(v1.3.0.9029) eucast rules fix, unique()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.3.0.9028
+Version: 1.3.0.9029
-Date: 2020-09-24
+Date: 2020-09-25
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NAMESPACE

@@ -58,6 +58,11 @@ S3method(skewness,matrix)
 S3method(summary,mic)
 S3method(summary,mo)
 S3method(summary,rsi)
+S3method(unique,ab)
+S3method(unique,disk)
+S3method(unique,mic)
+S3method(unique,mo)
+S3method(unique,rsi)
 export("%like%")
 export("%like_case%")
 export(ab_atc)
@@ -217,6 +222,7 @@ importFrom(graphics,arrows)
 importFrom(graphics,axis)
 importFrom(graphics,barplot)
 importFrom(graphics,par)
+importFrom(graphics,plot)
 importFrom(graphics,points)
 importFrom(graphics,text)
 importFrom(stats,complete.cases)

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 1.3.0.9028
+# AMR 1.3.0.9029
-## <small>Last updated: 24 September 2020</small>
+## <small>Last updated: 25 September 2020</small>
 
 Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!
 
@@ -63,6 +63,7 @@ Note: some changes in this version were suggested by anonymous reviewers from th
   * 'Penicillin G' (for intravenous use) is now named 'Benzylpenicillin' (code `PEN`)
   * 'Penicillin V' (for oral use, code `PNV`) was removed, since its actual entry 'Phenoxymethylpenicillin' (code `PHN`) already existed
   * The group name (`antibiotics$group`) of 'Linezolid' (`LNZ`), 'Cycloserine' (`CYC`), 'Tedizolid' (`TZD`) and 'Thiacetazone' (`THA`) is now "Oxazolidinones" instead of "Other antibacterials"
+* Added support for using `unique()` on classes `<rsi>`, `<mic>`, `<disk>`, `<ab>` and `<mo>`
 
 ### Other
 * Removed unnecessary references to the `base` package

R/ab.R

@@ -99,6 +99,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
   # remove diacritics
   x <- iconv(x, from = "UTF-8", to = "ASCII//TRANSLIT")
   x <- gsub('"', "", x, fixed = TRUE)
+  x <- gsub("(specimen|specimen date|specimen_date|spec_date)", "", x, ignore.case = TRUE, perl = TRUE)
   x_bak_clean <- x
   if (already_regex == FALSE) {
     x_bak_clean <- generalise_antibiotic_name(x_bak_clean)
@@ -212,26 +213,26 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
     }
     x_spelling <- x[i]
     if (already_regex == FALSE) {
-      x_spelling <- gsub("[IY]+", "[IY]+", x_spelling)
+      x_spelling <- gsub("[IY]+", "[IY]+", x_spelling, perl = TRUE)
-      x_spelling <- gsub("(C|K|Q|QU|S|Z|X|KS)+", "(C|K|Q|QU|S|Z|X|KS)+", x_spelling)
+      x_spelling <- gsub("(C|K|Q|QU|S|Z|X|KS)+", "(C|K|Q|QU|S|Z|X|KS)+", x_spelling, perl = TRUE)
-      x_spelling <- gsub("(PH|F|V)+", "(PH|F|V)+", x_spelling)
+      x_spelling <- gsub("(PH|F|V)+", "(PH|F|V)+", x_spelling, perl = TRUE)
-      x_spelling <- gsub("(TH|T)+", "(TH|T)+", x_spelling)
+      x_spelling <- gsub("(TH|T)+", "(TH|T)+", x_spelling, perl = TRUE)
-      x_spelling <- gsub("A+", "A+", x_spelling)
+      x_spelling <- gsub("A+", "A+", x_spelling, perl = TRUE)
-      x_spelling <- gsub("E+", "E+", x_spelling)
+      x_spelling <- gsub("E+", "E+", x_spelling, perl = TRUE)
-      x_spelling <- gsub("O+", "O+", x_spelling)
+      x_spelling <- gsub("O+", "O+", x_spelling, perl = TRUE)
       # allow any ending of -in/-ine and -im/-ime
-      x_spelling <- gsub("(\\[IY\\]\\+(N|M)|\\[IY\\]\\+(N|M)E\\+)$", "[IY]+(N|M)E*", x_spelling)
+      x_spelling <- gsub("(\\[IY\\]\\+(N|M)|\\[IY\\]\\+(N|M)E\\+)$", "[IY]+(N|M)E*", x_spelling, perl = TRUE)
       # allow any ending of -ol/-ole
-      x_spelling <- gsub("(O\\+L|O\\+LE\\+)$", "O+LE*", x_spelling)
+      x_spelling <- gsub("(O\\+L|O\\+LE\\+)$", "O+LE*", x_spelling, perl = TRUE)
       # allow any ending of -on/-one
-      x_spelling <- gsub("(O\\+N|O\\+NE\\+)$", "O+NE*", x_spelling)
+      x_spelling <- gsub("(O\\+N|O\\+NE\\+)$", "O+NE*", x_spelling, perl = TRUE)
       # replace multiple same characters to single one with '+', like "ll" -> "l+"
-      x_spelling <- gsub("(.)\\1+", "\\1+", x_spelling)
+      x_spelling <- gsub("(.)\\1+", "\\1+", x_spelling, perl = TRUE)
       # replace spaces and slashes with a possibility on both
-      x_spelling <- gsub("[ /]", "( .*|.*/)", x_spelling)
+      x_spelling <- gsub("[ /]", "( .*|.*/)", x_spelling, perl = TRUE)
       # correct for digital reading text (OCR)
-      x_spelling <- gsub("[NRD8B]", "[NRD8B]", x_spelling)
+      x_spelling <- gsub("[NRD8B]", "[NRD8B]", x_spelling, perl = TRUE)
-      x_spelling <- gsub("(O|0)", "(O|0)+", x_spelling)
+      x_spelling <- gsub("(O|0)", "(O|0)+", x_spelling, perl = TRUE)
       x_spelling <- gsub("++", "+", x_spelling, fixed = TRUE)
     }
     
