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(v1.7.1.9064) eucast 3.3 for mdro(), major change to repeated calling

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dr. M.S. (Matthijs) Berends 2021-12-11 13:41:31 +01:00
parent e18c49ed93
commit 77ba4318ea
64 changed files with 51141 additions and 9840 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.7.1.9063 Version: 1.7.1.9064
Date: 2021-12-09 Date: 2021-12-11
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

10
NEWS.md
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@ -1,5 +1,5 @@
# `AMR` 1.7.1.9063 # `AMR` 1.7.1.9064
## <small>Last updated: 9 December 2021</small> ## <small>Last updated: 11 December 2021</small>
### Breaking changes ### Breaking changes
* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version * Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
@ -7,7 +7,7 @@
* Removed all previously implemented `ggplot2::ggplot()` generics for classes `<mic>`, `<disk>`, `<rsi>` and `<resistance_predict>` as they did not follow the `ggplot2` logic. They were replaced with `ggplot2::autoplot()` generics. * Removed all previously implemented `ggplot2::ggplot()` generics for classes `<mic>`, `<disk>`, `<rsi>` and `<resistance_predict>` as they did not follow the `ggplot2` logic. They were replaced with `ggplot2::autoplot()` generics.
### New ### New
* Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021), effective in the `eucast_rules()` function. This is now the default guideline (all other guidelines are still available). * Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021). This is now the default EUCAST guideline in the package (all older guidelines are still available) for `eucast_rules()`, `mo_intrinsic_resistant()` and `mdro()`. The `intrinsic_resistant` data set was also updated accordingly.
* Support for Danish, and also added missing translations of all antimicrobial drugs in Italian, French and Portuguese * Support for Danish, and also added missing translations of all antimicrobial drugs in Italian, French and Portuguese
* Function `set_ab_names()` to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc. Its second argument can be a tidyverse way of selecting: * Function `set_ab_names()` to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc. Its second argument can be a tidyverse way of selecting:
```r ```r
@ -15,6 +15,7 @@
example_isolates %>% set_ab_names(AMC:GEN, property = "atc") example_isolates %>% set_ab_names(AMC:GEN, property = "atc")
``` ```
* Function `mo_lpsn()` to retrieve the [LPSN](https://lpsn.dsmz.de) record ID * Function `mo_lpsn()` to retrieve the [LPSN](https://lpsn.dsmz.de) record ID
* Function `ab_ddd_units()` to get units of DDDs (daily defined doses), deprecating the use of `ab_ddd(..., units = TRUE)` to be more consistent in data types of function output
### Changed ### Changed
* Updated the bacterial taxonomy to 5 October 2021 (according to [LPSN](https://lpsn.dsmz.de)), including all 11 new staphylococcal species named since 1 January last year * Updated the bacterial taxonomy to 5 October 2021 (according to [LPSN](https://lpsn.dsmz.de)), including all 11 new staphylococcal species named since 1 January last year
@ -38,9 +39,10 @@
example_isolates %>% select(ab_selector(oral_ddd > 1 & oral_units == "g")) # dplyr example_isolates %>% select(ab_selector(oral_ddd > 1 & oral_units == "g")) # dplyr
``` ```
* Added the selector `not_intrinsic_resistant()`, which only keeps antibiotic columns that are not intrinsic resistant for all microorganisms in a data set, based on the latest EUCAST guideline on intrinsic resistance. For example, if a data set contains only microorganism codes or names of *E. coli* and *K. pneumoniae* and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. * Added the selector `not_intrinsic_resistant()`, which only keeps antibiotic columns that are not intrinsic resistant for all microorganisms in a data set, based on the latest EUCAST guideline on intrinsic resistance. For example, if a data set contains only microorganism codes or names of *E. coli* and *K. pneumoniae* and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function.
* Added argument `only_treatable`, which defaults to `TRUE` and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)
* Fix for using selectors multiple times in one call (e.g., using them in `dplyr::filter()` and immediately after in `dplyr::select()`) * Fix for using selectors multiple times in one call (e.g., using them in `dplyr::filter()` and immediately after in `dplyr::select()`)
* Fix for using having multiple columns that are coerced to the same antibiotic agent * Fix for using having multiple columns that are coerced to the same antibiotic agent
* Added argument `only_treatable`, which defaults to `TRUE` and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high) * Fixed for using `all()` or `any()` on antibiotic selectors in an R Markdown file
* Fixed the Gram stain (`mo_gramstain()`) determination of the taxonomic class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as *Negativicoccus* and *Veillonella*. * Fixed the Gram stain (`mo_gramstain()`) determination of the taxonomic class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as *Negativicoccus* and *Veillonella*.
