*, *Staphylococcus* or *Streptococcus*. This group consequently contains all common Gram-negative bacteria, such as *Klebsiella*, *Pseudomonas* and *Legionella*.
 #' 
-#' Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is *Aspergillus*, *Bacteroides*, *Candida*, *Capnocytophaga*, *Chryseobacterium*, *Cryptococcus*, *Elisabethkingia*, *Flavobacterium*, *Fusobacterium*, *Giardia*, *Leptotrichia*, *Mycoplasma*, *Prevotella*, *Rhodotorula*, *Treponema*, *Trichophyton* or *Ureaplasma*. 
+#' Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is *Aspergillus*, *Bacteroides*, *Candida*, *Capnocytophaga*, *Chryseobacterium*, *Cryptococcus*, *Elisabethkingia*, *Flavobacterium*, *Fusobacterium*, *Giardia*, *Leptotrichia*, *Mycoplasma*, *Prevotella*, *Rhodotorula*, *Treponema*, *Trichophyton* or *Ureaplasma*. This group consequently contains all less common and rare human pathogens.
 #' 
-#' Group 3 (least prevalent microorganisms) consists of all other microorganisms.
+#' Group 3 (least prevalent microorganisms) consists of all other microorganisms. This group contains microorganisms most probably not found in humans.
 #' @inheritSection catalogue_of_life Catalogue of Life
 #  (source as a section here, so it can be inherited by other man pages:)
 #' @section Source:
@@ -106,7 +106,7 @@
 #' 3. Lancefield RC **A serological differentiation of human and other groups of hemolytic streptococci**. 1933. J Exp Med. 57(4): 571–95. <https://dx.doi.org/10.1084/jem.57.4.571>
 #' 4. Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]).
 #' @export
-#' @return A [`character`] vector with class [`mo`]
+#' @return A [`character`] [`vector`] with additional class [`mo`]
 #' @seealso [microorganisms] for the [`data.frame`] that is being used to determine ID's.
 #' 
 #' The [mo_property()] functions (like [mo_genus()], [mo_gramstain()]) to get properties based on the returned code.
@@ -177,6 +177,8 @@ as.mo <- function(x,
   
   # start off with replaced language-specific non-ASCII characters with ASCII characters
   x <- parse_and_convert(x)
+  # replace mo codes used in older package versions
+  x <- replace_old_mo_codes(x)
 
   # WHONET: xxx = no growth
   x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
@@ -288,6 +290,8 @@ exec_as.mo <- function(x,
   
   # start off with replaced language-specific non-ASCII characters with ASCII characters
   x <- parse_and_convert(x)
+  # replace mo codes used in older package versions
+  x <- replace_old_mo_codes(x)
   
   # WHONET: xxx = no growth
   x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
@@ -324,30 +328,6 @@ exec_as.mo <- function(x,
          & !identical(x, "")
          & !identical(x, "xxx")]
   
-  # conversion of old MO codes from v0.5.0 (ITIS) to later versions (Catalogue of Life)
-  if (any(x %like_case% "^[BFP]_[A-Z]{3,7}") & !all(x %in% microorganisms$mo)) {
-    leftpart <- gsub("^([BFP]_[A-Z]{3,7}).*", "\\1", x)
-    if (any(leftpart %in% names(mo_codes_v0.5.0))) {
-      old_mo_warning <- TRUE
-      rightpart <- gsub("^[BFP]_[A-Z]{3,7}(.*)", "\\1", x)
-      leftpart <- mo_codes_v0.5.0[leftpart]
-      x[!is.na(leftpart)] <- paste0(leftpart[!is.na(leftpart)], rightpart[!is.na(leftpart)])
-    }
-    # now check if some are still old
-    still_old <- x[x %in% names(mo_codes_v0.5.0)]
-    if (length(still_old) > 0) {
-      old_mo_warning <- TRUE
-      x[x %in% names(mo_codes_v0.5.0)] <- data.frame(old = still_old, stringsAsFactors = FALSE) %>%
-        left_join(data.frame(old = names(mo_codes_v0.5.0),
-                             new = mo_codes_v0.5.0,
-                             stringsAsFactors = FALSE), by = "old") %>%
-        # if they couldn't be found, replace them with the old ones again,
-        # so they will throw a warning in the end
-        mutate(new = ifelse(is.na(new), old, new)) %>%
-        pull(new)
-    }
-  }
-  
   # defined df to check for
   if (!is.null(reference_df)) {
     mo_source_isvalid(reference_df)
@@ -412,15 +392,6 @@ exec_as.mo <- function(x,
     #                            on = "mo",
     #                            ..property][[1]]
     
-  } else if (all(x %in% microorganisms.translation$mo_old)) {
-    # is an old mo code, used in previous versions of this package
-    old_mo_warning <- TRUE
-    x <- data.frame(mo_old = toupper(x), stringsAsFactors = FALSE) %>%
-      left_join(microorganisms.translation, by = "mo_old") %>%
-      rename(mo = mo_new) %>% 
-      left_join_MO_lookup(by = "mo") %>%
-      pull(property)
-    
   } else if (!all(x %in% microorganisms[, property])) {
     
     strip_whitespace <- function(x, dyslexia_mode) {
@@ -592,18 +563,6 @@ exec_as.mo <- function(x,
         next
       }
       
-      # old mo code, used in previous versions of this package ----
-      if (x_backup[i] %in% microorganisms.translation$mo_old) {
-        old_mo_warning <- TRUE
-        found <- lookup(mo_old == toupper(x_backup[i]), column = "mo_new", haystack = microorganisms.translation)
-        found <- lookup(mo == found)
-        if (!is.na(found)) {
-          # get property
-          x[i] <- found[1L]
-          next
-        }
-      }
-      
       if (x_backup[i] %like_case% "\\(unknown [a-z]+\\)" | tolower(x_backup_without_spp[i]) %in% c("other", "none", "unknown")) {
         # empty and nonsense values, ignore without warning
         x[i] <- lookup(mo == "UNKNOWN")
@@ -1584,12 +1543,14 @@ summary.mo <- function(object, ...) {
   x <- as.mo(object) # force again, could be mo from older pkg version
   top <- as.data.frame(table(x), responseName = "n", stringsAsFactors = FALSE)
   top_3 <- top[order(-top$n), 1][1:3]
-  c("Class" = "mo",
+  value <- c("Class" = "mo",
     "<NA>" = length(x[is.na(x)]),
     "Unique" = n_distinct(x[!is.na(x)]),
     "#1" = top_3[1],
     "#2" = top_3[2],
     "#3" = top_3[3])
+  class(value) <- c("summaryDefault", "table")
+  value
 }
 
 #' @method as.data.frame mo
@@ -1821,6 +1782,18 @@ parse_and_convert <- function(x) {
   parsed
 }
 
+replace_old_mo_codes <- function(x) {
+  if (any(toupper(x) %in% microorganisms.translation$mo_old, na.rm = TRUE)) {
+    # get the ones that match
+    matched <- match(toupper(x), microorganisms.translation$mo_old)
+    # and their new codes
+    mo_new <- microorganisms.translation$mo_new[matched]
+    # assign on places where a match was found
+    x[which(!is.na(matched))] <- mo_new[which(!is.na(matched))]
+  }
+  x
+}
+
 left_join_MO_lookup <- function(x, ...) {
   left_join(x = x, y = MO_lookup, ...)
 }

R/mo_property.R

@@ -437,8 +437,6 @@ mo_validate <- function(x, property, ...) {
   
   if (property == "mo") {
     return(to_class_mo(x))
-  } else if (property == "col_id") {
-    return(as.integer(x))
   } else if (property == "snomed") {
     return(as.double(eval(parse(text = x))))
   } else {

R/rsi.R

@@ -550,13 +550,15 @@ summary.rsi <- function(object, ...) {
   S <- sum(x == "S", na.rm = TRUE)
   I <- sum(x == "I", na.rm = TRUE)
   R <- sum(x == "R", na.rm = TRUE)
-  c(
+  value <- c(
     "Class" = "rsi",
     "%R" = paste0(percentage(R / n), " (n=", R, ")"),
     "%SI" = paste0(percentage((S + I) / n), " (n=", S + I, ")"),
     "- %S" = paste0(percentage(S / n), " (n=", S, ")"),
     "- %I" = paste0(percentage(I / n), " (n=", I, ")")
   )
+  class(value) <- c("summaryDefault", "table")
+  value
 }
 
