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custom mo update

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dr. M.S. (Matthijs) Berends 2022-12-28 14:20:10 +01:00
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commit ba3b237bdf
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR 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 Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

2
NEWS.md
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@ -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!)* *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*

82
R/add_custom_microorganisms.R
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@ -30,7 +30,7 @@
#' Add Custom Microorganisms to This Package #' Add Custom Microorganisms to This Package
#' #'
#' With [add_custom_microorganisms()] you can add your own custom antimicrobial drug codes to the `AMR` 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*. #' @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. #' **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: #' **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: #' 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: #' # Add custom antibiotic drug codes:
#' library(AMR) #' library(AMR)
#' add_custom_microorganisms( #' add_custom_microorganisms(
#' data.frame(mo = "ENT_ASB_CLO", #' data.frame(genus = "Enterobacter",
#' genus = "Enterobacter",
#' species = "asburiae/cloacae") #' species = "asburiae/cloacae")
#' ) #' )
#' ``` #' ```
@ -80,36 +79,32 @@
#' # now add a custom entry - it will be considered by as.mo() and #' # now add a custom entry - it will be considered by as.mo() and
#' # all mo_*() functions #' # all mo_*() functions
#' add_custom_microorganisms( #' add_custom_microorganisms(
#' data.frame(mo = "ENT_ASB_CLO", #' data.frame(genus = "Enterobacter",
#' genus = "Enterobacter",
#' species = "asburiae/cloacae" #' species = "asburiae/cloacae"
#' ) #' )
#' ) #' )
#' #'
#' # "ENT_ASB_CLO" is now a new microorganism: #' # E. asburiae/cloacae is now a new microorganism:
#' mo_name("Enterobacter asburiae/cloacae") #' 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: #' # all internal algorithms will work as well:
#' mo_name("Ent asburia cloacae") #' mo_name("Ent asburia cloacae")
#' #'
#' # and even the taxonomy was added based on the genus! #' # 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_gramstain("Enterobacter asburiae/cloacae")
#' #'
#' mo_info("ent_asb_clo") #' mo_info("Enterobacter asburiae/cloacae")
#' } #' }
add_custom_microorganisms <- function(x) { add_custom_microorganisms <- function(x) {
meet_criteria(x, allow_class = "data.frame") meet_criteria(x, allow_class = "data.frame")
required_cols <- c("mo", "genus", "species")
stop_ifnot( 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$mo]), " already exist in the internal `microorganisms` data set."
) )
# remove any extra class/type, such as grouped tbl, or data.table: # remove any extra class/type, such as grouped tbl, or data.table:
x <- as.data.frame(x, stringsAsFactors = FALSE) x <- as.data.frame(x, stringsAsFactors = FALSE)
# rename 'name' to 'fullname' if it's in the data set # rename 'name' to 'fullname' if it's in the data set
@ -126,14 +121,14 @@ add_custom_microorganisms <- function(x) {
x$genus <- trimws2(x$genus) x$genus <- trimws2(x$genus)
x$species <- trimws2(x$species) x$species <- trimws2(x$species)
x$subspecies <- trimws2(x$subspecies) x$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") "the 'genus' column must not contain spaces")
stop_if(any(x$species[!is.na(x$species)] %like% " "), stop_if(any(x$species %like% " "),
"the 'species' column must not contain spaces") "the 'species' column must not contain spaces")
stop_if(any(x$subspecies[!is.na(x$subspecies)] %like% " "), stop_if(any(x$subspecies %like% " "),
"the 'subspecies' column must not contain spaces") "the 'subspecies' column must not contain spaces")
if ("rank" %in% colnames(x)) { if ("rank" %in% colnames(x)) {
@ -147,14 +142,13 @@ add_custom_microorganisms <- function(x) {
call. = FALSE)))) call. = FALSE))))
} }
if (!"fullname" %in% colnames(x)) { 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)) { for (col in colnames(x)) {
if (is.list(AMR_env$MO_lookup[, col, drop = TRUE])) { if (is.list(AMR_env$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$order <- AMR_env$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$family <- AMR_env$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$kingdom_index <- AMR_env$MO_lookup$kingdom_index[match(x$genus, AMR_env$MO_lookup$genus)]
x$fullname_lower <- tolower(x$fullname) x$fullname_lower <- tolower(x$fullname)
x$full_first <- substr(x$fullname_lower, 1, 1) x$full_first <- substr(x$fullname_lower, 1, 1)
x$species_first <- tolower(substr(x$species, 1, 1)) x$species_first <- tolower(substr(x$species, 1, 1))
x$subspecies_first <- tolower(substr(x$subspecies, 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$mo) AMR_env$custom_mo_codes <- c(AMR_env$custom_mo_codes, x$mo)
class(AMR_env$MO_lookup$mo) <- "character" class(AMR_env$MO_lookup$mo) <- "character"
@ -193,8 +206,11 @@ add_custom_microorganisms <- function(x) {
# assign new values # assign new values
new_df[, col] <- x[, col, drop = TRUE] 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$MO_lookup <- unique(rbind(AMR_env$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$mo) <- c("mo", "character") class(AMR_env$MO_lookup$mo) <- c("mo", "character")
message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `microorganisms` data set.") message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `microorganisms` data set.")
} }

8
R/mo.R
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@ -182,9 +182,9 @@ as.mo <- function(x,
x_lower <- tolower(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 # 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)[.]*( |$))" "(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|serogr.?up|e?species|group|complex)[.]*( |$))"
) )
} }

20
man/add_custom_microorganisms.Rd
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@ -10,7 +10,7 @@ add_custom_microorganisms(x)
clear_custom_microorganisms() clear_custom_microorganisms()
} }
\arguments{ \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{ \description{
With \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} you can add your own custom antimicrobial drug codes to the \code{AMR} package. 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: \strong{Method 1:} Save the microorganisms to a local or remote file (can even be the internet). To use this method:
\enumerate{ \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: \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: \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: \if{html}{\out{<div class="sourceCode r">}}\preformatted{ # Add custom antibiotic drug codes:
library(AMR) library(AMR)
add_custom_microorganisms( add_custom_microorganisms(
data.frame(mo = "ENT_ASB_CLO", data.frame(genus = "Enterobacter",
genus = "Enterobacter",
species = "asburiae/cloacae") species = "asburiae/cloacae")
) )
}\if{html}{\out{</div>}} }\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 # now add a custom entry - it will be considered by as.mo() and
# all mo_*() functions # all mo_*() functions
add_custom_microorganisms( add_custom_microorganisms(
data.frame(mo = "ENT_ASB_CLO", data.frame(genus = "Enterobacter",
genus = "Enterobacter",
species = "asburiae/cloacae" species = "asburiae/cloacae"
) )
) )
# "ENT_ASB_CLO" is now a new microorganism: # E. asburiae/cloacae is now a new microorganism:
mo_name("Enterobacter asburiae/cloacae") 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: # all internal algorithms will work as well:
mo_name("Ent asburia cloacae") mo_name("Ent asburia cloacae")
# and even the taxonomy was added based on the genus! # 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_gramstain("Enterobacter asburiae/cloacae")
mo_info("ent_asb_clo") mo_info("Enterobacter asburiae/cloacae")
} }
} }
\seealso{ \seealso{