mirror of
https://github.com/msberends/AMR.git
synced 2025-07-09 01:22:25 +02:00
Fix for adding MO's
This commit is contained in:
@ -30,7 +30,7 @@
|
||||
#' Add Custom Microorganisms to This Package
|
||||
#'
|
||||
#' With [add_custom_microorganisms()] you can add your own custom microorganisms to the `AMR` package, such the non-taxonomic outcome of laboratory analysis.
|
||||
#' @param x a [data.frame] resembling the [microorganisms] data set, at least containing columns "genus" and "species"
|
||||
#' @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*.
|
||||
#'
|
||||
#' **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 "genus" and "species") 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 column "genus") 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:
|
||||
#'
|
||||
@ -98,16 +98,27 @@
|
||||
#' mo_gramstain("Enterobacter asburiae/cloacae")
|
||||
#'
|
||||
#' mo_info("Enterobacter asburiae/cloacae")
|
||||
#'
|
||||
#'
|
||||
#' # the function tries to be forgiving:
|
||||
#' add_custom_microorganisms(
|
||||
#' data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA",
|
||||
#' SPECIES = "SPECIES"))
|
||||
#' mo_name("ESCHERICHIA / KLEBSIELLA")
|
||||
#' mo_family("Escherichia/Klebsiella")
|
||||
#'
|
||||
#' add_custom_microorganisms(
|
||||
#' data.frame(genus = "Citrobacter", species = "freundii complex"))
|
||||
#' mo_name("C. freundii complex")
|
||||
#' mo_gramstain("C. freundii complex")
|
||||
#' }
|
||||
add_custom_microorganisms <- function(x) {
|
||||
meet_criteria(x, allow_class = "data.frame")
|
||||
stop_ifnot(
|
||||
all(c("genus", "species") %in% colnames(x)),
|
||||
paste0("`x` must contain columns ", vector_and(c("genus", "species"), sort = FALSE), ".")
|
||||
)
|
||||
stop_ifnot("genus" %in% tolower(colnames(x)), paste0("`x` must contain column 'genus'."))
|
||||
|
||||
# remove any extra class/type, such as grouped tbl, or data.table:
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
colnames(x) <- tolower(colnames(x))
|
||||
# rename 'name' to 'fullname' if it's in the data set
|
||||
if ("name" %in% colnames(x) && !"fullname" %in% colnames(x)) {
|
||||
colnames(x)[colnames(x) == "name"] <- "fullname"
|
||||
@ -116,21 +127,30 @@ add_custom_microorganisms <- function(x) {
|
||||
x <- x[, colnames(AMR_env$MO_lookup)[colnames(AMR_env$MO_lookup) %in% colnames(x)], drop = FALSE]
|
||||
|
||||
# clean the input ----
|
||||
if (!"subspecies" %in% colnames(x)) {
|
||||
x$subspecies <- NA_character_
|
||||
for (col in c("genus", "species", "subspecies")) {
|
||||
if (!col %in% colnames(x)) {
|
||||
x[, col] <- ""
|
||||
}
|
||||
if (is.factor(x[, col, drop = TRUE])) {
|
||||
x[, col] <- as.character(x[, col, drop = TRUE])
|
||||
}
|
||||
col_ <- x[, col, drop = TRUE]
|
||||
col_ <- tolower(trimws2(col_))
|
||||
col_[col_ %like% "(sub)?species"] <- ""
|
||||
col_ <- gsub(" *([/-]) *", "\\1", col_, perl = TRUE)
|
||||
# groups are in our taxonomic table with a capital G, and complexes might be added by the user
|
||||
col_ <- gsub(" group( |$)", " Group\\1", col_, perl = TRUE)
|
||||
col_ <- gsub(" complex( |$)", " Complex\\1", col_, perl = TRUE)
|
||||
|
||||
col_[is.na(col_)] <- ""
|
||||
if (col == "genus") {
|
||||
substr(col_, 1, 1) <- toupper(substr(col_, 1, 1))
|
||||
col_ <- gsub("/([a-z])", "/\\U\\1", col_, perl = TRUE)
|
||||
stop_if(any(col_ == ""), "the 'genus' column cannot be empty")
|
||||
stop_if(any(col_ %like% " "), "the 'genus' column must not contain spaces")
|