 #' @method plot rsi

R/zzz.R

@@ -27,10 +27,6 @@
   assign(x = "MO.old_lookup",
          value = create_MO.old_lookup(),
          envir = asNamespace("AMR"))
-  
-  assign(x = "mo_codes_v0.5.0",
-         value = make_trans_tbl(),
-         envir = asNamespace("AMR"))
 }
 
 # maybe add survey later: "https://www.surveymonkey.com/r/AMR_for_R"
@@ -44,8 +40,7 @@ create_MO_lookup <- function() {
   MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3
   MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
   
-  # use this paste instead of `fullname` to
+  # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
-  # work with Viridans Group Streptococci, etc.
   MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus, 
                                                    MO_lookup$species,
                                                    MO_lookup$subspecies)))
@@ -62,9 +57,6 @@ create_MO_lookup <- function() {
 
 create_MO.old_lookup <- function() {
   MO.old_lookup <- AMR::microorganisms.old
-  
-  # use this paste instead of `fullname` to
-  # work with Viridans Group Streptococci, etc.
   MO.old_lookup$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname)))
   
   # add a column with only "e coli" like combinations
@@ -73,202 +65,3 @@ create_MO.old_lookup <- function() {
   # so arrange data on prevalence first, then full name
   MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), ]
 }
-
-make_trans_tbl <- function() {
-  # conversion of old MO codes from v0.5.0 (ITIS) to later versions (Catalogue of Life)
-  c(B_ACHRMB = "B_ACHRM", B_ANNMA = "B_ACTNS", B_ACLLS = "B_ALCYC",
-    B_AHNGM = "B_ARCHN", B_ARMTM = "B_ARMTMN", B_ARTHR = "B_ARTHRB", B_ARTHRS = "B_ARTHR",
-    B_APHLS = "B_AZRHZP", B_BRCHA = "B_BRCHY", B_BCTRM = "B_BRVBCT",
-    B_CLRBCT = "B_CLRBC", B_CTRDM = "B_CLSTR", B_CPRMM = "B_CYLND",
-    B_DLCLN = "B_DPLCL", B_DMCLM = "B_DSLFT", B_DSLFVB = "B_DSLFV",
-    B_FCTRM = "B_FSBCT", B_GNRLA = "B_GRDNR", B_HNRBM = "B_HLNRB",
-    B_HPHGA = "B_HNPHGA", B_HCCCS = "B_HYDRC", B_MCRCLS = "B_MCRCL",
-    B_MTHYLS = "B_MLSMA", B_MARCLS = "B_MRCLS", B_MGCLS = "B_MSTGC",
-    B_MCLLA = "B_MTHYLC", B_MYCPLS = "B_MYCPL", B_NBCTR = "B_NTRBC",
-    B_OCLLS = "B_OCNBC", B_PTHRX = "B_PLNKT", B_PCCCS = "B_PRCHL",
-    B_PSPHN = "B_PRPHY", B_PDMNS = "B_PSDMN", B_SCCHRP = "B_SCCHR",
-    B_SRBCTR = "B_SHRBCTR", B_STRPTC = "B_STRPT", B_SHMNS = "B_SYNTR",
-    B_TRBCTR = "B_THRMN", P_ALBMN = "C_ABMNA", F_ACHLY = "C_ACHLY",
-    P_ACINT = "C_ACINT", P_ARTCL = "C_ACLNA", P_ACRVL = "C_ACRVL",
-    P_ADRCT = "C_ADRCT", P_AMPHS = "C_AHSRS", F_ALBUG = "C_ALBUG",
-    P_ALCNT = "C_ALCNT", P_ALFRD = "C_ALFRD", P_ALLGR = "C_ALLGR",
-    P_AMPHL = "C_ALPTS", F_ALTHR = "C_ALTHR", P_AMLLA = "C_AMLLA",
-    P_ANMLN = "C_AMLNA", P_AMMBC = "C_AMMBC", P_AMMDS = "C_AMMDS",
-    P_AMMLG = "C_AMMLG", P_AMMMR = "C_AMMMR", P_AMMMS = "C_AMMMS",
-    P_AMMON = "C_AMMON", P_AMMSC = "C_AMMSC", P_AMMSP = "C_AMMSP",
-    P_AMMST = "C_AMMST", P_AMMTM = "C_AMMTM", F_AMYCS = "C_AMYCS",
-    P_ANARM = "C_ANARM", P_ANGLD = "C_ANGLD", P_ANGLG = "C_ANGLG",
-    P_ANNLC = "C_ANNLC", F_ANSLP = "C_ANSLP", F_APDCH = "C_APDCH",
-    F_APHND = "C_APHND", F_APLNC = "C_APLNC", F_AQLND = "C_AQLND",
-    P_ARCHS = "C_ARCHAS", P_ASTRN = "C_ARNNN", P_ARNPR = "C_ARNPR",
-    F_ARSPR = "C_ARSPR", P_ARTST = "C_ARTSTR", P_AMPHC = "C_ARYNA",
-    P_ASCHM = "C_ASCHM", P_ASPDS = "C_ASPDS", P_ASTCL = "C_ASTCL",
-    P_ASTRG = "C_ASTRGR", P_ASTRM = "C_ASTRMM", P_ASTRR = "C_ASTRR",
-    P_ASTRT = "C_ASTRTR", F_ATKNS = "C_ATKNS", F_AYLLA = "C_AYLLA",
-    P_BAGGN = "C_BAGGN", P_BCCLL = "C_BCCLL", P_BDLLD = "C_BDLLD",
-    P_BGNRN = "C_BGNRN", P_BLCLN = "C_BLCLN", P_BLMND = "C_BLMND",
-    P_BLMNL = "C_BLMNL", P_BLPHR = "C_BLPHR", P_BLVNT = "C_BLVNT",
-    P_BOLVN = "C_BOLVN", P_BORLS = "C_BORLS", P_BRNNM = "C_BRNNM",
-    P_BRSLN = "C_BRSLN", P_BRSRD = "C_BRSRD", F_BRVLG = "C_BRVLG",
-    F_BNLLA = "C_BRVLGN", P_BSCCM = "C_BSCCM", F_BSDPH = "C_BSDPH",
-    P_BTHYS = "C_BTHYS", P_BTLLN = "C_BTLLN", P_BULMN = "C_BULMN",
-    P_CCLDM = "C_CCLDM", P_CDNLL = "C_CDNLL", P_CLPSS = "C_CDNLLP",
-    P_CHLDN = "C_CHLDNL", P_CHLST = "C_CHLST", P_CHNLM = "C_CHNLM",
-    P_CHRYS = "C_CHRYSL", P_CHTSP = "C_CHTSP", P_CBCDS = "C_CIBCDS",
-    P_CLCRN = "C_CLCRN", P_CLMNA = "C_CLMNA", P_CLPDM = "C_CLPDM",
-    P_CLPHR = "C_CLPHRY", P_CLVLN = "C_CLVLN", P_CMPNL = "C_CMPNL",
-    P_CNCRS = "C_CNCRS", P_CNTCH = "C_CNTCH", F_CNTRM = "C_CNTRMY",
-    P_COLPD = "C_COLPD", P_COLPS = "C_COLPS", P_CPRDS = "C_CPRDS",
-    P_CRNSP = "C_CPRMA", P_CRBNL = "C_CRBNL", P_CRBRB = "C_CRBRB",
-    P_CRBRG = "C_CRBRG", P_CRBRS = "C_CRBRS", P_CRCHS = "C_CRCHS",
-    P_CRCLC = "C_CRCLC", P_CRNLC = "C_CRNLC", P_CRNTH = "C_CRNTH",
-    P_CRPNT = "C_CRPNT", P_CRSTG = "C_CRSTG", P_CRTHN = "C_CRTHN",
