adding mo fixes

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9092
+Version: 1.8.2.9093
 Date: 2023-01-14
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9092
+# AMR 1.8.2.9093
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 

R/aa_helper_functions.R

@@ -1372,6 +1372,13 @@ percentage <- function(x, digits = NULL, ...) {
   )
 }
 
+add_intrinsic_resistance_to_AMR_env <- function() {
+  # for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
+  if (is.null(AMR_env$intrinsic_resistant)) {
+    AMR_env$intrinsic_resistant <- paste(AMR::intrinsic_resistant$mo, AMR::intrinsic_resistant$ab)
+  }
+}
+
 trimws2 <- function(..., whitespace = "[\u0009\u000A\u000B\u000C\u000D\u0020\u0085\u00A0\u1680\u180E\u2000\u2001\u2002\u2003\u2004\u2005\u2006\u2007\u2008\u2009\u200A\u200B\u200C\u200D\u2028\u2029\u202F\u205F\u2060\u3000\uFEFF]") {
   # this is even faster than trimws() itself which sets " \t\n\r".
   trimws(..., whitespace = whitespace)

R/custom_antimicrobials.R

@@ -27,9 +27,9 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-#' Add Custom Antimicrobials to This Package
+#' Add Custom Antimicrobials
 #'
-#' With [add_custom_antimicrobials()] you can add your own custom antimicrobial drug codes to the `AMR` package.
+#' With [add_custom_antimicrobials()] you can add your own custom antimicrobial drug names and codes.
 #' @param x a [data.frame] resembling the [antibiotics] data set, at least containing columns "ab" and "name"
 #' @details **Important:** Due to how \R works, the [add_custom_antimicrobials()] function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. 
 #' 
@@ -65,13 +65,13 @@
 #'       ```
 #'
 #' Use [clear_custom_antimicrobials()] to clear the previously added antimicrobials.
-#' @seealso [add_custom_microorganisms()] to add custom microorganisms to this package.
+#' @seealso [add_custom_microorganisms()] to add custom microorganisms.
 #' @rdname add_custom_antimicrobials
 #' @export
 #' @examples
 #' \donttest{
 #'
-#' # returns NA and throws a warning (which is now suppressed):
+#' # returns NA and throws a warning (which is suppressed here):
 #' suppressWarnings(
 #'   as.ab("testab")
 #' )

R/custom_microorganisms.R

@@ -27,9 +27,9 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-#' Add Custom Microorganisms to This Package
+#' Add Custom Microorganisms
 #'
-#' With [add_custom_microorganisms()] you can add your own custom microorganisms to the `AMR` package, such the non-taxonomic outcome of laboratory analysis.
+#' With [add_custom_microorganisms()] you can add your own custom microorganisms, such the non-taxonomic outcome of laboratory analysis.
 #' @param x a [data.frame] resembling the [microorganisms] data set, at least containing column "genus" (case-insensitive)
 #' @details This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see *Examples*.
 #' 
@@ -66,7 +66,7 @@
 #'       ```
 #'
 #' Use [clear_custom_microorganisms()] to clear the previously added antimicrobials.
-#' @seealso [add_custom_antimicrobials()] to add custom antimicrobials to this package.
+#' @seealso [add_custom_antimicrobials()] to add custom antimicrobials.
 #' @rdname add_custom_microorganisms
 #' @export
 #' @examples
@@ -102,15 +102,23 @@
 #' 
 #' # the function tries to be forgiving:
 #' add_custom_microorganisms(
-#'   data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA",
+#'   data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA SLASHLINE",
-#'              SPECIES = "SPECIES"))
+#'              SPECIES = "SPECIES")
+#' )
 #' mo_name("ESCHERICHIA / KLEBSIELLA")
+#' mo_rank("ESCHERICHIA / KLEBSIELLA")
+#' # taxonomy still works, although a slashline genus was given as input:
 #' mo_family("Escherichia/Klebsiella")
 #' 
+#' # for groups and complexes, set them as species or subspecies:
 #' add_custom_microorganisms(
-#'   data.frame(genus = "Citrobacter", species = "freundii complex"))
+#'   data.frame(genus = "Citrobacter", 
-#' mo_name("C. freundii complex")
+#'              species = c("freundii", "braakii complex"),
-#' mo_gramstain("C. freundii complex")
+#'              subspecies = c("complex", ""))
+#' )
+#' mo_name(c("C. freundii complex", "C. braakii complex"))
+#' mo_species(c("C. freundii complex", "C. braakii complex"))
+#' mo_gramstain(c("C. freundii complex", "C. braakii complex"))
 #' }
 add_custom_microorganisms <- function(x) {
   meet_criteria(x, allow_class = "data.frame")
@@ -135,12 +143,13 @@ add_custom_microorganisms <- function(x) {
       x[, col] <- as.character(x[, col, drop = TRUE])
     }
     col_ <- x[, col, drop = TRUE]
-    col_ <- tolower(trimws2(col_))
+    col_ <- tolower(col_)
+    col_ <- gsub("slashline", "", col_, fixed = TRUE)
+    col_ <- trimws2(col_)
     col_[col_ %like% "(sub)?species"] <- ""
     col_ <- gsub(" *([/-]) *", "\\1", col_, perl = TRUE)
-    # groups are in our taxonomic table with a capital G, and complexes might be added by the user
+    # groups are in our taxonomic table with a capital G
     col_ <- gsub(" group( |$)", " Group\\1", col_, perl = TRUE)
-    col_ <- gsub(" complex( |$)", " Complex\\1", col_, perl = TRUE)
     