* Dramatic speed improvement for `first_isolate()` * Dramatic speed improvement for `first_isolate()`
* Fix to prevent introducing `NA`s for old MO codes when running `as.mo()` on them * Fix to prevent introducing `NA`s for old MO codes when running `as.mo()` on them

0
R/globals.R → R/aa_globals.R
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68
R/aa_helper_functions.R
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@ -201,7 +201,7 @@ check_dataset_integrity <- function() {
} else { } else {
plural <- c(" is", "s", "") plural <- c(" is", "s", "")
} }
if (message_not_thrown_before("dataset_overwritten")) { if (message_not_thrown_before("check_dataset_integrity", overwritten)) {
warning_("The following data set", plural[1], warning_("The following data set", plural[1],
" overwritten by your global environment and prevent", plural[2], " overwritten by your global environment and prevent", plural[2],
" the AMR package from working correctly: ", " the AMR package from working correctly: ",
@ -323,7 +323,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
found <- found[1] found <- found[1]
if (!is.null(found) & info == TRUE) { if (!is.null(found) & info == TRUE) {
if (message_not_thrown_before(fn = paste0("search_", type))) { if (message_not_thrown_before("search_in_type", type)) {
msg <- paste0("Using column '", font_bold(found), "' as input for `col_", type, "`.") msg <- paste0("Using column '", font_bold(found), "' as input for `col_", type, "`.")
if (type %in% c("keyantibiotics", "keyantimicrobials", "specimen")) { if (type %in% c("keyantibiotics", "keyantimicrobials", "specimen")) {
msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.") msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
@ -804,14 +804,17 @@ meet_criteria <- function(object,
} }
get_current_data <- function(arg_name, call) { get_current_data <- function(arg_name, call) {
valid_df <- function(x) {
!is.null(x) && is.data.frame(x)
}
# try dplyr::cur_data_all() first to support dplyr groups # try dplyr::cur_data_all() first to support dplyr groups
# only useful for e.g. dplyr::filter(), dplyr::mutate() and dplyr::summarise() # only useful for e.g. dplyr::filter(), dplyr::mutate() and dplyr::summarise()
# not useful (throws error) with e.g. dplyr::select() - but that will be caught later in this function # not useful (throws error) with e.g. dplyr::select() - but that will be caught later in this function
cur_data_all <- import_fn("cur_data_all", "dplyr", error_on_fail = FALSE) cur_data_all <- import_fn("cur_data_all", "dplyr", error_on_fail = FALSE)
if (!is.null(cur_data_all)) { if (!is.null(cur_data_all)) {
out <- tryCatch(cur_data_all(), error = function(e) NULL) out <- tryCatch(cur_data_all(), error = function(e) NULL)
if (is.data.frame(out)) { if (valid_df(out)) {
return(structure(out, type = "dplyr_cur_data_all")) return(out)
} }
} }
@ -820,18 +823,18 @@ get_current_data <- function(arg_name, call) {
if (!is.null(env$`.Generic`)) { if (!is.null(env$`.Generic`)) {
# don't check `".Generic" %in% names(env)`, because in R < 3.2, `names(env)` is always NULL # don't check `".Generic" %in% names(env)`, because in R < 3.2, `names(env)` is always NULL
if (!is.null(env$`.data`) && is.data.frame(env$`.data`)) { if (valid_df(env$`.data`)) {
# an element `.data` will be in the environment when using `dplyr::select()` # an element `.data` will be in the environment when using `dplyr::select()`
# (but not when using `dplyr::filter()`, `dplyr::mutate()` or `dplyr::summarise()`) # (but not when using `dplyr::filter()`, `dplyr::mutate()` or `dplyr::summarise()`)
return(structure(env$`.data`, type = "dplyr_selector")) return(env$`.data`)
} else if (!is.null(env$xx) && is.data.frame(env$xx)) { } else if (valid_df(env$xx)) {
# an element `xx` will be in the environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]` # an element `xx` will be in the environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
return(structure(env$xx, type = "base_R")) return(env$xx)
} else if (!is.null(env$x) && is.data.frame(env$x)) { } else if (valid_df(env$x)) {
# an element `x` will be in the environment for only cols, e.g. `example_isolates[, carbapenems()]` # an element `x` will be in the environment for only cols, e.g. `example_isolates[, carbapenems()]`
return(structure(env$x, type = "base_R")) return(env$x)
} }
} }
} }
@ -901,32 +904,43 @@ is_null_or_grouped_tbl <- function(x) {
is.null(x) || inherits(x, "grouped_df") is.null(x) || inherits(x, "grouped_df")
} }
unique_call_id <- function(entire_session = FALSE) { unique_call_id <- function(entire_session = FALSE, match_fn = NULL) {
if (entire_session == TRUE) { if (entire_session == TRUE) {
c(envir = "session", return(c(envir = "session", call = "session"))
call = "session") }
} else {