||||
}
|
||||
x[, col] <- col_
|
||||
}
|
||||
x$genus <- trimws2(x$genus)
|
||||
x$species <- trimws2(x$species)
|
||||
x$subspecies <- trimws2(x$subspecies)
|
||||
x$genus[is.na(x$genus)] <- ""
|
||||
x$species[is.na(x$species)] <- ""
|
||||
x$subspecies[is.na(x$subspecies)] <- ""
|
||||
stop_if(any(x$genus %like% " "),
|
||||
"the 'genus' column must not contain spaces")
|
||||
stop_if(any(x$species %like% " "),
|
||||
"the 'species' column must not contain spaces")
|
||||
stop_if(any(x$subspecies %like% " "),
|
||||
"the 'subspecies' column must not contain spaces")
|
||||
|
||||
if ("rank" %in% colnames(x)) {
|
||||
stop_ifnot(all(x$rank %in% AMR_env$MO_lookup$rank),
|
||||
@ -139,7 +159,7 @@ add_custom_microorganisms <- function(x) {
|
||||
x$rank <- ifelse(x$subspecies != "", "subspecies",
|
||||
ifelse(x$species != "", "species",
|
||||
ifelse(x$genus != "", "genus",
|
||||
stop("in add_custom_microorganisms(): the 'genus' column cannot be empty",
|
||||
stop("in add_custom_microorganisms(): only microorganisms up to the genus level can be added",
|
||||
call. = FALSE))))
|
||||
}
|
||||
x$source <- "Added by user"
|
||||
@ -158,22 +178,29 @@ add_custom_microorganisms <- function(x) {
|
||||
x$family[is.na(x$family)] <- ""
|
||||
|
||||
for (col in colnames(x)) {
|
||||
if (is.factor(x[, col, drop = TRUE])) {
|
||||
x[, col] <- as.character(x[, col, drop = TRUE])
|
||||
}
|
||||
if (is.list(AMR_env$MO_lookup[, col, drop = TRUE])) {
|
||||
x[, col] <- as.list(x[, col, drop = TRUE])
|
||||
}
|
||||
}
|
||||
|
||||
# fill in other columns
|
||||
# fill in taxonomy based on genus
|
||||
genus_to_check <- gsub("^(.*)[^a-zA-Z].*", "\\1", x$genus, perl = TRUE)
|
||||
x$kingdom[which(x$kingdom == "" & genus_to_check != "")] <- AMR_env$MO_lookup$kingdom[match(genus_to_check[which(x$kingdom == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
|
||||
x$phylum[which(x$phylum == "" & genus_to_check != "")] <- AMR_env$MO_lookup$phylum[match(genus_to_check[which(x$phylum == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
|
||||
x$class[which(x$class == "" & genus_to_check != "")] <- AMR_env$MO_lookup$class[match(genus_to_check[which(x$class == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
|
||||
x$order[which(x$order == "" & genus_to_check != "")] <- AMR_env$MO_lookup$order[match(genus_to_check[which(x$order == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
|
||||
x$family[which(x$family == "" & genus_to_check != "")] <- AMR_env$MO_lookup$family[match(genus_to_check[which(x$family == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
|
||||
|
||||
# fill in other columns that are used in internal algorithms
|
||||
x$status <- "accepted"
|
||||
x$prevalence <- 1
|
||||
|
||||
x$kingdom[which(x$kingdom == "" & x$genus != "")] <- AMR_env$MO_lookup$kingdom[match(x$genus[which(x$kingdom == "" & x$genus != "")], AMR_env$MO_lookup$genus)]
|
||||
x$phylum[which(x$phylum == "" & x$genus != "")] <- AMR_env$MO_lookup$phylum[match(x$genus[which(x$phylum == "" & x$genus != "")], AMR_env$MO_lookup$genus)]
|
||||
x$class[which(x$class == "" & x$genus != "")] <- AMR_env$MO_lookup$class[match(x$genus[which(x$class == "" & x$genus != "")], AMR_env$MO_lookup$genus)]
|
||||
x$order[which(x$order == "" & x$genus != "")] <- AMR_env$MO_lookup$order[match(x$genus[which(x$order == "" & x$genus != "")], AMR_env$MO_lookup$genus)]
|
||||
x$family[which(x$family == "" & x$genus != "")] <- AMR_env$MO_lookup$family[match(x$genus[which(x$family == "" & x$genus != "")], AMR_env$MO_lookup$genus)]