-    P_CRTRN = "C_CRTRN", P_CYMBL = "C_CRTTA", P_CRYPT = "C_CRYPT",
-    P_CSHMN = "C_CSHMNL", P_CSSDL = "C_CSSDL", P_CLNDS = "C_CSSDLN",
-    P_CHRNA = "C_CTHRN", P_CTPSS = "C_CTPSS", P_CUNLN = "C_CUNLN",
-    P_CYLND = "C_CVLNA", P_CYCLC = "C_CYCLCB", P_CDNTA = "C_CYCLD",
-    P_CYCLG = "C_CYCLG", P_CYCLM = "C_CYCLM", P_CYRTL = "C_CYRTL",
-    P_CYSTM = "C_CYSTM", P_DCHLM = "C_DCHLM", P_DCRBS = "C_DCRBS",
-    P_DCTYC = "C_DCTYC", P_DIDNM = "C_DIDNM", P_DLPTS = "C_DLPTS",
-    P_DNTLN = "C_DNTLN", P_DNTST = "C_DNTST", P_DORTH = "C_DORTH",
-    P_DCTYP = "C_DPHMS", F_DPLCY = "C_DPLCY", P_DNDRT = "C_DRTNA",
-    P_DSCMM = "C_DSCMM", P_DSCRB = "C_DSCRB", P_DSCRN = "C_DSCRN",
-    P_DSCSP = "C_DSCSP", P_DSNBR = "C_DSNBR", P_DYCBC = "C_DYCBC",
-    F_DCTYC = "C_DYCHS", F_ECTRG = "C_ECTRG", B_EDWRD = "C_EDWRD",
-    P_EGGRL = "C_EGGRL", P_EHLYS = "C_EHLYS", P_EHRNB = "C_EHRNB",
-    P_ELPHD = "C_ELPHD", P_ENCHL = "C_ELYDM", P_EPHDM = "C_EPHDM",
-    P_EPLTS = "C_EPLTS", P_EPLXL = "C_EPLXL", P_EPNDL = "C_EPNDL",
-    P_EPNDS = "C_EPNDS", P_ENLLA = "C_EPSTM", P_EPSTY = "C_EPSTY",
-    F_ERYCH = "C_ERYCH", F_ESMDM = "C_ESMDM", P_ESSYR = "C_ESSYR",
-    P_FSCHR = "C_FHRNA", P_FLRLS = "C_FLRLS", P_FLNTN = "C_FNTNA",
-    P_FRNDC = "C_FRNDC", P_FRNTN = "C_FRNTN", P_FRSNK = "C_FRSNK",
-    P_FNLLA = "C_FSCHRN", P_FSSRN = "C_FSSRN", P_FVCSS = "C_FVCSS",
-    P_GDRYN = "C_GDRYN", F_GELGN = "C_GELGN", P_GERDA = "C_GERDA",
-    P_GLACM = "C_GLACM", P_GLBBL = "C_GLBBL", P_GLBGR = "C_GLBGR",
-    P_GLBLN = "C_GLBLN", P_GRTLA = "C_GLBRT", P_GLBTX = "C_GLBTX",
-    P_GLLNA = "C_GLLNA", P_GLMSP = "C_GLMSP", P_GLNDL = "C_GLNDL",
-    F_GNMCH = "C_GNMCH", P_GOSLL = "C_GOSLL", P_GRNDS = "C_GRNDS",
-    P_GRNTA = "C_GRNTA", P_GLBRT = "C_GTLLA", P_GTTLN = "C_GTTLN",
-    P_GVLNP = "C_GVLNP", P_GYPSN = "C_GYPSN", P_GYRDN = "C_GYRDN",
-    P_HALTR = "C_HALTR", P_HANZW = "C_HANZW", P_HAURN = "C_HAURN",
-    P_HELNN = "C_HELNN", P_HLPHR = "C_HHRYA", P_HLNTA = "C_HLNTA",
-    F_HLPHT = "C_HLPHT", P_HLSTC = "C_HLSTC", P_HMSPH = "C_HMSPH",
-    P_HMTRM = "C_HMTRM", P_HPKNS = "C_HPKNS", P_HPLPH = "C_HPLPH",
-    P_HPPCR = "C_HPPCR", P_HNLLA = "C_HPPCRP", P_HRMSN = "C_HRMSN",
-    P_HRNLL = "C_HRNLL", F_HRPCH = "C_HRPCH", P_HSTGR = "C_HSTGR",
-    P_HSTTL = "C_HSTTL", P_HTRST = "C_HTGNA", P_HTRLL = "C_HTRLL",
-    P_HTRPH = "C_HTRPH", F_HYPHC = "C_HYPHC", P_HYPRM = "C_HYPRM",
-    P_INTRN = "C_INTRN", P_IRIDI = "C_IRIDI", P_ISLND = "C_ISLND",
-    P_JCLLL = "C_JCLLL", P_KHLLL = "C_KHLLL", P_KRNPS = "C_KRNPS",
-    P_KRRRL = "C_KRRRL", P_LABOE = "C_LABOE", P_LAGEN = "C_LAGEN",
-    P_LBSLL = "C_LBSLL", F_LTHLA = "C_LBYRN", P_LCRYM = "C_LCRYM",
-    P_LEMBS = "C_LEMBS", F_LGNDM = "C_LGNDM", P_LGNMM = "C_LGNMM",
-    P_LGNPH = "C_LGNPHR", F_LGNSM = "C_LGNSM", P_LGYNP = "C_LGYNP",
-    P_LITTB = "C_LITTB", P_LITUL = "C_LITUL", P_LMBDN = "C_LMBDN",
-    P_LMRCK = "C_LMRCK", F_LBYRN = "C_LMYXA", P_LNGLN = "C_LNGLN",
-    P_LNTCL = "C_LNTCL", P_LOXDS = "C_LOXDS", F_LPTLG = "C_LPTLG",
-    F_LNLLA = "C_LPTLGN", F_LPTMT = "C_LPTMT", P_LRYNG = "C_LRYNG",
-    P_LTCRN = "C_LTCRN", P_LTHPL = "C_LTHPL", P_LTNTS = "C_LTNTS",
-    F_LTRST = "C_LTRST", P_LXPHY = "C_LXPHY", P_MCRTH = "C_MCRTH",
-    P_MELNS = "C_MELNS", P_MSDNM = "C_MESDNM", P_METPS = "C_METPS",
-    P_MIMSN = "C_MIMSN", P_MINCN = "C_MINCN", P_MLLNL = "C_MLLNL",
-    P_MLMMN = "C_MLMMN", F_MNDNL = "C_MNDNL", P_MNLYS = "C_MNLYS",
-    P_MNPSS = "C_MNPSS", P_MRGNL = "C_MRGNL", P_MRGNP = "C_MRGNP",
-    P_MRSPL = "C_MRSPL", P_MRTNT = "C_MRTNT", P_MSSLN = "C_MSSLN",
-    P_MSSSS = "C_MSSSS", P_MTCNT = "C_MTCNT", P_MYCHS = "C_MYCHS",
-    P_MYSCH = "C_MYSCH", F_MYZCY = "C_MYZCY", P_NASSL = "C_NASSL",
-    P_NBCLN = "C_NBCLN", P_NBCLR = "C_NBCLR", P_NCNRB = "C_NCNRB",
-    P_NDBCL = "C_NDBCL", P_NRLLA = "C_NDBCLR", P_NMMLC = "C_NMMLC",
-    F_NMTPH = "C_NMTPH", P_NNNLL = "C_NNNLL", P_NODSR = "C_NODSR",
-    P_NONIN = "C_NONIN", P_NOURI = "C_NOURI", P_OCLNA = "C_OCLNA",
-    P_OGLNA = "C_OGLNA", P_OPHTH = "C_OLMDM", F_OLPDP = "C_OLPDP",
-    P_ONYCH = "C_OMPSS", P_OOLIN = "C_OOLIN", P_OPRCL = "C_OPRCL",
-    P_ORBLN = "C_ORBLN", F_ORCAD = "C_ORCAD", P_ORDRS = "C_ORDRS",
-    P_OPHRY = "C_ORYDM", P_OSNGL = "C_OSNGL", P_OXYTR = "C_OXYTR",
-    P_PARRN = "C_PARRN", P_PATRS = "C_PATRS", P_PAVNN = "C_PAVNN",
-    P_PTYCH = "C_PCYLS", P_PDPHR = "C_PDPHR", P_PELSN = "C_PELSN",
-    F_PHGMY = "C_PHGMY", F_PSDSP = "C_PHRTA", P_PHRYG = "C_PHRYG",
-    P_PHYSL = "C_PHYSL", F_PHYTP = "C_PHYTP", P_PLACS = "C_PLACS",
-    P_PLCPS = "C_PLCPS", P_PLCPSL = "C_PLCPSL", P_PLCTN = "C_PLCTN",
-    P_PLGPH = "C_PLGPH", B_PLGTH = "C_PLGTH", P_PLMRN = "C_PLMRN",
-    P_PLNCT = "C_PLNCT", P_PLNDSC = "C_PLNDSC", P_PLNGY = "C_PLNGY",
-    P_PLNRBL = "C_PLNLLA", P_PLNLN = "C_PLNLN", P_PLNLR = "C_PLNLR",
-    P_PLNRB = "C_PLNRB", P_PLNSP = "C_PLNSPR", P_PLRNM = "C_PLRNM",