# combination of environment ID (such as "0x7fed4ee8c848") # combination of environment ID (such as "0x7fed4ee8c848")
# and highest system call # and relevant system call (where 'match_fn' is being called in)
call <- paste0(deparse(sys.calls()[[1]]), collapse = "") calls <- sys.calls()
if (!interactive() || call %like% "run_test_dir|test_all|tinytest|test_package|testthat") { int <- which(vapply(FUN.VALUE = logical(1),
# unit tests will keep the same call and environment - give them a unique ID calls,
call <- paste0(sample(c(c(0:9), letters[1:6]), size = 64, replace = TRUE), collapse = "") function(call, fun = match_fn) {
} call_clean <- gsub("[^a-zA-Z0-9_().-]", "", as.character(call), perl = TRUE)
c(envir = gsub("<environment: (.*)>", "\\1", utils::capture.output(sys.frames()[[1]])), any(call_clean %like% paste0(fun, "\\("), na.rm = TRUE)
call = call) }))[1L]
if (is.na(int)) {
int <- 1
} }
c(envir = gsub("<environment: (.*)>", "\\1", utils::capture.output(sys.frames()[[1]]), perl = TRUE),
call = paste0(deparse(calls[[int]]), collapse = ""))
} }
message_not_thrown_before <- function(fn, entire_session = FALSE) { #' @noRd
#' @param fn name of the function as a character
#' @param ... character elements to be pasted together as a 'salt'
#' @param entire_session show message once per session
message_not_thrown_before <- function(fn, ..., entire_session = FALSE) {
# this is to prevent that messages/notes will be printed for every dplyr group or more than once per session # this is to prevent that messages/notes will be printed for every dplyr group or more than once per session
# e.g. this would show a msg 4 times: example_isolates %>% group_by(hospital_id) %>% filter(mo_is_gram_negative()) # e.g. this would show a msg 4 times: example_isolates %>% group_by(hospital_id) %>% filter(mo_is_gram_negative())
not_thrown_before <- is.null(pkg_env[[paste0("thrown_msg.", fn)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn)]], salt <- gsub("[^a-zA-Z0-9|_-]", "?", paste(c(...), sep = "|", collapse = "|"), perl = TRUE)
unique_call_id(entire_session = entire_session)) not_thrown_before <- is.null(pkg_env[[paste0("thrown_msg.", fn, ".", salt)]]) ||
!identical(pkg_env[[paste0("thrown_msg.", fn, ".", salt)]],
unique_call_id(entire_session = entire_session,
match_fn = fn))
if (isTRUE(not_thrown_before)) { if (isTRUE(not_thrown_before)) {
# message was not thrown before - remember this so on the next run it will return FALSE: # message was not thrown before - remember this so on the next run it will return FALSE:
assign(x = paste0("thrown_msg.", fn), assign(x = paste0("thrown_msg.", fn, ".", salt),
value = unique_call_id(entire_session = entire_session), value = unique_call_id(entire_session = entire_session, match_fn = fn),
envir = pkg_env) envir = pkg_env)
} }
not_thrown_before not_thrown_before

4
R/ab_property.R
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@ -33,7 +33,7 @@
#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation. #' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
#' @param administration way of administration, either `"oral"` or `"iv"` #' @param administration way of administration, either `"oral"` or `"iv"`
#' @param open browse the URL using [utils::browseURL()] #' @param open browse the URL using [utils::browseURL()]
#' @param ... in case of [set_ab_names()] and `data` is a [data.frame]: variables to select (supports tidy selection like `AMX:VAN`), otherwise other arguments passed on to [as.ab()] #' @param ... in case of [set_ab_names()] and `data` is a [data.frame]: variables to select (supports tidy selection such as `column1:column4`), otherwise other arguments passed on to [as.ab()]
#' @param data a [data.frame] of which the columns need to be renamed, or a [character] vector of column names #' @param data a [data.frame] of which the columns need to be renamed, or a [character] vector of column names
#' @param snake_case a [logical] to indicate whether the names should be in so-called [snake case](https://en.wikipedia.org/wiki/Snake_case): in lower case and all spaces/slashes replaced with an underscore (`_`) #' @param snake_case a [logical] to indicate whether the names should be in so-called [snake case](https://en.wikipedia.org/wiki/Snake_case): in lower case and all spaces/slashes replaced with an underscore (`_`)
#' @param only_first a [logical] to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group) #' @param only_first a [logical] to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)
@ -359,7 +359,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_locale(),
} else { } else {
df <- data df <- data
} }
vars <- get_column_abx(df, info = FALSE, only_rsi_columns = FALSE, sort = FALSE) vars <- get_column_abx(df, info = FALSE, only_rsi_columns = FALSE, sort = FALSE, fn = "set_ab_names")
if (length(vars) == 0) { if (length(vars) == 0) {
message_("No columns with antibiotic results found for `set_ab_names()`, leaving names unchanged.") message_("No columns with antibiotic results found for `set_ab_names()`, leaving names unchanged.")