@@ -264,7 +265,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
       
       # try by removing all spaces
       if (x[i] %like% " ") {
-        found <- suppressWarnings(as.ab(gsub(" +", "", x[i]), initial_search = FALSE))
+        found <- suppressWarnings(as.ab(gsub(" +", "", x[i], perl = TRUE), initial_search = FALSE))
         if (length(found) > 0 & !is.na(found)) {
           x_new[i] <- note_if_more_than_one_found(found, i, from_text)
           next
@@ -273,7 +274,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
       
       # 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]), initial_search = FALSE))
+        found <- suppressWarnings(as.ab(gsub("[ 0-9]", "", x[i], perl = TRUE), initial_search = FALSE))
         if (length(found) > 0 & !is.na(found)) {
           x_new[i] <- note_if_more_than_one_found(found, i, from_text)
           next
@@ -318,7 +319,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
       
       # try by removing all trailing capitals
       if (x[i] %like_case% "[a-z]+[A-Z]+$") {
-        found <- suppressWarnings(as.ab(gsub("[A-Z]+$", "", x[i]), initial_search = FALSE))
+        found <- suppressWarnings(as.ab(gsub("[A-Z]+$", "", x[i], perl = TRUE), initial_search = FALSE))
         if (!is.na(found)) {
           x_new[i] <- note_if_more_than_one_found(found, i, from_text)
           next
@@ -326,7 +327,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
       }
       
       # keep only letters
-      found <- suppressWarnings(as.ab(gsub("[^A-Z]", "", x[i]), initial_search = FALSE))
+      found <- suppressWarnings(as.ab(gsub("[^A-Z]", "", x[i], perl = TRUE), initial_search = FALSE))
       if (!is.na(found)) {
         x_new[i] <- note_if_more_than_one_found(found, i, from_text)
         next
@@ -357,10 +358,10 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
       }
       
       # make all consonants facultative
-      search_str <- gsub("([BCDFGHJKLMNPQRSTVWXZ])", "\\1*", x[i])
+      search_str <- gsub("([BCDFGHJKLMNPQRSTVWXZ])", "\\1*", x[i], perl = TRUE)
       found <- suppressWarnings(as.ab(search_str, initial_search = FALSE, already_regex = TRUE))
       # keep at least 4 normal characters
-      if (nchar(gsub(".\\*", "", search_str)) < 4) {
+      if (nchar(gsub(".\\*", "", search_str, perl = TRUE)) < 4) {
         found <- NA
       }
       if (!is.na(found)) {
@@ -369,10 +370,10 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
       }
       
       # make all vowels facultative
-      search_str <- gsub("([AEIOUY])", "\\1*", x[i])
+      search_str <- gsub("([AEIOUY])", "\\1*", x[i], perl = TRUE)
       found <- suppressWarnings(as.ab(search_str, initial_search = FALSE, already_regex = TRUE))
       # keep at least 5 normal characters
-      if (nchar(gsub(".\\*", "", search_str)) < 5) {
+      if (nchar(gsub(".\\*", "", search_str, perl = TRUE)) < 5) {
         found <- NA
       }
       if (!is.na(found)) {
@@ -529,24 +530,33 @@ c.ab <- function(x, ...) {
   class_integrity_check(y, "antimicrobial code", antibiotics$ab)
 }
 
+#' @method unique ab
+#' @export
+#' @noRd
+unique.ab <- function(x, incomparables = FALSE, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+
 generalise_antibiotic_name <- function(x) {
   x <- toupper(x)
   # remove suffices
-  x <- gsub("_(MIC|RSI|DIS[CK])$", "", x)
+  x <- gsub("_(MIC|RSI|DIS[CK])$", "", x, perl = TRUE)
   # remove disk concentrations, like LVX_NM -> LVX
-  x <- gsub("_[A-Z]{2}[0-9_.]{0,3}$", "", x)
+  x <- gsub("_[A-Z]{2}[0-9_.]{0,3}$", "", x, perl = TRUE)
   # remove part between brackets if that's followed by another string
   x <- gsub("(.*)+ [(].*[)]", "\\1", x)
   # keep only max 1 space
-  x <- trimws2(gsub(" +", " ", x))
+  x <- trimws2(gsub(" +", " ", x, perl = TRUE))
   # non-character, space or number should be a slash
-  x <- gsub("[^A-Z0-9 -]", "/", x)
+  x <- gsub("[^A-Z0-9 -]", "/", x, perl = TRUE)
   # spaces around non-characters must be removed: amox + clav -> amox/clav
-  x <- gsub("(.*[A-Z0-9]) ([^A-Z0-9].*)", "\\1\\2", x)
+  x <- gsub("(.*[A-Z0-9]) ([^A-Z0-9].*)", "\\1\\2", x, perl = TRUE)
-  x <- gsub("(.*[^A-Z0-9]) ([A-Z0-9].*)", "\\1\\2", x)
+  x <- gsub("(.*[^A-Z0-9]) ([A-Z0-9].*)", "\\1\\2", x, perl = TRUE)
   # remove hyphen after a starting "co"
-  x <- gsub("^CO-", "CO", x)
+  x <- gsub("^CO-", "CO", x, perl = TRUE)
   # replace operators with a space
-  x <- gsub("(/| AND | WITH | W/|[+]|[-])+", " ", x)
+  x <- gsub("(/| AND | WITH | W/|[+]|[-])+", " ", x, perl = TRUE)
   x
 }

R/disk.R

@@ -177,3 +177,12 @@ c.disk <- function(x, ...) {
   attributes(y) <- attributes(x)
   y
 }
+
+#' @method unique disk
+#' @export
+#' @noRd
+unique.disk <- function(x, incomparables = FALSE, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}

R/eucast_rules.R

@@ -137,7 +137,7 @@ eucast_rules <- function(x,
                          ...) {
   
   x_deparsed <- deparse(substitute(x))
-  if (!x_deparsed %like% "[a-z]") {
+  if (length(x_deparsed) > 0 || !all(x_deparsed %like% "[a-z]")) {
     x_deparsed <- "your_data"
   }
   

R/mic.R

@@ -287,3 +287,12 @@ c.mic <- function(x, ...) {
   x <- as.character(x)
   as.mic(c(x, y))
 }
+
+#' @method unique mic
+#' @export
+#' @noRd
+unique.mic <- function(x, incomparables = FALSE, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}