-    P_PLRST = "C_PLRST", P_PLRTR = "C_PLRTR", F_PLSMD = "C_PLSMD",
-    P_PLTYC = "C_PLTYC", P_PSDBL = "C_PLVNA", P_PLYMR = "C_PLYMR",
-    P_PLTYN = "C_PNMTM", P_PNRPL = "C_PNRPL", F_PNTSM = "C_PNTSM",
-    P_PRCNT = "C_PRCNT", P_PRFSS = "C_PRFSS", P_PRMCM = "C_PRMCUM",
-    F_PRNSP = "C_PRNSP", P_PRPND = "C_PRPND", P_PRPYX = "C_PRPYX",
-    P_PRRDN = "C_PRRDN", P_PSDDF = "C_PSDDF", P_PSDMC = "C_PSDMC",
-    P_PSDND = "C_PSDND", P_PSDNN = "C_PSDNN", P_PSDPL = "C_PSDPLY",
-    P_PSMMS = "C_PSMMS", P_PTLLN = "C_PTLLN", P_PTLLND = "C_PTLLND",
-    F_PTRSN = "C_PTRSN", P_PULLN = "C_PULLN", P_PUTLN = "C_PUTLN",
-    P_PRTTR = "C_PYMNA", P_PYRGL = "C_PYRGL", P_PYRGO = "C_PYRGO",
-    P_PYRLN = "C_PYRLN", F_PYTHM = "C_PYTHIM", F_PYTHL = "C_PYTHL",
-    P_PYXCL = "C_PYXCL", P_QNQLC = "C_QNQLC", P_RAMLN = "C_RAMLN",
-    P_RBRTN = "C_RBRTN", P_RCRVD = "C_RCRVD", P_RCTBL = "C_RCTBL",
-    P_RCTCB = "C_RCTCB", P_RCTGL = "C_RCTGL", P_RCTVG = "C_RCTVG",
-    P_RDGDR = "C_RDGDR", P_REMNC = "C_REMNC", P_REPHX = "C_REPHX",
-    P_RHBDM = "C_RHBDMM", F_RHBDS = "C_RHBDSP", P_RHPDD = "C_RHPDD",
-    F_RHPDM = "C_RHPDM", F_RHZDMY = "C_RHZDM", P_RHZMM = "C_RHZMM",
-    P_RIVRN = "C_RIVRN", P_ROSLN = "C_ROSLN", P_ROTAL = "C_ROTAL",
-    P_RPHDP = "C_RPHDP", P_RPRTN = "C_RPRTN", P_RSSLL = "C_RSSLL",
-    P_RTLMM = "C_RTLMM", P_RTYLA = "C_RTYLA", P_RUGID = "C_RUGID",
-    F_RZLLP = "C_RZLLP", P_SAGRN = "C_SAGRN", P_SCCMM = "C_SCCMM",
-    P_SCCRH = "C_SCCRH", P_SCHLM = "C_SCHLM", F_SCLRS = "C_SCLRS",
-    P_SCTLR = "C_SCTLR", P_SEBRK = "C_SEBRK", P_SGMLN = "C_SGMLN",
-    P_SGMLP = "C_SGMLP", P_SGMMR = "C_SGMMR", P_SGMVR = "C_SGMVR",
-    F_SMMRS = "C_SMMRS", P_SNNDS = "C_SNNDS", P_SORTS = "C_SORTS",
-    P_SPHGN = "C_SPHGN", P_SPHNN = "C_SPHNN", P_SNLLA = "C_SPHNNL",
-    P_SPHTR = "C_SPHTR", P_SPHTX = "C_SPHTX", P_SPHVG = "C_SPHVG",
-    P_SPRDT = "C_SPRDT", P_SPRLC = "C_SPRLC", F_SPRLG = "C_SPRLG",
-    P_SPRLL = "C_SPRLL", F_SPRMY = "C_SPRMY", P_SPRPL = "C_SPRPL",
-    P_SPRSG = "C_SPRSG", P_SPRST = "C_SPRST", P_SPHNP = "C_SPRTA",
-    P_SPRZN = "C_SPRZN", P_SPHRG = "C_SPSNA", P_STHDM = "C_SPTHD",
-    P_SRCNR = "C_SRCNR", F_SRLPD = "C_SRLPD", F_SPNGS = "C_SSPRA",
-    F_STEIN = "C_STEIN", P_SPTHD = "C_STHDDS", P_STHRP = "C_STHRP",
-    P_STNFR = "C_STNFR", P_STNSM = "C_STNSM", P_STNTR = "C_STNTR",
-    P_STRBL = "C_STRBL", P_STRMB = "C_STRMB", P_STTSN = "C_STTSN",
-    P_STYLN = "C_SYCHA", F_SCHZC = "C_SYTRM", P_TBNLL = "C_TBNLL",
-    P_TRCHL = "C_TCHLS", P_TCHNT = "C_TCHNT", P_THRCL = "C_THRCL",
-    P_THRMM = "C_THRMM", P_TIARN = "C_TIARN", P_TKPHR = "C_TKPHR",
-    P_TLNMA = "C_TLNMA", P_TLYPM = "C_TLYPM", P_TMNDS = "C_TMNDS",
-    P_TMNTA = "C_TMNTA", P_TNTNN = "C_TNNDM", P_TTNNS = "C_TNTNN",
-    P_TNPSS = "C_TNTNNP", P_TONTN = "C_TONTN", P_TOSAI = "C_TOSAI",
-    P_TPHTR = "C_TPHTR", P_TRCHH = "C_TRCHH", P_TRPHS = "C_TRCHLR",
-    P_TMMNA = "C_TRCHM", P_TRCHS = "C_TRCHSP", P_TRFRN = "C_TRFRN",
-    P_TRLCL = "C_TRLCL", P_TRTXL = "C_TRTXL", P_TRTXS = "C_TRTXS",
-    P_TTRHY = "C_TTRHY", F_TTRMY = "C_TTRMY", P_TXTLR = "C_TXTLR",
-    F_THRST = "C_TYTRM", P_URLPT = "C_ULPTS", P_UNGLT = "C_UNGLT",
-    P_URCNT = "C_URCNT", P_URONM = "C_URONM", P_UROSM = "C_UROSM",
-    P_URTRC = "C_URTRC", P_URSTY = "C_UTYLA", P_UVGRN = "C_UVGRN",
-    P_VLVLN = "C_VALVLN", P_VGNLN = "C_VGNLN", P_VGNLNP = "C_VGNLNP",
-    P_VLNRA = "C_VLVLN", P_VGNCL = "C_VNCLA", P_VRGLN = "C_VRGLN",
-    P_VRGLNP = "C_VRGLNP", P_VRTCL = "C_VRTCL", P_WBBNL = "C_WBBNL",
-    P_WEBBN = "C_WEBBN", P_WSNRL = "C_WSNRL", P_ZTHMN = "C_ZHMNM",
-    B_ZOOGL = "C_ZOOGL", F_DDSCS = "F_DPDSC", F_SCCHR = "F_SMYCS",
-    P_AMTRN = "P_ACNTH", F_AMBDM = "P_AMBDM", F_ARCYR = "P_ARCYR",
-    F_BADHM = "P_BADHM", F_BDHMP = "P_BDHMP", F_BRBYL = "P_BRBYL",
-    F_BRFLD = "P_BRFLD", F_CLMYX = "P_CLMYX", F_CLSTD = "P_CLSTD",
-    F_CMTRC = "P_CMTRC", F_CRBRR = "P_CRBRR", F_CRTMY = "P_CRTMY",
-    F_CRTRM = "P_CRTRM", F_DCTYD = "P_DCTYD", F_DDYMM = "P_DDYMM",
-    F_DIACH = "P_DIACH", F_DIANM = "P_DIANM", F_DIDRM = "P_DIDRM",
-    F_ELMYX = "P_ELMYX", F_ESTLM = "P_ESTLM", F_FULIG = "P_FULIG",
-    F_HMTRC = "P_HMTRC", F_LCRPS = "P_LCRPS", F_LICEA = "P_LICEA",
-    F_LMPRD = "P_LMPRD", F_LPTDR = "P_LPTDR", F_LSTRL = "P_LSTRL",
-    F_LYCGL = "P_LYCGL", F_MCBRD = "P_MCBRD", F_MNKTL = "P_MNKTL",
-    F_MTTRC = "P_MTTRC", F_MUCLG = "P_MUCLG", F_PHYSR = "P_PHYSR",
-    F_PRCHN = "P_PRCHN", F_PRMBD = "P_PRMBD", F_PRTPH = "P_PRTPH",
-    F_PSRNA = "P_PSRNA", F_PYSRM = "P_PYSRM", F_RTCLR = "P_RTCLR",
-    F_STMNT = "P_STMNT", F_SYMPH = "P_SYMPH", F_TRBRK = "P_TRBRK",
-    F_TRICH = "P_TRICH", F_TUBFR = "P_TUBFR",
-    B_GRDNR = "B_GRLLA", B_SGMNS = "B_SNGMNS", B_TCLLS = "B_THBCL",
-    F_CCCCS = "F_CRYPT",
-    # renamings of old genus + species
-    # 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")
-}