|
||||
|
||||
x$kingdom_index <- AMR_env$MO_lookup$kingdom_index[match(x$genus, AMR_env$MO_lookup$genus)]
|
||||
x$ref <- paste("Self-added,", format(Sys.Date(), "%Y"))
|
||||
x$kingdom_index <- AMR_env$MO_lookup$kingdom_index[match(genus_to_check, AMR_env$MO_lookup$genus)]
|
||||
# complete missing kingdom index, so mo_matching_score() will not return NA
|
||||
x$kingdom_index[is.na(x$kingdom_index)] <- 1
|
||||
x$fullname_lower <- tolower(x$fullname)
|
||||
x$full_first <- substr(x$fullname_lower, 1, 1)
|
||||
x$species_first <- tolower(substr(x$species, 1, 1))
|
||||
@ -183,18 +210,19 @@ add_custom_microorganisms <- function(x) {
|
||||
# create the mo code
|
||||
x$mo <- NA_character_
|
||||
}
|
||||
x$mo <- trimws2(x$mo)
|
||||
x$mo <- trimws2(as.character(x$mo))
|
||||
x$mo[x$mo == ""] <- NA_character_
|
||||
current <- sum(AMR_env$MO_lookup$source == "Added by user", na.rm = TRUE)
|
||||
x$mo[is.na(x$mo)] <- paste0("CUSTOM",
|
||||
seq(from = sum(AMR_env$MO_lookup$source == "Added by user", na.rm = TRUE) + 1, to = nrow(x), by = 1),
|
||||
seq.int(from = current + 1, to = current + nrow(x), by = 1),
|
||||
"_",
|
||||
toupper(unname(abbreviate(gsub(" +", " _ ",
|
||||
gsub("[^A-Za-z0-9-]", " ",
|
||||
trimws2(paste(x$genus, x$species, x$subspecies)))),
|
||||
minlength = 10))))
|
||||
stop_if(anyDuplicated(c(as.character(AMR_env$MO_lookup$mo), x$mo)), "MO codes must be unique and not match existing MO codes of the AMR package")
|
||||
|
||||
# add to package ----
|
||||
|
||||
AMR_env$custom_mo_codes <- c(AMR_env$custom_mo_codes, x$mo)
|
||||
class(AMR_env$MO_lookup$mo) <- "character"
|
||||
|
||||
@ -215,7 +243,11 @@ add_custom_microorganisms <- function(x) {
|
||||
|
||||
AMR_env$MO_lookup <- unique(rbind(AMR_env$MO_lookup, new_df))
|
||||
class(AMR_env$MO_lookup$mo) <- c("mo", "character")
|
||||
message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `microorganisms` data set.")
|
||||
if (nrow(x) <= 3) {
|
||||
message_("Added ", vector_and(italicise(x$fullname), quotes = FALSE), " to the internal `microorganisms` data set.")
|
||||
} else {
|
||||
message_("Added ", nr2char(nrow(x)), " records to the internal `microorganisms` data set.")
|
||||
}
|
||||
}
|
||||
|
||||
#' @rdname add_custom_microorganisms
|
||||
71
R/mo.R
71
R/mo.R
@ -183,7 +183,7 @@ as.mo <- function(x,
|
||||
x_lower <- tolower(x)
|
||||
|
||||
complexes <- x[trimws2(x_lower) %like_case% " (complex|group)$"]
|
||||
if (length(complexes) > 0 && identical(remove_from_input, mo_cleaning_regex())) {
|
||||
if (length(complexes) > 0 && identical(remove_from_input, mo_cleaning_regex()) && !any(AMR_env$MO_lookup$fullname[which(AMR_env$MO_lookup$source == "Added by user")] %like% "(group|complex)", na.rm = TRUE)) {
|
||||
warning_("in `as.mo()`: 'complex' and 'group' were ignored from the input in ", length(complexes), " case", ifelse(length(complexes) > 1, "s", ""), ", as they are currently not supported.\nYou can add your own microorganism with `add_custom_microorganisms()`.", call = FALSE)
|
||||
}
|
||||
|
||||
@ -222,7 +222,7 @@ as.mo <- function(x,
|
||||
if (isTRUE(info) && message_not_thrown_before("as.mo", old, new, entire_session = TRUE) && any(is.na(old) & !is.na(new), na.rm = TRUE)) {
|
||||
message_(
|
||||
"Returning previously coerced value", ifelse(sum(is.na(old) & !is.na(new)) > 1, "s", ""),
|
||||
" for ", vector_and(x[is.na(old) & !is.na(new)]), ". Run `mo_reset_session()` to reset this."