R/mo.R

@@ -204,11 +204,11 @@ as.mo <- function(x,
     return(to_class_mo(x))
   }
   
-  if (tryCatch(all(tolower(x) %in% MO_lookup$fullname_lower, na.rm = TRUE)
+  if (tryCatch(all(x == "" | gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE) %in% MO_lookup$fullname_lower, na.rm = TRUE)
                & isFALSE(Becker)
                & isFALSE(Lancefield), error = function(e) FALSE)) {
     # to improve speed, special case for taxonomically correct full names (case-insensitive)
-    return(MO_lookup[match(tolower(x), MO_lookup$fullname_lower), "mo", drop = TRUE])
+    return(MO_lookup[match(gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE), MO_lookup$fullname_lower), "mo", drop = TRUE])
   }
   
   # start off with replaced language-specific non-ASCII characters with ASCII characters
@@ -481,8 +481,8 @@ exec_as.mo <- function(x,
       # also, make sure the trailing and leading characters are a-z or 0-9
       # in case of non-regex
       if (dyslexia_mode == FALSE) {
-        trimmed <- gsub("^[^a-zA-Z0-9)(]+", "", trimmed)
+        trimmed <- gsub("^[^a-zA-Z0-9)(]+", "", trimmed, perl = TRUE)
-        trimmed <- gsub("[^a-zA-Z0-9)(]+$", "", trimmed)
+        trimmed <- gsub("[^a-zA-Z0-9)(]+$", "", trimmed, perl = TRUE)
       }
       trimmed
     }
@@ -497,49 +497,49 @@ exec_as.mo <- function(x,
     x_backup[grepl("^(fungus|fungi)$", x)] <- "F_FUNGUS" # will otherwise become the kingdom
     
     # remove spp and species
-    x <- gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x)
+    x <- gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x, perl = TRUE)
-    x <- gsub("(spp.?|subsp.?|subspecies|biovar|serovar|species)", "", x)
+    x <- gsub("(spp.?|subsp.?|subspecies|biovar|serovar|species)", "", x, perl = TRUE)
-    x <- gsub("^([a-z]{2,4})(spe.?)$", "\\1", x) # when ending in SPE instead of SPP and preceded by 2-4 characters
+    x <- gsub("^([a-z]{2,4})(spe.?)$", "\\1", x, perl = TRUE) # when ending in SPE instead of SPP and preceded by 2-4 characters
     x <- strip_whitespace(x, dyslexia_mode)
     
     x_backup_without_spp <- x
     x_species <- paste(x, "species")
     # translate to English for supported languages of mo_property
-    x <- gsub("(gruppe|groep|grupo|gruppo|groupe)", "group", x)
+    x <- gsub("(gruppe|groep|grupo|gruppo|groupe)", "group", x, perl = TRUE)
     # no groups and complexes as ending
-    x <- gsub("(complex|group)$", "", x)
+    x <- gsub("(complex|group)$", "", x, perl = TRUE)
-    x <- gsub("((an)?aero+b)[a-z]*", "", x)
+    x <- gsub("((an)?aero+b)[a-z]*", "", x, perl = TRUE)
-    x <- gsub("^atyp[a-z]*", "", x)
+    x <- gsub("^atyp[a-z]*", "", x, perl = TRUE)
-    x <- gsub("(vergroen)[a-z]*", "viridans", x)
+    x <- gsub("(vergroen)[a-z]*", "viridans", x, perl = TRUE)
-    x <- gsub("[a-z]*diff?erent[a-z]*", "", x)
+    x <- gsub("[a-z]*diff?erent[a-z]*", "", x, perl = TRUE)
-    x <- gsub("(hefe|gist|gisten|levadura|lievito|fermento|levure)[a-z]*", "yeast", x)
+    x <- gsub("(hefe|gist|gisten|levadura|lievito|fermento|levure)[a-z]*", "yeast", x, perl = TRUE)
-    x <- gsub("(schimmels?|mofo|molde|stampo|moisissure|fungi)[a-z]*", "fungus", x)
+    x <- gsub("(schimmels?|mofo|molde|stampo|moisissure|fungi)[a-z]*", "fungus", x, perl = TRUE)
-    x <- gsub("fungus[ph|f]rya", "fungiphrya", x)
+    x <- gsub("fungus[ph|f]rya", "fungiphrya", x, perl = TRUE)
     # no contamination
-    x <- gsub("(contamination|kontamination|mengflora|contaminaci.n|contamina..o)", "", x)
+    x <- gsub("(contamination|kontamination|mengflora|contaminaci.n|contamina..o)", "", x, perl = TRUE)
     # remove non-text in case of "E. coli" except dots and spaces
-    x <- trimws(gsub("[^.a-zA-Z0-9/ \\-]+", " ", x))
+    x <- trimws(gsub("[^.a-zA-Z0-9/ \\-]+", " ", x, perl = TRUE))
     # but make sure that dots are followed by a space
-    x <- gsub("[.] ?", ". ", x)
+    x <- gsub("[.] ?", ". ", x, perl = TRUE)
     # replace minus by a space
-    x <- gsub("-+", " ", x)
+    x <- gsub("-+", " ", x, perl = TRUE)
     # replace hemolytic by haemolytic
-    x <- gsub("ha?emoly", "haemoly", x)
+    x <- gsub("ha?emoly", "haemoly", x, perl = TRUE)
     # place minus back in streptococci
-    x <- gsub("(alpha|beta|gamma).?ha?emoly", "\\1-haemoly", x)
+    x <- gsub("(alpha|beta|gamma).?ha?emoly", "\\1-haemoly", x, perl = TRUE)
     # remove genus as first word
-    x <- gsub("^genus ", "", x)
+    x <- gsub("^genus ", "", x, perl = TRUE)
     # remove 'uncertain'-like texts
-    x <- trimws(gsub("(uncertain|susp[ie]c[a-z]+|verdacht)", "", x))
+    x <- trimws(gsub("(uncertain|susp[ie]c[a-z]+|verdacht)", "", x, perl = TRUE))
     # allow characters that resemble others = dyslexia_mode ----
     if (dyslexia_mode == TRUE) {
       x <- tolower(x)
-      x <- gsub("[iy]+", "[iy]+", x)
+      x <- gsub("[iy]+", "[iy]+", x, perl = TRUE)
-      x <- gsub("(c|k|q|qu|s|z|x|ks)+", "(c|k|q|qu|s|z|x|ks)+", x)
+      x <- gsub("(c|k|q|qu|s|z|x|ks)+", "(c|k|q|qu|s|z|x|ks)+", x, perl = TRUE)
-      x <- gsub("(ph|hp|f|v)+", "(ph|hp|f|v)+", x)
+      x <- gsub("(ph|hp|f|v)+", "(ph|hp|f|v)+", x, perl = TRUE)
-      x <- gsub("(th|ht|t)+", "(th|ht|t)+", x)
+      x <- gsub("(th|ht|t)+", "(th|ht|t)+", x, perl = TRUE)
-      x <- gsub("a+", "a+", x)
+      x <- gsub("a+", "a+", x, perl = TRUE)
-      x <- gsub("u+", "u+", x)
+      x <- gsub("u+", "u+", x, perl = TRUE)
       # allow any ending of -um, -us, -ium, -icum, -ius, -icus, -ica, -ia and -a (needs perl for the negative backward lookup):
       x <- gsub("(u\\+\\(c\\|k\\|q\\|qu\\+\\|s\\|z\\|x\\|ks\\)\\+)(?![a-z])",
                 "(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, perl = TRUE)
@@ -549,11 +549,11 @@ exec_as.mo <- function(x,
                 "(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, perl = TRUE)
       x <- gsub("(\\[iy\\]\\+a\\+)(?![a-z])",
                 "([iy]*a+|[iy]+a*)", x, perl = TRUE)
-      x <- gsub("e+", "e+", x)
+      x <- gsub("e+", "e+", x, perl = TRUE)
-      x <- gsub("o+", "o+", x)
+      x <- gsub("o+", "o+", x, perl = TRUE)
-      x <- gsub("(.)\\1+", "\\1+", x)
+      x <- gsub("(.)\\1+", "\\1+", x, perl = TRUE)
       # allow multiplication of all other consonants
-      x <- gsub("([bdgjlnrw]+)", "\\1+", x)
+      x <- gsub("([bdgjlnrw]+)", "\\1+", x, perl = TRUE)
       # allow ending in -en or -us
       x <- gsub("e\\+n(?![a-z[])", "(e+n|u+(c|k|q|qu|s|z|x|ks)+)", x, perl = TRUE)
       # if the input is longer than 10 characters, allow any forgotten consonant between all characters, as some might just have forgotten one...
@@ -571,12 +571,12 @@ exec_as.mo <- function(x,
     