data-raw/microorganisms.txt

@@ -11207,6 +11207,7 @@
 "F_CANDD_KAZU"	"Candida kazuoi"	"Fungi"	"Ascomycota"	"Saccharomycetes"	"Saccharomycetales"	"(unknown family)"	"Candida"	"kazuoi"	""	"species"	"Nakase et al., 2007"	"3d20db459296758ec4a5beb7a56e3a44"	"CoL"	2	
 "F_CANDD_KRSN"	"Candida keroseneae"	"Fungi"	"Ascomycota"	"Saccharomycetes"	"Saccharomycetales"	"(unknown family)"	"Candida"	"keroseneae"	""	"species"	"Buddie et al., 2011"	"83b3ea8ab59f4c455de8a30e5b4d6a28"	"CoL"	2	
 "F_CANDD_KH-T"	"Candida khao-thaluensis"	"Fungi"	"Ascomycota"	"Saccharomycetes"	"Saccharomycetales"	"(unknown family)"	"Candida"	"khao-thaluensis"	""	"species"	"Groenew et al., 2011"	"3767929e75dd19022c79bde32143733f"	"CoL"	2	
+"F_CANDD_KRUS"	"Candida krusei"	"Fungi"	"Ascomycota"	"Saccharomycetes"	"Saccharomycetales"	"(unknown family)"	"Candida"	"krusei"	""	"species"		""	"manually added"	2	"444877006"
 "F_CANDD_KUOI"	"Candida kuoi"	"Fungi"	"Ascomycota"	"Saccharomycetes"	"Saccharomycetales"	"(unknown family)"	"Candida"	"kuoi"	""	"species"	"Kurtzman, 2012"	"2ddb2646cbee79c1aaaa725927e2e4c6"	"CoL"	2	
 "F_CANDD_LBDR"	"Candida labiduridarum"	"Fungi"	"Ascomycota"	"Saccharomycetes"	"Saccharomycetales"	"(unknown family)"	"Candida"	"labiduridarum"	""	"species"	"Suh et al., 2008"	"79db540254156bc73399caaca772652e"	"CoL"	2	
 "F_CANDD_LCT-"	"Candida lactis-condensi"	"Fungi"	"Ascomycota"	"Saccharomycetes"	"Saccharomycetales"	"(unknown family)"	"Candida"	"lactis-condensi"	""	"species"	"Mey et al., 1978"	"9f04e19bd4cba3af175dbebad0f84bf0"	"CoL"	2	

data-raw/reproduction_of_microorganisms.R

@@ -667,7 +667,16 @@ MOs <- MOs %>%
              ref = NA_character_,
              species_id = "",
              source = "manually added"),
-    # Blastocystis hominis does not exist (it means 'got a Bastocystis from humans', PMID 15634993)
+    # Candida krusei
+    MOs %>%
+      filter(genus == "Candida", species == "glabrata") %>% .[1,] %>%
+      mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_KRUS", mo),
+             species = "krusei" ,
+             fullname = "Candida krusei",
+             ref = NA_character_,
+             species_id = "",
+             source = "manually added"),
+    # Blastocystis hominis does not exist (it means 'got a Blastocystis from humans', PMID 15634993)
     # but let's be nice to the clinical people in microbiology
     MOs %>%
       filter(fullname == "Blastocystis") %>%
@@ -897,6 +906,7 @@ rsi_translation$mo <- as.mo(rsi_translation$mo)
 microorganisms.codes$mo <- as.mo(microorganisms.codes$mo)
 class(microorganisms.codes$mo) <- c("mo", "character")
 microorganisms.translation <- microorganisms.translation %>%
+  # (to do: add last package version to column pkg_version)
   left_join(microorganisms.old[, c("fullname", "fullname_new")], # microorganisms.old is now new and loaded
             by = c("mo_new" = "fullname")) %>%
   mutate(name = ifelse(!is.na(fullname_new), fullname_new, mo_new)) %>% 

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9035</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9035</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9035</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9035</span>
       </span>
     </div>
 

docs/extra.js

@@ -90,8 +90,9 @@ $( document ).ready(function() {
   }
   $(".template-authors").html(doct_tit($(".template-authors").html()));
   $(".template-citation-authors").html(doct_tit($(".template-citation-authors").html()));
+  $('.template-citation-authors h1').eq(0).text('How to cite');
+  $('.template-citation-authors h1').eq(1).text('All contributors');
   $(".developers").html(doct_tit($(".developers").html()));
-  // $("footer").html(doct_tit($("footer").html()));
 
   // Edit title of manual
   $('.template-reference-index h1').text('Manual');

docs/index.html

@@ -43,7 +43,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9035</span>
       </span>
     </div>
 

docs/news/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9035</span>
       </span>
     </div>
 
@@ -229,13 +229,13 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1209034" class="section level1">
+    <div id="amr-1209035" class="section level1">
-<h1 class="page-header" data-toc-text="1.2.0.9034">
+<h1 class="page-header" data-toc-text="1.2.0.9035">
-<a href="#amr-1209034" class="anchor"></a>AMR 1.2.0.9034<small> Unreleased </small>
+<a href="#amr-1209035" class="anchor"></a>AMR 1.2.0.9035<small> Unreleased </small>
 </h1>
-<div id="last-updated-13-jul-2020" class="section level2">
+<div id="last-updated-22-july-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-13-jul-2020" class="anchor"></a><small>Last updated: 13-Jul-2020</small>
+<a href="#last-updated-22-july-2020" class="anchor"></a><small>Last updated: 22 July 2020</small>
 </h2>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
@@ -262,14 +262,20 @@
 <h3 class="hasAnchor">
 <a href="#changed" class="anchor"></a>Changed</h3>
 <ul>
-<li>Improvements for <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> and all <code>count_*()</code>, <code>proportion_*()</code> functions:
+<li>
+<p>Big speed improvement for using any function on microorganism codes from earlier package versions (prior to <code>AMR</code> v1.2.0), such as <code><a href="../reference/as.mo.html">as.mo()</a></code>, <code><a href="../reference/mo_property.html">mo_name()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>, etc.</p>
+<p>As a consequence, very old microbial codes (from <code>AMR</code> v0.5.0 and lower) <strong>are not supported anymore</strong>. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> on your microorganism names or codes to transform them to current abbreviations used in this package.</p>
+</li>
+<li>
+<p>Improvements for <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> and all <code>count_*()</code>, <code>proportion_*()</code> functions:</p>
 <ul>
-<li>95% speed improvement (!) by using other base R functions for calculation</li>
+<li>95% speed improvement by using other base R functions for calculation</li>
 <li>Using unexisting columns wil now return an error instead of dropping them silently</li>
 <li>Using variables for column names (as well as selectors like <code><a href="https://dplyr.tidyverse.org/reference/reexports.html">dplyr::all_of()</a></code>) now works again</li>
 </ul>
 </li>
-<li>Improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code>:
+<li>
+<p>Improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code>:</p>
 <ul>
 <li>Dramatic improvement of the algorithm behind <code><a href="../reference/as.ab.html">as.ab()</a></code>, making many more input errors translatable, such as digitalised health care records, using too few or too many vowels or consonants and many more</li>
 <li>Added progress bar</li>
@@ -277,17 +283,15 @@
 <li>The <code><a href="../reference/as.ab.html">as.ab()</a></code> function will now throw a note if more than 1 antimicrobial drug could be retrieved from a single input value.</li>
 </ul>
 </li>
-<li>Fixed a bug where <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> would not work on a tibble when the <code>tibble</code> or <code>dplyr</code> package was loaded</li>
+<li><p>Fixed a bug where <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> would not work on a tibble when the <code>tibble</code> or <code>dplyr</code> package was loaded</p></li>
-<li>All <code>*_join_microorganisms()</code> functions and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> now return the original data class (e.g. <code>tibble</code>s and <code>data.table</code>s)</li>
+<li><p>All <code>*_join_microorganisms()</code> functions and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> now return the original data class (e.g. <code>tibble</code>s and <code>data.table</code>s)</p></li>
-<li>Fixed a bug for using grouped versions of <code><a href="../reference/proportion.html">rsi_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code> and <code><a href="../reference/count.html">count_df()</a></code>, and fixed a bug where not all different antimicrobial results were added as rows</li>
+<li><p>Fixed a bug for using grouped versions of <code><a href="../reference/proportion.html">rsi_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code> and <code><a href="../reference/count.html">count_df()</a></code>, and fixed a bug where not all different antimicrobial results were added as rows</p></li>
-<li>Improved auto-determination for columns of types <code>&lt;mo&gt;</code> and <code>&lt;Date&gt;</code>
+<li><p>Improved auto-determination for columns of types <code>&lt;mo&gt;</code> and <code>&lt;Date&gt;</code></p></li>
-</li>
+<li><p>Fixed a bug in <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> for when only one antibiotic was in the input data</p></li>
-<li>Fixed a bug in <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> for when only one antibiotic was in the input data</li>
+<li><p>Changed the summary for class <code>&lt;rsi&gt;</code>, to highlight the %SI vs. %R</p></li>
-<li>Changed the summary for class <code>&lt;mo&gt;</code>, to highlight the %SI vs. %R</li>
+<li><p>Improved error handling, giving more useful info when functions return an error</p></li>
-<li>Improved error handling, giving more useful info when functions return an error</li>
+<li><p>Any progress bar will now only show in interactive mode (i.e. not in R Markdown)</p></li>
-<li>Any progress bar will now only show in interactive mode (i.e. not in R Markdown)</li>
+<li><p>Speed improvement for <code><a href="../reference/mdro.html">mdro()</a></code> and <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code></p></li>
-<li>Speed improvement for <code><a href="../reference/mdro.html">mdro()</a></code> and <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code>
-</li>
 </ul>
 </div>
 <div id="other" class="section level3">