     col_[is.na(col_)] <- ""
     if (col == "genus") {
@@ -151,6 +160,10 @@ add_custom_microorganisms <- function(x) {
     }
     x[, col] <- col_
   }
+  # if subspecies is a group or complex, add it to the species and empty the subspecies
+  x$species[which(x$subspecies %in% c("group", "Group", "complex"))] <- paste(x$species[which(x$subspecies %in% c("group", "Group", "complex"))],
+                                                                              x$subspecies[which(x$subspecies %in% c("group", "Group", "complex"))])
+  x$subspecies[which(x$subspecies %in% c("group", "Group", "complex"))] <- ""
   
   if ("rank" %in% colnames(x)) {
     stop_ifnot(all(x$rank %in% AMR_env$MO_lookup$rank),

R/mo.R

@@ -236,9 +236,8 @@ as.mo <- function(x,
     x[trimws2(x) %like% translate_into_language("no .*growth", language = language)] <- NA_character_
     x[trimws2(x) %like% paste0("^(", translate_into_language("no|not", language = language), ") ")] <- NA_character_
 
-    # groups are in our taxonomic table with a capital G, and complexes might be added by the user
+    # groups are in our taxonomic table with a capital G
     x <- gsub(" group( |$)", " Group\\1", x, perl = TRUE)
-    x <- gsub(" complex( |$)", " Complex\\1", x, perl = TRUE)
 
     # run over all unique leftovers
     x_unique <- unique(x[is.na(out) & !is.na(x)])

R/zzz.R

@@ -239,10 +239,3 @@ create_MO_lookup <- function() {
   MO_lookup$subspecies_first <- tolower(substr(MO_lookup$subspecies, 1, 1)) # tolower for Salmonella serovars
   MO_lookup
 }
-
-add_intrinsic_resistance_to_AMR_env <- function() {
-  # for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
-  if (is.null(AMR_env$intrinsic_resistant)) {
-    AMR_env$intrinsic_resistant <- paste(AMR::intrinsic_resistant$mo, AMR::intrinsic_resistant$ab)
-  }
-}

inst/tinytest/test-mo_property.R

@@ -95,6 +95,7 @@ expect_equal(mo_synonyms("Escherichia coli"), NULL)
 expect_true(length(mo_synonyms("Candida albicans")) > 1)
 expect_inherits(mo_synonyms(c("Candida albicans", "Escherichia coli")), "list")
 expect_equal(names(mo_info("Escherichia coli")), c(
+  "identifier",
   "kingdom", "phylum", "class", "order",
   "family", "genus", "species", "subspecies",
   "status", "synonyms", "gramstain", "url", "ref",

man/add_custom_antimicrobials.Rd

@@ -3,7 +3,7 @@
 \name{add_custom_antimicrobials}
 \alias{add_custom_antimicrobials}
 \alias{clear_custom_antimicrobials}
-\title{Add Custom Antimicrobials to This Package}
+\title{Add Custom Antimicrobials}
 \usage{
 add_custom_antimicrobials(x)
 