     x_trimmed <- x
     x_trimmed_species <- paste(x_trimmed, "species")
-    x_trimmed_without_group <- gsub(" gro.u.p$", "", x_trimmed)
+    x_trimmed_without_group <- gsub(" gro.u.p$", "", x_trimmed, perl = TRUE)
     # remove last part from "-" or "/"
     x_trimmed_without_group <- gsub("(.*)[-/].*", "\\1", x_trimmed_without_group)
     # replace space and dot by regex sign
-    x_withspaces <- gsub("[ .]+", ".* ", x)
+    x_withspaces <- gsub("[ .]+", ".* ", x, perl = TRUE)
-    x <- gsub("[ .]+", ".*", x)
+    x <- gsub("[ .]+", ".*", x, perl = TRUE)
     # add start en stop regex
     x <- paste0("^", x, "$")
     
@@ -616,7 +616,7 @@ exec_as.mo <- function(x,
       }
       
       # valid fullname ----
-      found <- lookup(fullname_lower %in% gsub("[^a-zA-Z0-9_. -]", "", tolower(c(x_backup[i], x_backup_without_spp[i]))))
+      found <- lookup(fullname_lower %in% gsub("[^a-zA-Z0-9_. -]", "", tolower(c(x_backup[i], x_backup_without_spp[i])), perl = TRUE))
       # added the gsub() for "(unknown fungus)", since fullname_lower does not contain brackets
       if (!is.na(found)) {
         x[i] <- found[1L]
@@ -670,7 +670,7 @@ exec_as.mo <- function(x,
       
       # very probable: is G. species ----
       found <- lookup(g_species %in% gsub("[^a-z0-9/ \\-]+", "", 
-                                          tolower(c(x_backup[i], x_backup_without_spp[i]))))
+                                          tolower(c(x_backup[i], x_backup_without_spp[i])), perl = TRUE))
       if (!is.na(found)) {
         x[i] <- found[1L]
         next
@@ -1121,8 +1121,8 @@ exec_as.mo <- function(x,
             if (isTRUE(debug)) {
               cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (4) strip values between brackets\n"))
             }
-            a.x_backup_stripped <- gsub("( *[(].*[)] *)", " ", a.x_backup)
+            a.x_backup_stripped <- gsub("( *[(].*[)] *)", " ", a.x_backup, perl = TRUE)
-            a.x_backup_stripped <- trimws(gsub(" +", " ", a.x_backup_stripped))
+            a.x_backup_stripped <- trimws(gsub(" +", " ", a.x_backup_stripped, perl = TRUE))
             if (isTRUE(debug)) {
               message("Running '", a.x_backup_stripped, "'")
             }
@@ -1612,7 +1612,7 @@ format_uncertainty_as_df <- function(uncertainty_level,
 pillar_shaft.mo <- function(x, ...) {
   out <- format(x)
   # grey out the kingdom (part until first "_")
-  out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(font_subtle("\\1"), "\\2"), out[!is.na(x)])
+  out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(font_subtle("\\1"), "\\2"), out[!is.na(x)], perl = TRUE)
   # and grey out every _
   out[!is.na(x)] <- gsub("_", font_subtle("_"), out[!is.na(x)])
   
@@ -1747,6 +1747,15 @@ c.mo <- function(x, ...) {
                                                    as.character(microorganisms.translation$mo_old)))
 }
 