docs/pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   WHONET: WHONET.html
   benchmarks: benchmarks.html
   resistance_predict: resistance_predict.html
-last_built: 2020-07-13T07:17Z
+last_built: 2020-07-22T08:18Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles

docs/reference/as.mo.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9035</span>
       </span>
     </div>
 
@@ -285,7 +285,7 @@
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> vector with class <code>mo</code></p>
+    <p>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> with additional class <code>mo</code></p>
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     
@@ -306,7 +306,7 @@
                             C (Chromista), F (Fungi), P (Protozoa)
 </pre>
 
-<p>Values that cannot be coered will be considered 'unknown' and will get the MO code <code>UNKNOWN</code>.</p>
+<p>Values that cannot be coerced will be considered 'unknown' and will get the MO code <code>UNKNOWN</code>.</p>
 <p>Use the <code><a href='mo_property.html'>mo_*</a></code> functions to get properties based on the returned code, see Examples.</p>
 <p>The algorithm uses data from the Catalogue of Life (see below) and from one other source (see <a href='microorganisms.html'>microorganisms</a>).</p>
 <p>The <code>as.mo()</code> function uses several coercion rules for fast and logical results. It assesses the input matching criteria in the following order:</p><ol>
@@ -327,17 +327,17 @@
 <li><p>Uncertainty level 3: allow all of level 1 and 2, strip off text elements from the end, allow any part of a taxonomic name.</p></li>
 </ul>
 
-<p>This leads to e.g.:</p><ul>
+<p>The level of uncertainty can be set using the argument <code>allow_uncertain</code>. The default is <code>allow_uncertain = TRUE</code>, which is equal to uncertainty level 2. Using <code>allow_uncertain = FALSE</code> is equal to uncertainty level 0 and will skip all rules. You can also use e.g. <code>as.mo(..., allow_uncertain = 1)</code> to only allow up to level 1 uncertainty.</p>
+<p>With the default setting (<code>allow_uncertain = TRUE</code>, level 2), below examples will lead to valid results:</p><ul>
 <li><p><code>"Streptococcus group B (known as S. agalactiae)"</code>. The text between brackets will be removed and a warning will be thrown that the result <em>Streptococcus group B</em> (<code>B_STRPT_GRPB</code>) needs review.</p></li>
 <li><p><code>"S. aureus - please mind: MRSA"</code>. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result <em>Staphylococcus aureus</em> (<code>B_STPHY_AURS</code>) needs review.</p></li>
 <li><p><code>"Fluoroquinolone-resistant Neisseria gonorrhoeae"</code>. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result <em>Neisseria gonorrhoeae</em> (<code>B_NESSR_GNRR</code>) needs review.</p></li>
 </ul>
 
-<p>The level of uncertainty can be set using the argument <code>allow_uncertain</code>. The default is <code>allow_uncertain = TRUE</code>, which is equal to uncertainty level 2. Using <code>allow_uncertain = FALSE</code> is equal to uncertainty level 0 and will skip all rules. You can also use e.g. <code>as.mo(..., allow_uncertain = 1)</code> to only allow up to level 1 uncertainty.</p>
+<p>There are three helper functions that can be run after using the <code>as.mo()</code> function:</p><ul>
-<p>There are three helper functions that can be run after then <code>as.mo()</code> function:</p><ul>
+<li><p>Use <code>mo_uncertainties()</code> to get a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with all values that were coerced to a valid value, but with uncertainty. The output contains a score, that is calculated as \((n - 0.5 * L) / n\), where <em>n</em> is the number of characters of the full taxonomic name of the microorganism, and <em>L</em> is the <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> between that full name and the user input.</p></li>
-<li><p>Use <code>mo_uncertainties()</code> to get a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with all values that were coerced to a valid value, but with uncertainty. The output contains a score, that is calculated as \((n - 0.5 * L) / n\), where <em>n</em> is the number of characters of the returned full name of the microorganism, and <em>L</em> is the <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> between that full name and the user input.</p></li>
+<li><p>Use <code>mo_failures()</code> to get a <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> with all values that could not be coerced to a valid value.</p></li>
-<li><p>Use <code>mo_failures()</code> to get a <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> with all values that could not be coerced to a valid value.</p></li>
+<li><p>Use <code>mo_renamed()</code> to get a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with all values that could be coerced based on old, previously accepted taxonomic names.</p></li>
-<li><p>Use <code>mo_renamed()</code> to get a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with all values that could be coerced based on an old, previously accepted taxonomic name.</p></li>
 </ul>
 
 
@@ -345,9 +345,9 @@
 
 
 <p>The intelligent rules consider the prevalence of microorganisms in humans grouped into three groups, which is available as the <code>prevalence</code> columns in the <a href='microorganisms.html'>microorganisms</a> and <a href='microorganisms.old.html'>microorganisms.old</a> data sets. The grouping into prevalence groups is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence.</p>
-<p>Group 1 (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is  <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacteriales.</p>
+<p>Group 1 (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is  <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Klebsiella</em>, <em>Pseudomonas</em> and <em>Legionella</em>.</p>
-<p>Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Aspergillus</em>, <em>Bacteroides</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Chryseobacterium</em>, <em>Cryptococcus</em>, <em>Elisabethkingia</em>, <em>Flavobacterium</em>, <em>Fusobacterium</em>, <em>Giardia</em>, <em>Leptotrichia</em>, <em>Mycoplasma</em>, <em>Prevotella</em>, <em>Rhodotorula</em>, <em>Treponema</em>, <em>Trichophyton</em> or <em>Ureaplasma</em>.</p>
+<p>Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Aspergillus</em>, <em>Bacteroides</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Chryseobacterium</em>, <em>Cryptococcus</em>, <em>Elisabethkingia</em>, <em>Flavobacterium</em>, <em>Fusobacterium</em>, <em>Giardia</em>, <em>Leptotrichia</em>, <em>Mycoplasma</em>, <em>Prevotella</em>, <em>Rhodotorula</em>, <em>Treponema</em>, <em>Trichophyton</em> or <em>Ureaplasma</em>. This group consequently contains all less common and rare human pathogens.</p>
-<p>Group 3 (least prevalent microorganisms) consists of all other microorganisms.</p>
+<p>Group 3 (least prevalent microorganisms) consists of all other microorganisms. This group contains microorganisms most probably not found in humans.</p>
 