|
||||
" for ", vector_and(x[is.na(old) & !is.na(new)]), ". Run `mo_reset_session()` to reset this. This note will be shown once per session for this input."
|
||||
)
|
||||
}
|
||||
|
||||
@ -236,8 +236,9 @@ as.mo <- function(x,
|
||||
x[trimws2(x) %like% translate_into_language("no .*growth", language = language)] <- NA_character_
|
||||
x[trimws2(x) %like% paste0("^(", translate_into_language("no|not", language = language), ") ")] <- NA_character_
|
||||
|
||||
# groups are in our taxonomic table with a capital G
|
||||
x <- gsub(" group ", " Group ", x, fixed = TRUE)
|
||||
# groups are in our taxonomic table with a capital G, and complexes might be added by the user
|
||||
x <- gsub(" group( |$)", " Group\\1", x, perl = TRUE)
|
||||
x <- gsub(" complex( |$)", " Complex\\1", x, perl = TRUE)
|
||||
|
||||
# run over all unique leftovers
|
||||
x_unique <- unique(x[is.na(out) & !is.na(x)])
|
||||
@ -281,11 +282,11 @@ as.mo <- function(x,
|
||||
first_chars <- paste0("(^| )", "[", paste(substr(x_parts, 1, 1), collapse = ""), "]")
|
||||
filtr <- which(AMR_env$MO_lookup$full_first %like_case% first_chars)
|
||||
} else if (nchar(x_out) == 4) {
|
||||
# no space and 4 characters - probably a code such as STAU or ESCO!
|
||||
# no space and 4 characters - probably a code such as STAU or ESCO
|
||||
msg <- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on ", vector_and(c(substr(x_out, 1, 2), substr(x_out, 3, 4)), sort = FALSE)))
|
||||
filtr <- which(AMR_env$MO_lookup$fullname_lower %like_case% paste0("(^| )", substr(x_out, 1, 2), ".* ", substr(x_out, 3, 4)))
|
||||
} else if (nchar(x_out) <= 6) {
|
||||
# no space and 5-6 characters - probably a code such as STAAUR or ESCCOL!
|
||||
# no space and 5-6 characters - probably a code such as STAAUR or ESCCOL
|
||||
first_part <- paste0(substr(x_out, 1, 2), "[a-z]*", substr(x_out, 3, 3))
|
||||
second_part <- substr(x_out, 4, nchar(x_out))
|
||||
msg <- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on ", vector_and(c(gsub("[a-z]*", "(...)", first_part, fixed = TRUE), second_part), sort = FALSE)))
|
||||
@ -992,6 +993,9 @@ italicise <- function(x) {
|
||||
gsub("Salmonella ", "", x[x %like_case% "Salmonella [A-Z]"]))
|
||||
out[x %like_case% "Streptococcus [A-Z]"] <- paste(font_italic("Streptococcus"),
|
||||
gsub("Streptococcus ", "", x[x %like_case% "Streptococcus [A-Z]"]))
|
||||
if (has_colour()) {
|
||||
out <- gsub("(Group|group|Complex|complex)(\033\\[23m)?", "\033[23m\\1", out, perl = TRUE)
|
||||
}
|
||||
out
|
||||
}
|
||||
|
||||
@ -1009,33 +1013,36 @@ nr2char <- function(x) {
|
||||
|
||||
parse_and_convert <- function(x) {
|
||||
if (tryCatch(is.character(x) && all(Encoding(x) == "unknown", na.rm = TRUE), error = function(e) FALSE)) {
|
||||
return(trimws2(x))
|
||||
}
|
||||
tryCatch(
|
||||
{
|
||||
if (!is.null(dim(x))) {
|
||||
if (NCOL(x) > 2) {
|
||||
stop("a maximum of two columns is allowed", call. = FALSE)
|
||||
} else if (NCOL(x) == 2) {
|
||||
# support Tidyverse selection like: df %>% select(colA, colB)
|
||||
# paste these columns together
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
colnames(x) <- c("A", "B")
|
||||
x <- paste(x$A, x$B)
|
||||
} else {
|
||||
# support Tidyverse selection like: df %>% select(colA)
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)[[1]]
|
||||
out <- x
|
||||
} else {
|
||||
out <- tryCatch(
|
||||
{
|
||||
if (!is.null(dim(x))) {
|
||||
if (NCOL(x) > 2) {
|
||||
stop("a maximum of two columns is allowed", call. = FALSE)
|
||||
} else if (NCOL(x) == 2) {
|
||||
# support Tidyverse selection like: df %>% select(colA, colB)
|
