custom mo update

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.2.9071
+Version: 1.8.2.9072
-Date: 2022-12-27
+Date: 2022-12-28
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9071
+# AMR 1.8.2.9072
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 

R/add_custom_microorganisms.R

@@ -30,7 +30,7 @@
 #' Add Custom Microorganisms to This Package
 #'
 #' With [add_custom_microorganisms()] you can add your own custom antimicrobial drug codes to the `AMR` package.
-#' @param x a [data.frame] resembling the [microorganisms] data set, at least containing columns "mo", "genus" and "species"
+#' @param x a [data.frame] resembling the [microorganisms] data set, at least containing columns "genus" and "species"
 #' @details This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see *Examples*.
 #' 
 #' **Important:** Due to how \R works, the [add_custom_microorganisms()] function has to be run in every \R session - added microorganisms are not stored between sessions and are thus lost when \R is exited. 
@@ -39,7 +39,7 @@
 #' 
 #' **Method 1:** Save the microorganisms to a local or remote file (can even be the internet). To use this method:
 #' 
-#'    1. Create a data set in the structure of the [microorganisms] data set (containing at the very least columns "ab" and "name") and save it with [saveRDS()] to a location of choice, e.g. `"~/my_custom_mo.rds"`, or any remote location.
+#'    1. Create a data set in the structure of the [microorganisms] data set (containing at the very least columns "genus" and "species") and save it with [saveRDS()] to a location of choice, e.g. `"~/my_custom_mo.rds"`, or any remote location.
 #'    
 #'    2. Set the file location to the `AMR_custom_mo` \R option: `options(AMR_custom_mo = "~/my_custom_mo.rds")`. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the `.Rprofile` file so that it will loaded on start-up of \R. To do this, open the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`, add this text and save the file:
 #'
@@ -60,8 +60,7 @@
 #'        # Add custom antibiotic drug codes:
 #'        library(AMR)
 #'        add_custom_microorganisms(
-#'          data.frame(mo = "ENT_ASB_CLO",
+#'          data.frame(genus = "Enterobacter",
-#'                     genus = "Enterobacter",
 #'                     species = "asburiae/cloacae")
 #'        )
 #'       ```
@@ -80,36 +79,32 @@
 #' # now add a custom entry - it will be considered by as.mo() and
 #' # all mo_*() functions
 #' add_custom_microorganisms(
-#'   data.frame(mo = "ENT_ASB_CLO",
+#'   data.frame(genus = "Enterobacter",
-#'              genus = "Enterobacter",
 #'              species = "asburiae/cloacae"
 #'   )
 #' )
 #'
-#' # "ENT_ASB_CLO" is now a new microorganism:
+#' # E. asburiae/cloacae is now a new microorganism:
 #' mo_name("Enterobacter asburiae/cloacae")
-#' as.mo("ent_asb_clo")
+#' # its code:
-#' mo_name("ent_asb_clo")
+#' as.mo("Enterobacter asburiae/cloacae")
+
 #' # all internal algorithms will work as well:
 #' mo_name("Ent asburia cloacae")
 #' 
 #' # and even the taxonomy was added based on the genus!
-#' mo_family("ent_asb_clo")
+#' mo_family("E. asburiae/cloacae")
 #' mo_gramstain("Enterobacter asburiae/cloacae")
 #'
-#' mo_info("ent_asb_clo")
+#' mo_info("Enterobacter asburiae/cloacae")
 #' }
 add_custom_microorganisms <- function(x) {
   meet_criteria(x, allow_class = "data.frame")
-  required_cols <- c("mo", "genus", "species")
   stop_ifnot(
-    all(required_cols %in% colnames(x)),
+    all(c("genus", "species") %in% colnames(x)),
-    paste0("`x` must contain columns ", vector_and(required_cols, sort = FALSE), ".")
+    paste0("`x` must contain columns ", vector_and(c("genus", "species"), sort = FALSE), ".")
-  )
-  stop_if(
-    any(x$mo %in% AMR_env$MO_lookup$mo),
-    "Microorganism code(s) ", vector_and(x$mo[x$mo %in% AMR_env$MO_lookup$mo]), " already exist in the internal `microorganisms` data set."
   )
+  
   # remove any extra class/type, such as grouped tbl, or data.table:
   x <- as.data.frame(x, stringsAsFactors = FALSE)
   # rename 'name' to 'fullname' if it's in the data set
@@ -126,14 +121,14 @@ add_custom_microorganisms <- function(x) {
   x$genus <- trimws2(x$genus)
   x$species <- trimws2(x$species)
   x$subspecies <- trimws2(x$subspecies)
-  x$genus[x$genus == ""] <- NA_character_
+  x$genus[is.na(x$genus)] <- ""
-  x$species[x$species == ""] <- NA_character_
+  x$species[is.na(x$species)] <- ""
-  x$subspecies[x$subspecies == ""] <- NA_character_
+  x$subspecies[is.na(x$subspecies)] <- ""
-  stop_if(any(x$genus[!is.na(x$genus)] %like% " "),
+  stop_if(any(x$genus %like% " "),
           "the 'genus' column must not contain spaces")
-  stop_if(any(x$species[!is.na(x$species)] %like% " "),
+  stop_if(any(x$species %like% " "),
           "the 'species' column must not contain spaces")
-  stop_if(any(x$subspecies[!is.na(x$subspecies)] %like% " "),
+  stop_if(any(x$subspecies %like% " "),
           "the 'subspecies' column must not contain spaces")
   