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
 

docs/reference/guess_ab_col.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9035</span>
       </span>
     </div>
 
@@ -282,7 +282,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
 <span class='co'># [1] "tetr"</span>
 
 <span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"J01AA07"</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='co'># Note: Using column `tetr` as input for "J01AA07".</span>
+<span class='co'># NOTE: Using column `tetr` as input for `J01AA07` (tetracycline).</span>
 <span class='co'># [1] "tetr"</span>
 
 <span class='co'># WHONET codes</span>

docs/reference/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9034</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9035</span>
       </span>
     </div>
 
@@ -484,7 +484,7 @@
         <td>
           <p><code><a href="microorganisms.html">microorganisms</a></code> </p>
         </td>
-        <td><p>Data set with 67,150 microorganisms</p></td>
+        <td><p>Data set with 67,151 microorganisms</p></td>
       </tr><tr>
         
         <td>

docs/reference/microorganisms.html

@@ -6,7 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-<title>Data set with 67,150 microorganisms — microorganisms • AMR (for R)</title>
+<title>Data set with 67,151 microorganisms — microorganisms • AMR (for R)</title>
 
 <!-- favicons -->
 <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
   <link href="../extra.css" rel="stylesheet">
   <script src="../extra.js"></script>
 
-<meta property="og:title" content="Data set with 67,150 microorganisms — microorganisms" />
+<meta property="og:title" content="Data set with 67,151 microorganisms — microorganisms" />
 <meta property="og:description" content="A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using as.mo()." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
 
@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9035</span>
       </span>
     </div>
 
@@ -226,7 +226,7 @@
 <div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>Data set with 67,150 microorganisms</h1>
+    <h1>Data set with 67,151 microorganisms</h1>
     <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
     <div class="hidden name"><code>microorganisms.Rd</code></div>
     </div>
@@ -240,7 +240,7 @@
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 67,150 observations and 16 variables:</p><ul>
+    <p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 67,151 observations and 16 variables:</p><ul>
 <li><p><code>mo</code><br /> ID of microorganism as used by this package</p></li>
 <li><p><code>fullname</code><br /> Full name, like <code>"Escherichia coli"</code></p></li>
 <li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br /> Taxonomic rank of the microorganism</p></li>
@@ -256,13 +256,14 @@
 
     <p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p>
 <p>Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786</p>
-<p>Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <a href='https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date'>https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date</a> (check included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p>
+<p>Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <a href='https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date'>https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date</a> and <a href='https://lpsn.dsmz.de'>https://lpsn.dsmz.de</a> (check included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p>
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     <p>Manually added were:</p><ul>
 <li><p>11 entries of <em>Streptococcus</em> (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)</p></li>
 <li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative (CoNS) and coagulase-positive (CoPS))</p></li>
 <li><p>3 entries of <em>Trichomonas</em> (<em>Trichomonas vaginalis</em>, and its family and genus)</p></li>
+<li><p>1 entry of <em>Candida</em> (<em>Candida krusei</em>), that is not (yet) in the Catalogue of Life</p></li>
 <li><p>1 entry of <em>Blastocystis</em> (<em>Blastocystis hominis</em>), although it officially does not exist (Noel <em>et al.</em> 2005, PMID 15634993)</p></li>
 <li><p>5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)</p></li>
 <li><p>6 families under the Enterobacterales order, according to Adeolu <em>et al.</em> (2016, PMID 27620848), that are not (yet) in the Catalogue of Life</p></li>
@@ -284,8 +285,9 @@
 
     
 
-<p>Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.</p>
+<p>Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
-<p>From: <a href='https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date/complete-list-readme'>https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date/complete-list-readme</a></p>
+<em>(from <a href='https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date/complete-list-readme'>https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date/complete-list-readme</a>)</em></p>
+<p>In February 2020, the DSMZ records were merged with the List of Prokaryotic names with Standing in Nomenclature (LPSN).</p>
     <h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
 
     

docs/reference/rsi_translation.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9035</span>
       </span>
     </div>
 
@@ -255,7 +255,7 @@
 
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
-    <p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.</p>
+    <p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically.</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>
 
     

git_premaster.sh

@@ -85,7 +85,7 @@ if [ -z "$3" ]; then
   # combine tag (e.g. 0.1.0) and commit number (like 40) increased by 9000 to indicate beta version
   new_version="$current_tag.$((current_commit + 9000))" # results in 0.1.0.9040
   # add date to 2nd line of NEWS.md when no version number was set
-  sed -i -- "2s/.*/## \<small\>Last updated: $(date '+%d-%b-%Y')\<\/small\>/" NEWS.md
+  sed -i -- "2s/.*/## \<small\>Last updated: $(date '+%e %B %Y')\<\/small\>/" NEWS.md
 else
   # version number set in command
   new_version=$3

man/as.mo.Rd

@@ -44,7 +44,7 @@ This excludes \emph{Enterococci} at default (who are in group D), use \code{Lanc
 \item{...}{other parameters passed on to functions}
 }
 \value{
-A \code{\link{character}} vector with class \code{\link{mo}}
+A \code{\link{character}} \code{\link{vector}} with additional class \code{\link{mo}}
 }
 \description{
 Use this function to determine a valid microorganism ID (\code{\link{mo}}). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), an abbreviation known in the field (like \code{"MRSA"}), or just a genus. Please see \emph{Examples}.
@@ -66,7 +66,7 @@ A microorganism ID from this package (class: \code{\link{mo}}) typically looks l
                             C (Chromista), F (Fungi), P (Protozoa)
 }
 
-Values that cannot be coered will be considered 'unknown' and will get the MO code \code{UNKNOWN}.
+Values that cannot be coerced will be considered 'unknown' and will get the MO code \code{UNKNOWN}.
 
 Use the \code{\link[=mo_property]{mo_*}} functions to get properties based on the returned code, see Examples.
 
@@ -92,20 +92,20 @@ In addition, the \code{\link[=as.mo]{as.mo()}} function can differentiate four l
 \item Uncertainty level 3: allow all of level 1 and 2, strip off text elements from the end, allow any part of a taxonomic name.
 }
 
-This leads to e.g.:
+The level of uncertainty can be set using the argument \code{allow_uncertain}. The default is \code{allow_uncertain = TRUE}, which is equal to uncertainty level 2. Using \code{allow_uncertain = FALSE} is equal to uncertainty level 0 and will skip all rules. You can also use e.g. \code{as.mo(..., allow_uncertain = 1)} to only allow up to level 1 uncertainty.
+
+With the default setting (\code{allow_uncertain = TRUE}, level 2), below examples will lead to valid results:
 \itemize{
 \item \code{"Streptococcus group B (known as S. agalactiae)"}. The text between brackets will be removed and a warning will be thrown that the result \emph{Streptococcus group B} (\code{B_STRPT_GRPB}) needs review.
 \item \code{"S. aureus - please mind: MRSA"}. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result \emph{Staphylococcus aureus} (\code{B_STPHY_AURS}) needs review.
 \item \code{"Fluoroquinolone-resistant Neisseria gonorrhoeae"}. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result \emph{Neisseria gonorrhoeae} (\code{B_NESSR_GNRR}) needs review.
 }
 