||||
# paste these columns together
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
colnames(x) <- c("A", "B")
|
||||
x <- paste(x$A, x$B)
|
||||
} else {
|
||||
# support Tidyverse selection like: df %>% select(colA)
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)[[1]]
|
||||
}
|
||||
}
|
||||
}
|
||||
parsed <- iconv(as.character(x), to = "UTF-8")
|
||||
parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT")
|
||||
parsed <- gsub('"', "", parsed, fixed = TRUE)
|
||||
parsed <- gsub(" +", " ", parsed, perl = TRUE)
|
||||
parsed
|
||||
},
|
||||
error = function(e) stop(e$message, call. = FALSE)
|
||||
) # this will also be thrown when running `as.mo(no_existing_object)`
|
||||
trimws2(parsed)
|
||||
parsed <- iconv(as.character(x), to = "UTF-8")
|
||||
parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT")
|
||||
parsed <- gsub('"', "", parsed, fixed = TRUE)
|
||||
parsed
|
||||
},
|
||||
error = function(e) stop(e$message, call. = FALSE)
|
||||
) # this will also be thrown when running `as.mo(no_existing_object)`
|
||||
}
|
||||
out <- trimws2(out)
|
||||
out <- gsub(" +", " ", out, perl = TRUE)
|
||||
out <- gsub(" ?/ ? ", "/", out, perl = TRUE)
|
||||
out
|
||||
}
|
||||
|
||||
replace_old_mo_codes <- function(x, property) {
|
||||
|
||||
@ -39,7 +39,9 @@
|
||||
#' @section Matching Score for Microorganisms:
|
||||
#' With ambiguous user input in [as.mo()] and all the [`mo_*`][mo_property()] functions, the returned results are chosen based on their matching score using [mo_matching_score()]. This matching score \eqn{m}, is calculated as:
|
||||
#'
|
||||
#' \ifelse{latex}{\deqn{m_{(x, n)} = \frac{l_{n} - 0.5 \cdot \min \begin{cases}l_{n} \\ \textrm{lev}(x, n)\end{cases}}{l_{n} \cdot p_{n} \cdot k_{n}}}}{\ifelse{html}{\figure{mo_matching_score.png}{options: width="300" alt="mo matching score"}}{m(x, n) = ( l_n * min(l_n, lev(x, n) ) ) / ( l_n * p_n * k_n )}}
|
||||
#' \ifelse{latex}{\deqn{m_{(x, n)} = \frac{l_{n} - 0.5 \cdot \min \begin{cases}l_{n} \\ \textrm{lev}(x, n)\end{cases}}{l_{n} \cdot p_{n} \cdot k_{n}}}}{
|
||||
#'
|
||||
#' \ifelse{html}{\figure{mo_matching_score.png}{options: width="300" alt="mo matching score"}}{m(x, n) = ( l_n * min(l_n, lev(x, n) ) ) / ( l_n * p_n * k_n )}}
|
||||
#'
|
||||
#' where:
|
||||
#'
|
||||
@ -47,7 +49,7 @@
|
||||
#' * \eqn{n} is a taxonomic name (genus, species, and subspecies);
|
||||
#' * \eqn{l_n} is the length of \eqn{n};
|
||||
#' * \eqn{lev} is the [Levenshtein distance function](https://en.wikipedia.org/wiki/Levenshtein_distance) (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change \eqn{x} into \eqn{n};
|
||||
#' * \eqn{p_{n}} is the human pathogenic prevalence group of \eqn{n}, as described below;
|
||||
#' * \eqn{p_n} is the human pathogenic prevalence group of \eqn{n}, as described below;
|
||||
#' * \eqn{k_n} is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.
|
||||
#'
|
||||
#' The grouping into human pathogenic prevalence \eqn{p} is based on recent work from Bartlett *et al.* (2022, \doi{10.1099/mic.0.001269}) who extensively studied medical-scientific literature to categorise all bacterial species into these groups:
|
||||
|
||||
@ -777,6 +777,7 @@ mo_info <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A
|
||||
|
||||
info <- lapply(x, function(y) {
|
||||
c(
|
||||
list(identifier = x),
|
||||
mo_taxonomy(y, language = language, keep_synonyms = keep_synonyms),
|
||||
list(
|
||||
status = mo_status(y, language = language, keep_synonyms = keep_synonyms),
|
||||
|
||||
Reference in New Issue
Block a user