   if ("rank" %in% colnames(x)) {
@@ -147,14 +142,13 @@ add_custom_microorganisms <- function(x) {
                                         call. = FALSE))))
   }
   if (!"fullname" %in% colnames(x)) {
-    x$fullname <- paste(x$genus, x$species, x$subspecies)
+    x$fullname <- trimws2(paste(x$genus, x$species, x$subspecies))
-    x$fullname <- gsub(" NA", "", x$fullname)
   }
-  if (!"kingdom" %in% colnames(x)) x$kingdom <- NA_character_
+  if (!"kingdom" %in% colnames(x)) x$kingdom <- ""
-  if (!"phylum" %in% colnames(x)) x$phylum <- NA_character_
+  if (!"phylum" %in% colnames(x)) x$phylum <- ""
-  if (!"class" %in% colnames(x)) x$class <- NA_character_
+  if (!"class" %in% colnames(x)) x$class <- ""
-  if (!"order" %in% colnames(x)) x$order <- NA_character_
+  if (!"order" %in% colnames(x)) x$order <- ""
-  if (!"family" %in% colnames(x)) x$family <- NA_character_
+  if (!"family" %in% colnames(x)) x$family <- ""
 
   for (col in colnames(x)) {
     if (is.list(AMR_env$MO_lookup[, col, drop = TRUE])) {
@@ -171,13 +165,32 @@ add_custom_microorganisms <- function(x) {
   x$order <- AMR_env$MO_lookup$order[match(x$genus, AMR_env$MO_lookup$genus)]
   x$family <- AMR_env$MO_lookup$family[match(x$genus, AMR_env$MO_lookup$genus)]
   
+  x$kingdom[is.na(x$kingdom)] <- ""
+  x$phylum[is.na(x$phylum)] <- ""
+  x$class[is.na(x$class)] <- ""
+  x$order[is.na(x$order)] <- ""
+  x$family[is.na(x$family)] <- ""
+  
   x$kingdom_index <- AMR_env$MO_lookup$kingdom_index[match(x$genus, AMR_env$MO_lookup$genus)]
   x$fullname_lower <- tolower(x$fullname)
   x$full_first <- substr(x$fullname_lower, 1, 1)
   x$species_first <- tolower(substr(x$species, 1, 1))
   x$subspecies_first <- tolower(substr(x$subspecies, 1, 1))
   
-  # add to pacakge ----
+  if (!"mo" %in% colnames(x)) {
+    # create the mo code
+    x$mo <- NA_character_
+  }
+  x$mo <- trimws2(x$mo)
+  x$mo[x$mo == ""] <- NA_character_
+  x$mo[is.na(x$mo)] <- paste0("CUSTOM_",
+                              toupper(abbreviate(gsub(" +", " _ ",
+                                                      gsub("[^A-Za-z0-9-]", " ",
+                                                                        trimws2(paste(x$genus, x$species, x$subspecies)))),
+                                                 minlength = 10,
+                                                 named = FALSE)))
+  
+  # add to package ----
   
   AMR_env$custom_mo_codes <- c(AMR_env$custom_mo_codes, x$mo)
   class(AMR_env$MO_lookup$mo) <- "character"
@@ -193,8 +206,11 @@ add_custom_microorganisms <- function(x) {
     # assign new values
     new_df[, col] <- x[, col, drop = TRUE]
   }
+  
+  # clear previous coercions
+  suppressMessages(mo_reset_session())
+  
   AMR_env$MO_lookup <- unique(rbind(AMR_env$MO_lookup, new_df))
-  AMR_env$mo_previously_coerced <- AMR_env$mo_previously_coerced[which(!AMR_env$mo_previously_coerced$mo %in% new_df$mo), , drop = FALSE]
   class(AMR_env$MO_lookup$mo) <- c("mo", "character")
   message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `microorganisms` data set.")
 }