return(data) return(data)

35
R/ab_selectors.R
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@ -181,7 +181,8 @@ ab_selector <- function(filter,
# but it only takes a couple of milliseconds # but it only takes a couple of milliseconds
vars_df <- get_current_data(arg_name = NA, call = -2) vars_df <- get_current_data(arg_name = NA, call = -2)
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE) ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns,
sort = FALSE, fn = "ab_selector")
call <- substitute(filter) call <- substitute(filter)
agents <- tryCatch(AMR::antibiotics[which(eval(call, envir = AMR::antibiotics)), "ab", drop = TRUE], agents <- tryCatch(AMR::antibiotics[which(eval(call, envir = AMR::antibiotics)), "ab", drop = TRUE],
error = function(e) stop_(e$message, call = -5)) error = function(e) stop_(e$message, call = -5))
@ -383,7 +384,8 @@ administrable_per_os <- function(only_rsi_columns = FALSE, ...) {
# but it only takes a couple of milliseconds # but it only takes a couple of milliseconds
vars_df <- get_current_data(arg_name = NA, call = -2) vars_df <- get_current_data(arg_name = NA, call = -2)
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE) ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns,
sort = FALSE, fn = "administrable_per_os")
agents_all <- antibiotics[which(!is.na(antibiotics$oral_ddd)), "ab", drop = TRUE] agents_all <- antibiotics[which(!is.na(antibiotics$oral_ddd)), "ab", drop = TRUE]
agents <- antibiotics[which(antibiotics$ab %in% ab_in_data & !is.na(antibiotics$oral_ddd)), "ab", drop = TRUE] agents <- antibiotics[which(antibiotics$ab %in% ab_in_data & !is.na(antibiotics$oral_ddd)), "ab", drop = TRUE]
agents <- ab_in_data[ab_in_data %in% agents] agents <- ab_in_data[ab_in_data %in% agents]
@ -410,7 +412,8 @@ administrable_iv <- function(only_rsi_columns = FALSE, ...) {
# but it only takes a couple of milliseconds # but it only takes a couple of milliseconds
vars_df <- get_current_data(arg_name = NA, call = -2) vars_df <- get_current_data(arg_name = NA, call = -2)
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE) ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns,
sort = FALSE, fn = "administrable_iv")
agents_all <- antibiotics[which(!is.na(antibiotics$iv_ddd)), "ab", drop = TRUE] agents_all <- antibiotics[which(!is.na(antibiotics$iv_ddd)), "ab", drop = TRUE]
agents <- antibiotics[which(antibiotics$ab %in% ab_in_data & !is.na(antibiotics$iv_ddd)), "ab", drop = TRUE] agents <- antibiotics[which(antibiotics$ab %in% ab_in_data & !is.na(antibiotics$iv_ddd)), "ab", drop = TRUE]
agents <- ab_in_data[ab_in_data %in% agents] agents <- ab_in_data[ab_in_data %in% agents]
@ -432,7 +435,8 @@ not_intrinsic_resistant <- function(only_rsi_columns = FALSE, col_mo = NULL, ver
# but it only takes a couple of milliseconds # but it only takes a couple of milliseconds
vars_df <- get_current_data(arg_name = NA, call = -2) vars_df <- get_current_data(arg_name = NA, call = -2)
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE) ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns,
sort = FALSE, fn = "not_intrinsic_resistant")
# intrinsic vars # intrinsic vars
vars_df_R <- tryCatch(sapply(eucast_rules(vars_df, vars_df_R <- tryCatch(sapply(eucast_rules(vars_df,
col_mo = col_mo, col_mo = col_mo,
@ -445,7 +449,7 @@ not_intrinsic_resistant <- function(only_rsi_columns = FALSE, col_mo = NULL, ver
agents <- ab_in_data[ab_in_data %in% names(vars_df_R[which(vars_df_R)])] agents <- ab_in_data[ab_in_data %in% names(vars_df_R[which(vars_df_R)])]
if (length(agents) > 0 && if (length(agents) > 0 &&
message_not_thrown_before(paste0("not_intrinsic_resistant.", paste(sort(agents), collapse = "|")))) { message_not_thrown_before("not_intrinsic_resistant", sort(agents))) {
agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'") agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL) agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
need_name <- generalise_antibiotic_name(agents) != generalise_antibiotic_name(agents_names) need_name <- generalise_antibiotic_name(agents) != generalise_antibiotic_name(agents_names)
@ -470,11 +474,13 @@ ab_select_exec <- function(function_name,
# but it only takes a couple of milliseconds # but it only takes a couple of milliseconds
vars_df <- get_current_data(arg_name = NA, call = -3) vars_df <- get_current_data(arg_name = NA, call = -3)
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE) ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns,
sort = FALSE, fn = function_name)
# untreatable drugs # untreatable drugs
untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate"), "ab", drop = TRUE] if (only_treatable == TRUE) {
if (only_treatable == TRUE & any(untreatable %in% names(ab_in_data))) { untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening"), "ab", drop = TRUE]
if (message_not_thrown_before(paste0("ab_class.untreatable.", function_name), entire_session = TRUE)) { if (any(untreatable %in% names(ab_in_data))) {
if (message_not_thrown_before(function_name, "ab_class", "untreatable", entire_session = TRUE)) {
warning_("Some agents in `", function_name, "()` were ignored since they cannot be used for treating patients: ", warning_("Some agents in `", function_name, "()` were ignored since they cannot be used for treating patients: ",
vector_and(ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable], vector_and(ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable],
language = NULL, language = NULL,
@ -486,6 +492,7 @@ ab_select_exec <- function(function_name,
} }
ab_in_data <- ab_in_data[!names(ab_in_data) %in% untreatable] ab_in_data <- ab_in_data[!names(ab_in_data) %in% untreatable]
} }
}
if (length(ab_in_data) == 0) { if (length(ab_in_data) == 0) {
message_("No antimicrobial agents found in the data.") message_("No antimicrobial agents found in the data.")