+#' @method unique mo
+#' @export
+#' @noRd
+unique.mo <- function(x, incomparables = FALSE, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+
 #' @rdname as.mo
 #' @export
 mo_failures <- function() {

R/resistance_predict.R

@@ -294,7 +294,7 @@ rsi_predict <- resistance_predict
 
 #' @method plot resistance_predict
 #' @export
-#' @importFrom graphics axis arrows points
+#' @importFrom graphics plot axis arrows points
 #' @rdname resistance_predict
 plot.resistance_predict <- function(x, main = paste("Resistance Prediction of", x_name), ...) {
   x_name <- paste0(ab_name(attributes(x)$ab), " (", attributes(x)$ab, ")")
@@ -304,12 +304,7 @@ plot.resistance_predict <- function(x, main = paste("Resistance Prediction of",
   } else {
     ylab <- "%IR"
   }
-  # get plot() generic; this was moved from the 'graphics' pkg to the 'base' pkg in R 4.0.0
+
-  if (as.integer(R.Version()$major) >= 4) {
-    plot <- import_fn("plot", "base")
-  } else {
-    plot <- import_fn("plot", "graphics")
-  }
   plot(x = x$year,
        y = x$value,
        ylim = c(0, 1),

R/rsi.R

@@ -19,7 +19,7 @@
 # Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
-#' Interpret MIC and disk, or clean raw R/SI data
+#' Interpret MIC and disk values, or clean raw R/SI data
 #'
 #' Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class [`rsi`], which is an ordered factor with levels `S < I < R`. Values that cannot be interpreted will be returned as `NA` with a warning.
 #' @inheritSection lifecycle Stable lifecycle
@@ -339,6 +339,7 @@ as.rsi.mic <- function(x,
                            ab_name(ab_coerced, tolower = TRUE), ")", mo_var_found, 
                            " according to ", font_bold(guideline_coerced), " ... ")),
           appendLF = FALSE)
+  
   result <- exec_as.rsi(method = "mic",
                         x = x,
                         mo = mo_coerced,
@@ -482,7 +483,7 @@ as.rsi.data.frame <- function(x,
     ab <- colnames(x)[i]
     if (length(sel) == 0 || (length(sel) > 0 && ab %in% sel)) {
       ab_coerced <- suppressWarnings(as.ab(ab))
-      if (is.na(ab_coerced) | !ab %in% sel) {
+      if (is.na(ab_coerced) || (length(sel) > 0 & !ab %in% sel)) {
         # not even a valid AB code
         return(FALSE)
       } else {
@@ -494,7 +495,7 @@ as.rsi.data.frame <- function(x,
           message(font_blue(paste0("NOTE: Assuming column `", ab, "` (",
                                    ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
                                    ab_name(ab_coerced, tolower = TRUE), ") contains disk zones.")))
-        } else if (!is.rsi(y)) {
+        } else if (!check & !is.rsi(y)) {
           message(font_blue(paste0("NOTE: Assuming column `", ab, "` (",
                                    ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
                                    ab_name(ab_coerced, tolower = TRUE), ") must be cleaned to valid R/SI values.")))
@@ -581,11 +582,20 @@ exec_as.rsi <- function(method,
   warned <- FALSE
   method_param <- toupper(method)
   
-  mo_genus <- as.mo(mo_genus(mo))
+  genera <- mo_genus(mo)
+  mo_genus <- as.mo(genera)
   mo_family <- as.mo(mo_family(mo))
   mo_order <- as.mo(mo_order(mo))
+  if (any(genera == "Staphylococcus", na.rm = TRUE)) {
     mo_becker <- as.mo(mo, Becker = TRUE)
+  } else {
+    mo_becker <- mo
+  }
+  if (any(genera == "Streptococcus", na.rm = TRUE)) {
     mo_lancefield <- as.mo(mo, Lancefield = TRUE)
+  } else {
+    mo_lancefield <- mo
+  }
   mo_other <- as.mo(rep("UNKNOWN", length(mo)))
   
   guideline_coerced <- get_guideline(guideline)
@@ -781,7 +791,7 @@ summary.rsi <- function(object, ...) {
 
 #' @method plot rsi
 #' @export
-#' @importFrom graphics text axis
+#' @importFrom graphics plot text axis
 #' @rdname plot
 plot.rsi <- function(x,
                      lwd = 2,
@@ -810,12 +820,6 @@ plot.rsi <- function(x,
   
   ymax <- pm_if_else(max(data$s) > 95, 105, 100)
   
-  # get plot() generic; this was moved from the 'graphics' pkg to the 'base' pkg in R 4.0.0
-  if (as.integer(R.Version()$major) >= 4) {
-    plot <- import_fn("plot", "base")
-  } else {
-    plot <- import_fn("plot", "graphics")
-  }
   plot(x = data$x,
        y = data$s,
        lwd = lwd,
@@ -896,3 +900,12 @@ c.rsi <- function(x, ...) {
   x <- as.character(x)
   as.rsi(c(x, y))
 }
+
+#' @method unique rsi
+#' @export
+#' @noRd
+unique.rsi <- function(x, incomparables = FALSE, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}

R/zzz.R

@@ -90,10 +90,10 @@ create_MO_lookup <- function() {
                                                    MO_lookup$subspecies)))
   ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname)
   MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
-  MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower))
+  MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
   
   # add a column with only "e coli" like combinations
-  MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower)
+  MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)
   