-The level of uncertainty can be set using the argument \code{allow_uncertain}. The default is \code{allow_uncertain = TRUE}, which is equal to uncertainty level 2. Using \code{allow_uncertain = FALSE} is equal to uncertainty level 0 and will skip all rules. You can also use e.g. \code{as.mo(..., allow_uncertain = 1)} to only allow up to level 1 uncertainty.
+There are three helper functions that can be run after using the \code{\link[=as.mo]{as.mo()}} function:
-
-There are three helper functions that can be run after then \code{\link[=as.mo]{as.mo()}} function:
 \itemize{
-\item Use \code{\link[=mo_uncertainties]{mo_uncertainties()}} to get a \code{\link{data.frame}} with all values that were coerced to a valid value, but with uncertainty. The output contains a score, that is calculated as \eqn{(n - 0.5 * L) / n}, where \emph{n} is the number of characters of the returned full name of the microorganism, and \emph{L} is the \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{Levenshtein distance} between that full name and the user input.
+\item Use \code{\link[=mo_uncertainties]{mo_uncertainties()}} to get a \code{\link{data.frame}} with all values that were coerced to a valid value, but with uncertainty. The output contains a score, that is calculated as \eqn{(n - 0.5 * L) / n}, where \emph{n} is the number of characters of the full taxonomic name of the microorganism, and \emph{L} is the \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{Levenshtein distance} between that full name and the user input.
-\item Use \code{\link[=mo_failures]{mo_failures()}} to get a \code{\link{vector}} with all values that could not be coerced to a valid value.
+\item Use \code{\link[=mo_failures]{mo_failures()}} to get a \code{\link{character}} \code{\link{vector}} with all values that could not be coerced to a valid value.
-\item Use \code{\link[=mo_renamed]{mo_renamed()}} to get a \code{\link{data.frame}} with all values that could be coerced based on an old, previously accepted taxonomic name.
+\item Use \code{\link[=mo_renamed]{mo_renamed()}} to get a \code{\link{data.frame}} with all values that could be coerced based on old, previously accepted taxonomic names.
 }
 }
 
@@ -113,11 +113,11 @@ There are three helper functions that can be run after then \code{\link[=as.mo]{
 
 The intelligent rules consider the prevalence of microorganisms in humans grouped into three groups, which is available as the \code{prevalence} columns in the \link{microorganisms} and \link{microorganisms.old} data sets. The grouping into prevalence groups is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence.
 
-Group 1 (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is  \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacteriales.
+Group 1 (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is  \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Klebsiella}, \emph{Pseudomonas} and \emph{Legionella}.
 
-Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Aspergillus}, \emph{Bacteroides}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Chryseobacterium}, \emph{Cryptococcus}, \emph{Elisabethkingia}, \emph{Flavobacterium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Leptotrichia}, \emph{Mycoplasma}, \emph{Prevotella}, \emph{Rhodotorula}, \emph{Treponema}, \emph{Trichophyton} or \emph{Ureaplasma}.
+Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Aspergillus}, \emph{Bacteroides}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Chryseobacterium}, \emph{Cryptococcus}, \emph{Elisabethkingia}, \emph{Flavobacterium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Leptotrichia}, \emph{Mycoplasma}, \emph{Prevotella}, \emph{Rhodotorula}, \emph{Treponema}, \emph{Trichophyton} or \emph{Ureaplasma}. This group consequently contains all less common and rare human pathogens.
 
-Group 3 (least prevalent microorganisms) consists of all other microorganisms.
+Group 3 (least prevalent microorganisms) consists of all other microorganisms. This group contains microorganisms most probably not found in humans.
 }
 }
 \section{Source}{

man/guess_ab_col.Rd

@@ -43,7 +43,7 @@ guess_ab_col(df, "J01AA07") # ATC code of tetracycline
 # [1] "tetr"
 
 guess_ab_col(df, "J01AA07", verbose = TRUE)
-# Note: Using column `tetr` as input for "J01AA07".
+# NOTE: Using column `tetr` as input for `J01AA07` (tetracycline).
 # [1] "tetr"
 
 # WHONET codes

man/microorganisms.Rd

@@ -3,9 +3,9 @@
 \docType{data}
 \name{microorganisms}
 \alias{microorganisms}
-\title{Data set with 67,150 microorganisms}
+\title{Data set with 67,151 microorganisms}
 \format{
-A \code{\link{data.frame}} with 67,150 observations and 16 variables:
+A \code{\link{data.frame}} with 67,151 observations and 16 variables:
 \itemize{
 \item \code{mo}\cr ID of microorganism as used by this package
 \item \code{fullname}\cr Full name, like \code{"Escherichia coli"}
@@ -23,7 +23,7 @@ Catalogue of Life: Annual Checklist (public online taxonomic database), \url{htt
 
 Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
 
-Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, \url{https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date} (check included version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
+Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, \url{https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date} and \url{https://lpsn.dsmz.de} (check included version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
 }
 \usage{
 microorganisms
@@ -37,6 +37,7 @@ Manually added were:
 \item 11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
 \item 2 entries of \emph{Staphylococcus} (coagulase-negative (CoNS) and coagulase-positive (CoPS))
 \item 3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)
+\item 1 entry of \emph{Candida} (\emph{Candida krusei}), that is not (yet) in the Catalogue of Life
 \item 1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
 \item 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
 \item 6 families under the Enterobacterales order, according to Adeolu \emph{et al.} (2016, PMID 27620848), that are not (yet) in the Catalogue of Life
@@ -58,8 +59,9 @@ The file in R format (with preserved data structure) can be found here:
 \section{About the records from DSMZ (see source)}{
 
 Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
+\emph{(from \url{https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date/complete-list-readme})}
 
-From: \url{https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date/complete-list-readme}
+In February 2020, the DSMZ records were merged with the List of Prokaryotic names with Standing in Nomenclature (LPSN).
 }
 
 \section{Catalogue of Life}{

man/rsi_translation.Rd

@@ -26,7 +26,7 @@ rsi_translation
 Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
 }
 \details{
-The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
+The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically.
 }
 \section{Read more on our website!}{
 

pkgdown/extra.js

@@ -90,8 +90,9 @@ $( document ).ready(function() {
   }
   $(".template-authors").html(doct_tit($(".template-authors").html()));
   $(".template-citation-authors").html(doct_tit($(".template-citation-authors").html()));
+  $('.template-citation-authors h1').eq(0).text('How to cite');
+  $('.template-citation-authors h1').eq(1).text('All contributors');
   $(".developers").html(doct_tit($(".developers").html()));
-  // $("footer").html(doct_tit($("footer").html()));
 
   // Edit title of manual
   $('.template-reference-index h1').text('Manual');

tests/testthat/test-data.R

@@ -38,6 +38,7 @@ test_that("data sets are valid", {
   expect_true(all(rsi_translation$mo %in% microorganisms$mo))
   expect_false(any(is.na(microorganisms.codes$code)))
   expect_false(any(is.na(microorganisms.codes$mo)))
+  expect_false(any(microorganisms.translation$mo_old %in% microorganisms$mo))
 
   # antibiotic names must always be coercible to their original AB code
   expect_identical(antibiotics$ab, as.ab(antibiotics$name))
@@ -63,9 +64,6 @@ test_that("creation of data sets is valid", {
   expect_true(all(c("fullname", "fullname_new", "ref", "prevalence",
                     "fullname_lower", "g_species") %in% colnames(olddf)))
 
-  old <- make_trans_tbl()
-  expect_gt(length(old), 0)
-  
 })
 
 test_that("CoL version info works", {

tests/testthat/test-mo.R

@@ -25,6 +25,8 @@ test_that("as.mo works", {
   
   skip_on_cran()
   
+  library(dplyr)
+ 
   MOs <- microorganisms %>% filter(!is.na(mo), nchar(mo) > 3)
   expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo)))
   
@@ -50,7 +52,6 @@ test_that("as.mo works", {
   expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
   expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
   expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
-  expect_equal(as.character(suppressWarnings(as.mo("B_STRPTC"))), "B_STRPT") # old MO code (<=v0.5.0)
   expect_equal(as.character(suppressWarnings(as.mo("B_STRPT_PNE"))), "B_STRPT_PNMN") # old MO code (<=v0.8.0)
   
   expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("B_STRPT_GRPA", "B_STRPT_GRPB"))
@@ -145,8 +146,6 @@ test_that("as.mo works", {
   expect_identical(as.character(as.mo("S. salivarius",  Lancefield = FALSE)), "B_STRPT_SLVR")
   expect_identical(as.character(as.mo("S. salivarius",  Lancefield = TRUE)),  "B_STRPT_GRPK") # group K
 
-  library(dplyr)
-  
   # select with one column
   expect_identical(
     example_isolates[1:10, ] %>%
@@ -260,10 +259,6 @@ test_that("as.mo works", {
   
   expect_error(translate_allow_uncertain(5))
 
-  # very old MO codes (<= v0.5.0)
-  expect_equal(suppressWarnings(as.character(as.mo("F_CCCCS_NEO"))), "F_CRYPT_NFRM")
-  expect_equal(suppressWarnings(as.character(as.mo("F_CANDD_GLB"))), "F_CANDD_GLBR")
-  
   # debug mode
   expect_output(print(suppressMessages(suppressWarnings(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3)))))