@ -666,14 +673,14 @@ any.ab_selector_any_all <- function(..., na.rm = FALSE) {
} }
is_any <- function(el1) { is_any <- function(el1) {
syscall <- paste0(trimws(deparse(sys.calls()[[1]])), collapse = " ") syscalls <- paste0(trimws(deparse(sys.calls())), collapse = " ")
el1 <- gsub("(.*),.*", "\\1", el1) el1 <- gsub("(.*),.*", "\\1", el1)
syscall %like% paste0("[^_a-zA-Z0-9]any\\(", "(c\\()?", el1) syscalls %like% paste0("[^_a-zA-Z0-9]any\\(", "(c\\()?", el1)
} }
is_all <- function(el1) { is_all <- function(el1) {
syscall <- paste0(trimws(deparse(sys.calls()[[1]])), collapse = " ") syscalls <- paste0(trimws(deparse(sys.calls())), collapse = " ")
el1 <- gsub("(.*),.*", "\\1", el1) el1 <- gsub("(.*),.*", "\\1", el1)
syscall %like% paste0("[^_a-zA-Z0-9]all\\(", "(c\\()?", el1) syscalls %like% paste0("[^_a-zA-Z0-9]all\\(", "(c\\()?", el1)
} }
find_ab_group <- function(ab_class_args) { find_ab_group <- function(ab_class_args) {
@ -714,7 +721,7 @@ find_ab_names <- function(ab_group, n = 3) {
} }
message_agent_names <- function(function_name, agents, ab_group = NULL, examples = "", ab_class_args = NULL, call = NULL) { message_agent_names <- function(function_name, agents, ab_group = NULL, examples = "", ab_class_args = NULL, call = NULL) {
if (message_not_thrown_before(paste0(function_name, ".", paste(sort(agents), collapse = "|")))) { if (message_not_thrown_before(function_name, sort(agents))) {
if (length(agents) == 0) { if (length(agents) == 0) {
if (is.null(ab_group)) { if (is.null(ab_group)) {
message_("For `", function_name, "()` no antimicrobial agents found", examples, ".") message_("For `", function_name, "()` no antimicrobial agents found", examples, ".")

14
R/data.R
View File

@ -262,20 +262,24 @@
#' #'
#' Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations. #' Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.
#' @format A [data.frame] with `r format(nrow(intrinsic_resistant), big.mark = ",")` observations and `r ncol(intrinsic_resistant)` variables: #' @format A [data.frame] with `r format(nrow(intrinsic_resistant), big.mark = ",")` observations and `r ncol(intrinsic_resistant)` variables:
#' - `microorganism`\cr Name of the microorganism #' - `microorganism`\cr Official taxonomic name of the microorganism, according to the LPSN
#' - `antibiotic`\cr Name of the antibiotic drug #' - `antibiotic`\cr Official name of the antibiotic drug, according to the WHOCC
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt>. This file **allows for machine reading EUCAST guidelines about intrinsic resistance**, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically. #' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt>. This file **allows for machine reading EUCAST guidelines about intrinsic resistance**, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
#' #'
#' This data set is based on `r format_eucast_version_nr(3.2)`. #' This data set is based on `r format_eucast_version_nr(3.3)`.
#' @inheritSection AMR Reference Data Publicly Available #' @inheritSection AMR Reference Data Publicly Available
#' @inheritSection AMR Read more on Our Website! #' @inheritSection AMR Read more on Our Website!
#' @examples #' @examples
#' subset(intrinsic_resistant,
#' antibiotic == "Vancomycin" & microorganism %like% "Enterococcus")$microorganism
#' #> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
#'
#' \donttest{ #' \donttest{
#' if (require("dplyr")) { #' if (require("dplyr")) {
#' intrinsic_resistant %>% #' intrinsic_resistant %>%
#' filter(antibiotic == "Vancomycin", microorganism %like% "Enterococcus") %>% #' filter(antibiotic == "Vancomycin" & microorganism %like% "Enterococcus") %>%
#' pull(microorganism) #' pull(microorganism)
#' # [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" #' #> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
#' } #' }
#' } #' }
"intrinsic_resistant" "intrinsic_resistant"

3
R/eucast_rules.R
View File

@ -305,6 +305,7 @@ eucast_rules <- function(x,
verbose = verbose, verbose = verbose,
info = info, info = info,
only_rsi_columns = only_rsi_columns, only_rsi_columns = only_rsi_columns,
fn = "eucast_rules",
...) ...)
if (!"AMP" %in% names(cols_ab) & "AMX" %in% names(cols_ab)) { if (!"AMP" %in% names(cols_ab) & "AMX" %in% names(cols_ab)) {
@ -1055,7 +1056,7 @@ eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 11.0)
meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS))) meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS)))
# show used version_breakpoints number once per session (pkg_env will reload every session) # show used version_breakpoints number once per session (pkg_env will reload every session)
if (message_not_thrown_before(paste0("eucast_dosage_v", gsub("[^0-9]", "", version_breakpoints)), entire_session = TRUE)) { if (message_not_thrown_before("eucast_dosage", "v", gsub("[^0-9]", "", version_breakpoints), entire_session = TRUE)) {
message_("Dosages for antimicrobial drugs, as meant for ", message_("Dosages for antimicrobial drugs, as meant for ",
format_eucast_version_nr(version_breakpoints, markdown = FALSE), ". ", format_eucast_version_nr(version_breakpoints, markdown = FALSE), ". ",
font_red("This note will be shown once per session.")) font_red("This note will be shown once per session."))