   # so arrange data on prevalence first, then kingdom, then full name
   MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), ]

data-raw/eucast_rules.tsv

@@ -216,20 +216,19 @@ genus_species	is	Aeromonas dhakensis			aminopenicillins, AMC, SAM, FOX	R	Table 1
 genus_species	is	Aeromonas caviae			aminopenicillins, AMC, SAM, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
 genus_species	is	Aeromonas jandaei			aminopenicillins, AMC, SAM, TIC,  CZO, CEP, LEX, CFR, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
 genus	one_of	Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas			PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	
-fullname	like	^Acinetobacter (baumannii|pittii|nosocomialis)			aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	
+fullname	like	^Acinetobacter (baumannii|pittii|nosocomialis)			aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	Additional rules from header added in separate rule (genus is one of…)
-genus	is	Acinetobacter			DOX, TCY	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	
+genus	is	Acinetobacter			DOX, TCY	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	Additional rules from header added in separate rule (genus is one of…)
-genus_species	is	Achromobacter xylosoxidans 			aminopenicillins, CRO, CTX, ETP	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	
+genus_species	is	Achromobacter xylosoxidans 			aminopenicillins, CRO, CTX, ETP	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	Additional rules from header added in separate rule (genus is one of…)
-fullname	like	^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis)			aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CRO, CTX, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	
+fullname	like	^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis)			aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CRO, CTX, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	Additional rules from header added in separate rule (genus is one of…)
-genus_species	is	Elizabethkingia meningoseptica			aminopenicillins, AMC, SAM, TIC, TCC, PIP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	
+genus_species	is	Elizabethkingia meningoseptica			aminopenicillins, AMC, SAM, TIC, TCC, PIP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	Additional rules from header added in separate rule (genus is one of…)
-genus_species	is	Ochrobactrum anthropi			aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	
+genus_species	is	Ochrobactrum anthropi			aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	Additional rules from header added in separate rule (genus is one of…)
-genus_species	is	Pseudomonas aeruginosa			aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, TMP, tetracyclines, TGC	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	
+genus_species	is	Pseudomonas aeruginosa			aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, KAN, NEO, TMP, tetracyclines, TGC	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	Additional rules from header added in separate rule (genus is one of…)
-genus_species	is	Stenotrophomonas maltophilia			aminopenicillins, AMC, SAM, TIC, PIP, TZP, CRO, CTX, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, DOX, TCY, polymyxins	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	
+genus_species	is	Stenotrophomonas maltophilia			aminopenicillins, AMC, SAM, TIC, PIP, TZP, CRO, CTX, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.2	Additional rules from header added in separate rule (genus is one of…)
-genus	one_of	Haemophilus, Moraxella, Neisseria, Campylobacter			glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.2	
+genus_species	is	Haemophilus influenzae			FUS, streptogramins, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.2	
-genus_species	is	Haemophilus influenzae			FUS, streptogramins	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.2	
+genus_species	is	Moraxella catarrhalis			TMP, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.2	
-genus_species	is	Moraxella catarrhalis			TMP	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.2	
+genus	is	Neisseria			TMP, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.2	
-genus	is	Neisseria			TMP	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.2	
+genus_species	is	Campylobacter fetus			FUS, streptogramins, TMP, NAL, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.2	
-genus_species	is	Campylobacter fetus			FUS, streptogramins, TMP, NAL	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.2	
+fullname	like	^Campylobacter (jejuni|coli)			FUS, streptogramins, TMP, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.2	
-fullname	like	^Campylobacter (jejuni|coli)			FUS, streptogramins, TMP	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.2	
 gramstain	is	Gram-positive			ATM, TEM, polymyxins, NAL	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.2	
 genus_species	is	Staphylococcus saprophyticus			FUS, CAZ, FOS, NOV	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.2	
 genus_species	is	Staphylococcus cohnii			CAZ, NOV	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.2	
@@ -263,6 +262,7 @@ genus	one_of	Arsenophonus, Biostraticola, Brenneria, Buchnera, Budvicia, Buttiau
 fullname	like	^(Serratia|Providencia|Morganella morganii)			TGC	R	Expert Rules on Enterobacterales	Expert Rules	3.2	
 genus	is	Salmonella			cephalosporins_2nd	R	Expert Rules on Salmonella	Expert Rules	3.2	
 genus	is	Salmonella			aminoglycosides	R	Expert Rules on Salmonella	Expert Rules	3.2	
+genus	is	Salmonella	PEF	R	CIP	R	Expert Rules on Salmonella	Expert Rules	3.2	
 genus_species	is	Staphylococcus aureus	FOX1	R	all_betalactams	R	Expert Rules on Staphylococcus	Expert Rules	3.2	
 genus_species	is	Staphylococcus aureus	FOX1	S	all_betalactams	S	Expert Rules on Staphylococcus	Expert Rules	3.2	
 genus_species	one_of	Staphylococcus aureus, Staphylococcus lugdunensis	PEN	R	AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC	R	Expert Rules on Staphylococcus	Expert Rules	3.2	all penicillins without beta-lactamse inhibitor
@@ -278,6 +278,7 @@ fullname	like	^Enterococcus (faecalis|faecium)	AMP	R	ureidopenicillins, IPM	R	Ex
 fullname	like	^Enterococcus (faecalis|faecium)	AMX	R	ureidopenicillins, IPM	R	Expert Rules on Enterococcus	Expert Rules	3.2	
 genus	is	Enterococcus	NOR	S	CIP, LVX	S	Expert Rules on Enterococcus	Expert Rules	3.2	
 genus	is	Enterococcus	VAN	S	lipoglycopeptides	S	Expert Rules on Enterococcus	Expert Rules	3.2	
+genus_species	is	Enterococcus faecium			CLI	R	Expert Rules on Enterococcus	Expert Rules	3.2	
 genus_species	one_of	Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G	PEN	S	aminopenicillins, cephalosporins, carbapenems	S	Expert Rules on Streptococcus A, B, C and G	Expert Rules	3.2	
 genus_species	one_of	Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G	NOR	S	LVX, MFX	S	Expert Rules on Streptococcus A, B, C and G	Expert Rules	3.2	
 genus_species	one_of	Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G	NOR	R	LVX, MFX	R	Expert Rules on Streptococcus A, B, C and G	Expert Rules	3.2	

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">1.3.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9029</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">1.3.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9029</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">1.3.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9029</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">1.3.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9029</span>
       </span>
     </div>
 

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">1.3.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9029</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">1.3.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9029</span>
       </span>
     </div>
 