R/mo.R

@@ -182,9 +182,9 @@ as.mo <- function(x,
 
   x_lower <- tolower(x)
   
-  complexes <- x[trimws2(x_lower) %like_case% "complex$"]
+  complexes <- x[trimws2(x_lower) %like_case% " (complex|group)$"]
-  if (length(complexes) > 0) {
+  if (length(complexes) > 0 && identical(remove_from_input, mo_cleaning_regex())) {
-    warning_("in `as.mo()`: translation of complexes is not supported at the moment - the input text 'complex' was ignored in ", length(complexes), " cases.", call = FALSE)
+    warning_("in `as.mo()`: 'complex' and 'group' were ignored from the input in ", length(complexes), " case", ifelse(length(complexes) > 1, "s", ""), ", as they are currently not supported.\nYou can add your own microorganism with `add_custom_microorganisms()`.", call = FALSE)
   }
   
   # WHONET: xxx = no growth
@@ -536,7 +536,7 @@ mo_cleaning_regex <- function() {
     "|",
     "([({]|\\[).+([})]|\\])",
     "|",
-    "(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|serogr.?up|e?species|complex)[.]*( |$))"
+    "(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|serogr.?up|e?species|group|complex)[.]*( |$))"
   )
 }
 

man/add_custom_microorganisms.Rd

@@ -10,7 +10,7 @@ add_custom_microorganisms(x)
 clear_custom_microorganisms()
 }
 \arguments{
-\item{x}{a \link{data.frame} resembling the \link{microorganisms} data set, at least containing columns "mo", "genus" and "species"}
+\item{x}{a \link{data.frame} resembling the \link{microorganisms} data set, at least containing columns "genus" and "species"}
 }
 \description{
 With \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} you can add your own custom antimicrobial drug codes to the \code{AMR} package.
@@ -24,7 +24,7 @@ There are two ways to automate this process:
 
 \strong{Method 1:} Save the microorganisms to a local or remote file (can even be the internet). To use this method:
 \enumerate{
-\item Create a data set in the structure of the \link{microorganisms} data set (containing at the very least columns "ab" and "name") and save it with \code{\link[=saveRDS]{saveRDS()}} to a location of choice, e.g. \code{"~/my_custom_mo.rds"}, or any remote location.
+\item Create a data set in the structure of the \link{microorganisms} data set (containing at the very least columns "genus" and "species") and save it with \code{\link[=saveRDS]{saveRDS()}} to a location of choice, e.g. \code{"~/my_custom_mo.rds"}, or any remote location.
 \item Set the file location to the \code{AMR_custom_mo} \R option: \code{options(AMR_custom_mo = "~/my_custom_mo.rds")}. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the \code{.Rprofile} file so that it will loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file:
 
 \if{html}{\out{<div class="sourceCode r">}}\preformatted{# Add custom microorganism codes:
@@ -42,8 +42,7 @@ Upon package load, this file will be loaded and run through the \code{\link[=add
 \if{html}{\out{<div class="sourceCode r">}}\preformatted{ # Add custom antibiotic drug codes:
  library(AMR)
  add_custom_microorganisms(
-   data.frame(mo = "ENT_ASB_CLO",
+   data.frame(genus = "Enterobacter",
-              genus = "Enterobacter",
               species = "asburiae/cloacae")
  )
 }\if{html}{\out{</div>}}
@@ -61,24 +60,23 @@ mo_name("Enterobacter asburiae/cloacae")
 # now add a custom entry - it will be considered by as.mo() and
 # all mo_*() functions
 add_custom_microorganisms(
-  data.frame(mo = "ENT_ASB_CLO",
+  data.frame(genus = "Enterobacter",
-             genus = "Enterobacter",
              species = "asburiae/cloacae"
   )
 )
 
-# "ENT_ASB_CLO" is now a new microorganism:
+# E. asburiae/cloacae is now a new microorganism:
 mo_name("Enterobacter asburiae/cloacae")
-as.mo("ent_asb_clo")
+# its code:
-mo_name("ent_asb_clo")
+as.mo("Enterobacter asburiae/cloacae")
 # all internal algorithms will work as well:
 mo_name("Ent asburia cloacae")
 
 # and even the taxonomy was added based on the genus!
-mo_family("ent_asb_clo")
+mo_family("E. asburiae/cloacae")
 mo_gramstain("Enterobacter asburiae/cloacae")
 
-mo_info("ent_asb_clo")
+mo_info("Enterobacter asburiae/cloacae")
 }
 }
 \seealso{