8
R/first_isolate.R
View File

@ -256,7 +256,7 @@ first_isolate <- function(x = NULL,
if (method == "phenotype-based" & !any_col_contains_rsi) { if (method == "phenotype-based" & !any_col_contains_rsi) {
method <- "episode-based" method <- "episode-based"
} }
if (info == TRUE & message_not_thrown_before("first_isolate.method")) { if (info == TRUE & message_not_thrown_before("first_isolate", "method")) {
message_(paste0("Determining first isolates ", message_(paste0("Determining first isolates ",
ifelse(method %in% c("episode-based", "phenotype-based"), ifelse(method %in% c("episode-based", "phenotype-based"),
ifelse(is.infinite(episode_days), ifelse(is.infinite(episode_days),
@ -360,7 +360,7 @@ first_isolate <- function(x = NULL,
testcodes_exclude <- NULL testcodes_exclude <- NULL
} }
# remove testcodes # remove testcodes
if (!is.null(testcodes_exclude) & info == TRUE & message_not_thrown_before("first_isolate.excludingtestcodes")) { if (!is.null(testcodes_exclude) & info == TRUE & message_not_thrown_before("first_isolate", "excludingtestcodes")) {
message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE), message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE),
add_fn = font_black, add_fn = font_black,
as_note = FALSE) as_note = FALSE)
@ -373,7 +373,7 @@ first_isolate <- function(x = NULL,
# filter on specimen group and keyantibiotics when they are filled in # filter on specimen group and keyantibiotics when they are filled in
if (!is.null(specimen_group)) { if (!is.null(specimen_group)) {
check_columns_existance(col_specimen, x) check_columns_existance(col_specimen, x)
if (info == TRUE & message_not_thrown_before("first_isolate.excludingspecimen")) { if (info == TRUE & message_not_thrown_before("first_isolate", "excludingspecimen")) {
message_("Excluding other than specimen group '", specimen_group, "'", message_("Excluding other than specimen group '", specimen_group, "'",
add_fn = font_black, add_fn = font_black,
as_note = FALSE) as_note = FALSE)
@ -445,7 +445,7 @@ first_isolate <- function(x = NULL,
# Analysis of first isolate ---- # Analysis of first isolate ----
if (!is.null(col_keyantimicrobials)) { if (!is.null(col_keyantimicrobials)) {
if (info == TRUE & message_not_thrown_before("first_isolate.type")) { if (info == TRUE & message_not_thrown_before("first_isolate", "type")) {
if (type == "keyantimicrobials") { if (type == "keyantimicrobials") {
message_("Basing inclusion on key antimicrobials, ", message_("Basing inclusion on key antimicrobials, ",
ifelse(ignore_I == FALSE, "not ", ""), ifelse(ignore_I == FALSE, "not ", ""),

49
R/guess_ab_col.R
View File

@ -75,7 +75,8 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_r
meet_criteria(search_string, allow_class = "character", has_length = 1, allow_NULL = FALSE) meet_criteria(search_string, allow_class = "character", has_length = 1, allow_NULL = FALSE)
} }
all_found <- get_column_abx(x, info = verbose, only_rsi_columns = only_rsi_columns, verbose = verbose) all_found <- get_column_abx(x, info = verbose, only_rsi_columns = only_rsi_columns,
verbose = verbose, fn = "guess_ab_col")
search_string.ab <- suppressWarnings(as.ab(search_string)) search_string.ab <- suppressWarnings(as.ab(search_string))
ab_result <- unname(all_found[names(all_found) == search_string.ab]) ab_result <- unname(all_found[names(all_found) == search_string.ab])
@ -104,10 +105,12 @@ get_column_abx <- function(x,
info = TRUE, info = TRUE,
only_rsi_columns = FALSE, only_rsi_columns = FALSE,
sort = TRUE, sort = TRUE,
reuse_previous_result = TRUE) { reuse_previous_result = TRUE,
fn = NULL) {
# check if retrieved before, then get it from package environment # check if retrieved before, then get it from package environment
if (isTRUE(reuse_previous_result) && identical(unique_call_id(entire_session = FALSE), pkg_env$get_column_abx.call)) { if (isTRUE(reuse_previous_result) && identical(unique_call_id(entire_session = FALSE,
match_fn = fn),
pkg_env$get_column_abx.call)) {
# so within the same call, within the same environment, we got here again. # so within the same call, within the same environment, we got here again.
# but we could've come from another function within the same call, so now only check the columns that changed # but we could've come from another function within the same call, so now only check the columns that changed
@ -194,6 +197,8 @@ get_column_abx <- function(x,
# such as get_column_abx(example_isolates %>% rename(thisone = AMX), amox = "thisone") # such as get_column_abx(example_isolates %>% rename(thisone = AMX), amox = "thisone")
all_okay <- TRUE all_okay <- TRUE
dots <- list(...) dots <- list(...)