@@ -236,13 +236,13 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1309028" class="section level1">
+    <div id="amr-1309029" class="section level1">
-<h1 class="page-header" data-toc-text="1.3.0.9028">
+<h1 class="page-header" data-toc-text="1.3.0.9029">
-<a href="#amr-1309028" class="anchor"></a>AMR 1.3.0.9028<small> Unreleased </small>
+<a href="#amr-1309029" class="anchor"></a>AMR 1.3.0.9029<small> Unreleased </small>
 </h1>
-<div id="last-updated-24-september-2020" class="section level2">
+<div id="last-updated-25-september-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-24-september-2020" class="anchor"></a><small>Last updated: 24 September 2020</small>
+<a href="#last-updated-25-september-2020" class="anchor"></a><small>Last updated: 25 September 2020</small>
 </h2>
 <p>Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!</p>
 <div id="new" class="section level3">
@@ -329,6 +329,7 @@
 <li>The group name (<code>antibiotics$group</code>) of ‘Linezolid’ (<code>LNZ</code>), ‘Cycloserine’ (<code>CYC</code>), ‘Tedizolid’ (<code>TZD</code>) and ‘Thiacetazone’ (<code>THA</code>) is now “Oxazolidinones” instead of “Other antibacterials”</li>
 </ul>
 </li>
+<li><p>Added support for using <code><a href="https://rdrr.io/r/base/unique.html">unique()</a></code> on classes <code>&lt;rsi&gt;</code>, <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code>, <code>&lt;ab&gt;</code> and <code>&lt;mo&gt;</code></p></li>
 </ul>
 </div>
 <div id="other" class="section level3">
@@ -437,7 +438,7 @@
 <p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
 <p>Negative effects of this change are:</p>
 <ul>
-<li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>.</li>
+<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
 <li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</code> anymore. This is purely a visual effect.</del></li>
 <li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
 <li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
@@ -774,7 +775,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </pre></div>
 <p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
 </li>
-<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
+<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code>freq()</code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
 <li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
 </ul>
 </div>
@@ -1043,7 +1044,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>The <code><a href="../reference/age.html">age()</a></code> function gained a new parameter <code>exact</code> to determine ages with decimals</li>
 <li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
 </li>
-<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>):
+<li>Frequency tables (<code>freq()</code>):
 <ul>
 <li><p>speed improvement for microbial IDs</p></li>
 <li><p>fixed factor level names for R Markdown</p></li>
@@ -1052,12 +1053,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <p>support for boxplots:</p>
 <div class="sourceCode" id="cb20"><pre class="downlit">
 <span class="kw">septic_patients</span> <span class="op">%&gt;%</span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>) <span class="op">%&gt;%</span> 
+  <span class="fu">freq</span>(<span class="kw">age</span>) <span class="op">%&gt;%</span> 
   <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
 <span class="co"># grouped boxplots:</span>
 <span class="kw">septic_patients</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">hospital_id</span>) <span class="op">%&gt;%</span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>) <span class="op">%&gt;%</span>
+  <span class="fu">freq</span>(<span class="kw">age</span>) <span class="op">%&gt;%</span>
   <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
 </pre></div>
 </li>
@@ -1068,7 +1069,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
 </li>
 <li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
-<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
+<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
 </li>
 <li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
 <li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
@@ -1309,7 +1310,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 </li>
-<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function):
+<li>Frequency tables (<code>freq()</code> function):
 <ul>
 <li>
 <p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
@@ -1318,15 +1319,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="co"># OLD WAY</span>
 <span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(genus = <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>)) <span class="op">%&gt;%</span>
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">genus</span>)
+  <span class="fu">freq</span>(<span class="kw">genus</span>)
 <span class="co"># NEW WAY</span>
 <span class="kw">septic_patients</span> <span class="op">%&gt;%</span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>))
+  <span class="fu">freq</span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>))
 
 <span class="co"># Even supports grouping variables:</span>
 <span class="kw">septic_patients</span> <span class="op">%&gt;%</span>
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">gender</span>) <span class="op">%&gt;%</span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>))
+  <span class="fu">freq</span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>))
 </pre></div>
 </li>
 <li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
@@ -1410,21 +1411,21 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below parameter <code>minimum</code></p></li>
 <li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li>
 <li>
-<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>:</p>
+<p>Frequency tables - <code>freq()</code>:</p>
 <ul>
 <li>
 <p>Support for grouping variables, test with:</p>
 <div class="sourceCode" id="cb32"><pre class="downlit">
 <span class="kw">septic_patients</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">hospital_id</span>) <span class="op">%&gt;%</span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">gender</span>)
+  <span class="fu">freq</span>(<span class="kw">gender</span>)
 </pre></div>
 </li>
 <li>
 <p>Support for (un)selecting columns:</p>
 <div class="sourceCode" id="cb33"><pre class="downlit">
 <span class="kw">septic_patients</span> <span class="op">%&gt;%</span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">hospital_id</span>) <span class="op">%&gt;%</span> 
+  <span class="fu">freq</span>(<span class="kw">hospital_id</span>) <span class="op">%&gt;%</span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw">count</span>, <span class="op">-</span><span class="kw">cum_count</span>) <span class="co"># only get item, percent, cum_percent</span>
 </pre></div>
 </li>
@@ -1443,7 +1444,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
 <li><p>Fix for <code>mo_property</code> not working properly</p></li>
 <li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
-<li><p>Support for named vectors of class <code>mo</code>, useful for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">top_freq()</a></code></p></li>
+<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
 <li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> parameter</p></li>
 <li>
 <p>AI improvements for <code>as.mo</code>:</p>
@@ -1610,13 +1611,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <p>Support for types (classes) list and matrix for <code>freq</code></p>
 <div class="sourceCode" id="cb40"><pre class="downlit">
 <span class="kw">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span>(<span class="kw">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="kw">age</span>, <span class="kw">gender</span>), ncol = <span class="fl">2</span>))
-<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">my_matrix</span>)
+<span class="fu">freq</span>(<span class="kw">my_matrix</span>)
 </pre></div>
 <p>For lists, subsetting is possible:</p>
 <div class="sourceCode" id="cb41"><pre class="downlit">
 <span class="kw">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(age = <span class="kw">septic_patients</span><span class="op">$</span><span class="kw">age</span>, gender = <span class="kw">septic_patients</span><span class="op">$</span><span class="kw">gender</span>)
-<span class="kw">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>)
+<span class="kw">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span>(<span class="kw">age</span>)
-<span class="kw">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">gender</span>)
+<span class="kw">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span>(<span class="kw">gender</span>)
 </pre></div>
 </li>
 </ul>
@@ -1691,13 +1692,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>A vignette to explain its usage</li>
 <li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
-<li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(table(x, y))</a></code>
+<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</code>
 </li>
 <li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
 </li>
 <li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
 </li>
-<li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
+<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
 </li>
 <li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
 <li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>

