adding mo fixes

2023-01-14 19:50:25 +01:00 · 2023-01-14 19:50:25 +01:00 · b94bc6c67b
parent ca79068604
commit b94bc6c67b
12 changed files with 69 additions and 44 deletions
--- a/2
+++ b/2
@ -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)
--- a/NEWS.md
+++ b/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!)*

--- a/R/aa_helper_functions.R
+++ b/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)
--- a/R/custom_antimicrobials.R
+++ b/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")
 #' )
--- a/R/custom_microorganisms.R
+++ b/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",
-#'              SPECIES = "SPECIES"))
+#'   data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA SLASHLINE",
+#'              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"))
-#' mo_name("C. freundii complex")
-#' mo_gramstain("C. freundii complex")
+#'   data.frame(genus = "Citrobacter", 
+#'              species = c("freundii", "braakii 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),
--- a/R/mo.R
+++ b/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)])
--- a/R/zzz.R
+++ b/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)
-  }
-}
--- a/inst/tinytest/test-mo_property.R
+++ b/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",
--- a/man/add_custom_antimicrobials.Rd
+++ b/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.
 }
--- a/man/add_custom_microorganisms.Rd
+++ b/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",
-             SPECIES = "SPECIES"))
+  data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA SLASHLINE",
+             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"))
-mo_name("C. freundii complex")
-mo_gramstain("C. freundii complex")
+  data.frame(genus = "Citrobacter", 
+             species = c("freundii", "braakii 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.
 }
--- a/pkgdown/extra.css
+++ b/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],
--- a/pkgdown/extra.js
+++ b/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:second").text("How to Cite");
+  $(".citation h2:nth(0)").text("All contributors");
+  $(".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;
-    const regex2 = /(\n|<br>)*# \}/ig;
-    $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll(regex1, ""));
-    $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll(regex2, ""));
+    $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\donttest{", ""));
+    $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\dontrun{", ""));
+    $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# }", ""));
  }

  // remove leading newline in code examples on changelog