# remove data.frames, since this is also used running `eucast_rules(eucast_rules_df = df)`
dots <- dots[!vapply(FUN.VALUE = logical(1), dots, is.data.frame)]
if (length(dots) > 0) { if (length(dots) > 0) {
newnames <- suppressWarnings(as.ab(names(dots), info = FALSE)) newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
if (any(is.na(newnames))) { if (any(is.na(newnames))) {
@ -228,7 +233,7 @@ get_column_abx <- function(x,
if (info == TRUE & all_okay == TRUE) { if (info == TRUE & all_okay == TRUE) {
message_("No columns found.") message_("No columns found.")
} }
pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE) pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE, match_fn = fn)
pkg_env$get_column_abx.checked_cols <- colnames(x.bak) pkg_env$get_column_abx.checked_cols <- colnames(x.bak)
pkg_env$get_column_abx.out <- out pkg_env$get_column_abx.out <- out
return(out) return(out)
@ -240,31 +245,39 @@ get_column_abx <- function(x,
} }
# only keep the first hits, no duplicates # only keep the first hits, no duplicates
duplicates <- c(out[duplicated(names(out))], out[duplicated(unname(out))]) duplicates <- c(out[duplicated(names(out))], out[duplicated(unname(out))])
out <- out[!duplicated(names(out))] if (length(duplicates) > 0) {
out <- out[!duplicated(unname(out))] all_okay <- FALSE
if (sort == TRUE) {
out <- out[order(names(out), out)]
} }
# succeeded with auto-guessing if (info == TRUE) {
if (info == TRUE & all_okay == TRUE) { if (all_okay == TRUE) {
message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE) message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
} else {
message_(" WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
} }
for (i in seq_len(length(out))) { for (i in seq_len(length(out))) {
if (info == TRUE & verbose == TRUE & !names(out[i]) %in% names(duplicates)) { if (verbose == TRUE & !names(out[i]) %in% names(duplicates)) {
message_("Using column '", font_bold(out[i]), "' as input for ", names(out)[i], message_("Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
" (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ").") " (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ").")
} }
if (info == TRUE & names(out[i]) %in% names(duplicates)) { if (names(out[i]) %in% names(duplicates)) {
warning_(paste0("Using column '", font_bold(out[i]), "' as input for ", names(out)[i], already_set_as <- out[unname(out) == unname(out[i])][1L]
" (", ab_name(names(out)[i], tolower = TRUE, language = NULL), warning_(paste0("Column '", font_bold(out[i]), "' will not be used for ",
"), although it was matched for multiple antibiotics or columns."), names(out)[i], " (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ")",
", as it is already set for ",
names(already_set_as), " (", ab_name(names(already_set_as), tolower = TRUE, language = NULL), ")"),
add_fn = font_red, add_fn = font_red,
call = FALSE, call = FALSE,
immediate = verbose) immediate = verbose)
} }
} }
}
out <- out[!duplicated(names(out))]
out <- out[!duplicated(unname(out))]
if (sort == TRUE) {
out <- out[order(names(out), out)]
}
if (!is.null(hard_dependencies)) { if (!is.null(hard_dependencies)) {
hard_dependencies <- unique(hard_dependencies) hard_dependencies <- unique(hard_dependencies)
@ -288,7 +301,7 @@ get_column_abx <- function(x,
} }
} }
pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE) pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE, match_fn = fn)
pkg_env$get_column_abx.checked_cols <- colnames(x.bak) pkg_env$get_column_abx.checked_cols <- colnames(x.bak)
pkg_env$get_column_abx.out <- out pkg_env$get_column_abx.out <- out
out out

7
R/key_antimicrobials.R
View File

@ -142,7 +142,7 @@ key_antimicrobials <- function(x = NULL,
# force regular data.frame, not a tibble or data.table # force regular data.frame, not a tibble or data.table
x <- as.data.frame(x, stringsAsFactors = FALSE) x <- as.data.frame(x, stringsAsFactors = FALSE)
cols <- get_column_abx(x, info = FALSE, only_rsi_columns = only_rsi_columns) cols <- get_column_abx(x, info = FALSE, only_rsi_columns = only_rsi_columns, fn = "key_antimicrobials")
# try to find columns based on type # try to find columns based on type
# -- mo # -- mo
@ -171,7 +171,7 @@ key_antimicrobials <- function(x = NULL,
if (values_new_length < values_old_length & if (values_new_length < values_old_length &
any(filter, na.rm = TRUE) & any(filter, na.rm = TRUE) &
message_not_thrown_before(paste0("key_antimicrobials.", name))) { message_not_thrown_before("key_antimicrobials", name)) {
warning_(ifelse(values_new_length == 0, warning_(ifelse(values_new_length == 0,
"No columns available ", "No columns available ",
paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")), paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")),
@ -238,7 +238,8 @@ all_antimicrobials <- function(x = NULL,
# force regular data.frame, not a tibble or data.table # force regular data.frame, not a tibble or data.table
x <- as.data.frame(x, stringsAsFactors = FALSE) x <- as.data.frame(x, stringsAsFactors = FALSE)