docs/pkgdown.yml

@@ -2,7 +2,7 @@ pandoc: 2.7.3
 pkgdown: 1.5.1.9000
 pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
 articles: []
-last_built: 2020-09-24T10:36Z
+last_built: 2020-09-25T12:44Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles

docs/reference/as.rsi.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>Interpret MIC and disk, or clean raw R/SI data — as.rsi • AMR (for R)</title>
+<title>Interpret MIC and disk values, or clean raw R/SI data — as.rsi • 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="Interpret MIC and disk, or clean raw R/SI data — as.rsi" />
+<meta property="og:title" content="Interpret MIC and disk values, or clean raw R/SI data — as.rsi" />
 <meta property="og:description" content="Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Values that cannot be interpreted will be returned as NA with a warning." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
 
@@ -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">1.3.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9029</span>
       </span>
     </div>
 
@@ -233,7 +233,7 @@
 <div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>Interpret MIC and disk, or clean raw R/SI data</h1>
+    <h1>Interpret MIC and disk values, or clean raw R/SI data</h1>
     <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/rsi.R'><code>R/rsi.R</code></a></small>
     <div class="hidden name"><code>as.rsi.Rd</code></div>
     </div>

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">1.3.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9029</span>
       </span>
     </div>
 
@@ -425,7 +425,7 @@
         <td>
           <p><code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">is.rsi()</a></code> <code><a href="as.rsi.html">is.rsi.eligible()</a></code> </p>
         </td>
-        <td><p>Interpret MIC and disk, or clean raw R/SI data</p></td>
+        <td><p>Interpret MIC and disk values, or clean raw R/SI data</p></td>
       </tr><tr>
         
         <td>

docs/survey.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">1.3.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9029</span>
       </span>
     </div>
 

man/as.rsi.Rd

@@ -8,7 +8,7 @@
 \alias{as.rsi.mic}
 \alias{as.rsi.disk}
 \alias{as.rsi.data.frame}
-\title{Interpret MIC and disk, or clean raw R/SI data}
+\title{Interpret MIC and disk values, or clean raw R/SI data}
 \usage{
 as.rsi(x, ...)
 

tests/testthat.R

@@ -19,7 +19,7 @@
 # Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
-library(testthat)
+library(testthat, warn.conflicts = FALSE)
 library(AMR)
 
 test_check("AMR")

tests/testthat/test-ab.R

@@ -67,6 +67,7 @@ test_that("as.ab works", {
   expect_s3_class(x[1], "ab")
   expect_s3_class(x[[1]], "ab")
   expect_s3_class(c(x[1], x[9]), "ab")
+  expect_s3_class(unique(x[1], x[9]), "ab")
   expect_warning(x[1] <- "invalid code")
   expect_warning(x[[1]] <- "invalid code")
   expect_warning(c(x[1], "test"))

tests/testthat/test-disk.R

@@ -29,8 +29,11 @@ test_that("disk works", {
   expect_equal(suppressWarnings(as.logical(as.disk("INVALID VALUE"))), NA)
 
   # all levels should be valid disks
-  expect_silent(as.disk(levels(as.disk(15))))
+  x <- as.disk(c(20, 40))
-
+  expect_s3_class(x[1], "disk")
+  expect_s3_class(x[[1]], "disk")
+  expect_s3_class(c(x[1], x[9]), "disk")
+  expect_s3_class(unique(x[1], x[9]), "disk")
   expect_warning(as.disk("INVALID VALUE"))
   
   expect_output(print(as.disk(12)))

tests/testthat/test-ggplot_rsi.R

@@ -30,6 +30,8 @@ test_that("ggplot_rsi works", {
   library(dplyr)
   library(ggplot2)
   
+  pdf(NULL) # prevent Rplots.pdf being created
+
   # data should be equal
   expect_equal(
     (example_isolates %>% select(AMC, CIP) %>% ggplot_rsi())$data %>% summarise_all(resistance) %>% as.double(),

tests/testthat/test-import_fn.R

@@ -19,6 +19,8 @@
 # Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
+context("import_fn.R")
+
 test_that("imports work", {
   skip_on_cran()
   

tests/testthat/test-mic.R

@@ -34,8 +34,11 @@ test_that("mic works", {
   expect_equal(suppressWarnings(as.logical(as.mic("INVALID VALUE"))), NA)
 
   # all levels should be valid MICs
-  expect_silent(as.mic(levels(as.mic(1))))
+  x <- as.mic(c(2, 4))
-
+  expect_s3_class(x[1], "mic")
+  expect_s3_class(x[[1]], "mic")
+  expect_s3_class(c(x[1], x[9]), "mic")
+  expect_s3_class(unique(x[1], x[9]), "mic")
   expect_warning(as.mic("INVALID VALUE"))
 
   pdf(NULL) # prevent Rplots.pdf being created

tests/testthat/test-pca.R

@@ -44,6 +44,8 @@ test_that("PCA works", {
   
   expect_s3_class(pca_model, "pca")
   
+  pdf(NULL) # prevent Rplots.pdf being created
+  
   ggplot_pca(pca_model, ellipse = TRUE)
   ggplot_pca(pca_model, arrows_textangled = FALSE)
 })

tests/testthat/test-rsi.R

@@ -28,6 +28,13 @@ test_that("rsi works", {
   expect_true(as.rsi("I") < as.rsi("R"))
   expect_true(is.rsi(as.rsi("S")))
   
+  
+  x <- example_isolates$AMX
+  expect_s3_class(x[1], "rsi")
+  expect_s3_class(x[[1]], "rsi")
+  expect_s3_class(c(x[1], x[9]), "rsi")
+  expect_s3_class(unique(x[1], x[9]), "rsi")
+  
   pdf(NULL) # prevent Rplots.pdf being created
   expect_silent(barplot(as.rsi(c("S", "I", "R"))))
   expect_silent(plot(as.rsi(c("S", "I", "R"))))