@@ -13,7 +13,7 @@ clear_custom_antimicrobials()
 \item{x}{a \link{data.frame} resembling the \link{antibiotics} data set, at least containing columns "ab" and "name"}
 }
 \description{
-With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own custom antimicrobial drug codes to the \code{AMR} package.
+With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own custom antimicrobial drug names and codes.
 }
 \details{
 \strong{Important:} Due to how \R works, the \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited.
@@ -52,7 +52,7 @@ Use \code{\link[=clear_custom_antimicrobials]{clear_custom_antimicrobials()}} to
 \examples{
 \donttest{
 
-# returns NA and throws a warning (which is now suppressed):
+# returns NA and throws a warning (which is suppressed here):
 suppressWarnings(
   as.ab("testab")
 )
@@ -101,5 +101,5 @@ x[, betalactams()]
 }
 }
 \seealso{
-\code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} to add custom microorganisms to this package.
+\code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} to add custom microorganisms.
 }

man/add_custom_microorganisms.Rd

@@ -3,7 +3,7 @@
 \name{add_custom_microorganisms}
 \alias{add_custom_microorganisms}
 \alias{clear_custom_microorganisms}
-\title{Add Custom Microorganisms to This Package}
+\title{Add Custom Microorganisms}
 \usage{
 add_custom_microorganisms(x)
 
@@ -13,7 +13,7 @@ clear_custom_microorganisms()
 \item{x}{a \link{data.frame} resembling the \link{microorganisms} data set, at least containing column "genus" (case-insensitive)}
 }
 \description{
-With \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} you can add your own custom microorganisms to the \code{AMR} package, such the non-taxonomic outcome of laboratory analysis.
+With \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} you can add your own custom microorganisms, such the non-taxonomic outcome of laboratory analysis.
 }
 \details{
 This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see \emph{Examples}.
@@ -83,17 +83,25 @@ mo_info("Enterobacter asburiae/cloacae")
 
 # the function tries to be forgiving:
 add_custom_microorganisms(
-  data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA",
+  data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA SLASHLINE",
-             SPECIES = "SPECIES"))
+             SPECIES = "SPECIES")
+)
 mo_name("ESCHERICHIA / KLEBSIELLA")
+mo_rank("ESCHERICHIA / KLEBSIELLA")
+# taxonomy still works, although a slashline genus was given as input:
 mo_family("Escherichia/Klebsiella")
 
+# for groups and complexes, set them as species or subspecies:
 add_custom_microorganisms(
-  data.frame(genus = "Citrobacter", species = "freundii complex"))
+  data.frame(genus = "Citrobacter", 
-mo_name("C. freundii complex")
+             species = c("freundii", "braakii complex"),
-mo_gramstain("C. freundii complex")
+             subspecies = c("complex", ""))
+)
+mo_name(c("C. freundii complex", "C. braakii complex"))
+mo_species(c("C. freundii complex", "C. braakii complex"))
+mo_gramstain(c("C. freundii complex", "C. braakii complex"))
 }
 }
 \seealso{
-\code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} to add custom antimicrobials to this package.
+\code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} to add custom antimicrobials.
 }

pkgdown/extra.css

@@ -78,6 +78,11 @@ pre .co, .co {
   color: #999999 !important;
   font-style: italic !important;
 }
+pre code .r-out,
+pre code .r-msg {
+  /* output of functions */
+  color: #555555 !important;
+}
 code a[href],
 a[href] code,
 pre a[href],

pkgdown/extra.js

@@ -33,15 +33,14 @@ $(document).ready(function() {
 
   // Replace 'Developers' with 'Maintainers' on the main page, and "Contributors" on the Authors page
   $(".developers h2").text("Maintainers");
-  $(".citation h2:first").text("All contributors");
+  $(".citation h2:nth(0)").text("All contributors");
-  $(".citation h2:second").text("How to Cite");
+  $(".citation h2:nth(1)").text("How to Cite");
 
   // remove \donttest and \dontrun texts in Examples
   if ($("#ref-examples ~ div pre").length > 0) {
-    const regex1 = /# \\dont(test|run)\{(\n|<br>)*/ig;
+    $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\donttest{", ""));
-    const regex2 = /(\n|<br>)*# \}/ig;
+    $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\dontrun{", ""));
-    $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll(regex1, ""));
+    $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# }", ""));
-    $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll(regex2, ""));
   }
 
   // remove leading newline in code examples on changelog