cols <- get_column_abx(x, only_rsi_columns = only_rsi_columns, info = FALSE, sort = FALSE) cols <- get_column_abx(x, only_rsi_columns = only_rsi_columns, info = FALSE,
sort = FALSE, fn = "all_antimicrobials")
generate_antimcrobials_string(x[ , cols, drop = FALSE]) generate_antimcrobials_string(x[ , cols, drop = FALSE])
} }

2
R/like.R
View File

@ -69,7 +69,7 @@
#' # get isolates whose name start with 'Ent' or 'ent' #' # get isolates whose name start with 'Ent' or 'ent'
#' example_isolates[which(mo_name(example_isolates$mo) %like% "^ent"), ] #' example_isolates[which(mo_name(example_isolates$mo) %like% "^ent"), ]
#' \donttest{ #' \donttest{
#' # faster way, only works in R 3.2 and later: #' # faster way, since mo_name() is context-aware:
#' example_isolates[which(mo_name() %like% "^ent"), ] #' example_isolates[which(mo_name() %like% "^ent"), ]
#' #'
#' if (require("dplyr")) { #' if (require("dplyr")) {

128
R/mdro.R
View File

@ -51,7 +51,11 @@
#' #'
#' Magiorakos AP, Srinivasan A *et al.* "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) ([link](https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext)) #' Magiorakos AP, Srinivasan A *et al.* "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) ([link](https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext))
#' #'
#' * `guideline = "EUCAST3.2"` (or simply `guideline = "EUCAST"`) #' * `guideline = "EUCAST3.3"` (or simply `guideline = "EUCAST"`)
#'
#' The European international guideline - EUCAST Expert Rules Version 3.3 "Intrinsic Resistance and Unusual Phenotypes" ([link](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf))
#'
#' * `guideline = "EUCAST3.2"`
#' #'
#' The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" ([link](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf)) #' The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" ([link](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf))
#' #'
@ -73,7 +77,6 @@
#' #'
#' Please suggest your own (country-specific) guidelines by letting us know: <https://github.com/msberends/AMR/issues/new>. #' Please suggest your own (country-specific) guidelines by letting us know: <https://github.com/msberends/AMR/issues/new>.
#' #'
#'
#' @section Using Custom Guidelines: #' @section Using Custom Guidelines:
#' #'
#' Custom guidelines can be set with the [custom_mdro_guideline()] function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data. #' Custom guidelines can be set with the [custom_mdro_guideline()] function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.
@ -325,10 +328,17 @@ mdro <- function(x = NULL,
} else if (guideline$code == "eucast3.2") { } else if (guideline$code == "eucast3.2") {
guideline$name <- "EUCAST Expert Rules, \"Intrinsic Resistance and Unusual Phenotypes\"" guideline$name <- "EUCAST Expert Rules, \"Intrinsic Resistance and Unusual Phenotypes\""
guideline$author <- "EUCAST (European Committee on Antimicrobial Susceptibility Testing)" guideline$author <- "EUCAST (European Committee on Antimicrobial Susceptibility Testing)"
guideline$version <- "3.2, 2020" guideline$version <- "3.2, February 2020"
guideline$source_url <- "https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf" guideline$source_url <- "https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf"
guideline$type <- "EUCAST Unusual Phenotypes" guideline$type <- "EUCAST Unusual Phenotypes"
} else if (guideline$code == "eucast3.3") {
guideline$name <- "EUCAST Expert Rules, \"Intrinsic Resistance and Unusual Phenotypes\""
guideline$author <- "EUCAST (European Committee on Antimicrobial Susceptibility Testing)"
guideline$version <- "3.3, October 2021"
guideline$source_url <- "https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf"
guideline$type <- "EUCAST Unusual Phenotypes"
} else if (guideline$code == "tb") { } else if (guideline$code == "tb") {
guideline$name <- "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" guideline$name <- "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis"
guideline$author <- "WHO (World Health Organization)" guideline$author <- "WHO (World Health Organization)"
@ -474,6 +484,7 @@ mdro <- function(x = NULL,
verbose = verbose, verbose = verbose,
info = info, info = info,
only_rsi_columns = only_rsi_columns, only_rsi_columns = only_rsi_columns,
fn = "mdro",
...) ...)
} else if (guideline$code == "eucast3.2") { } else if (guideline$code == "eucast3.2") {
cols_ab <- get_column_abx(x = x, cols_ab <- get_column_abx(x = x,
@ -502,6 +513,36 @@ mdro <- function(x = NULL,
verbose = verbose, verbose = verbose,
info = info, info = info,
only_rsi_columns = only_rsi_columns, only_rsi_columns = only_rsi_columns,
fn = "mdro",
...)
} else if (guideline$code == "eucast3.3") {
cols_ab <- get_column_abx(x = x,
soft_dependencies = c("AMP",
"AMX",
"CIP",
"DAL",
"DAP",
"ERV",
"FDX",
"GEN",
"LNZ",
"MEM",
"MTR",
"OMC",
"ORI",
"PEN",
"QDA",
"RIF",
"TEC",
"TGC",
"TLV",
"TOB",
"TZD",
"VAN"),
verbose = verbose,
info = info,
only_rsi_columns = only_rsi_columns,
fn = "mdro",
...) ...)
} else if (guideline$code == "tb") { } else if (guideline$code == "tb") {
cols_ab <- get_column_abx(x = x, cols_ab <- get_column_abx(x = x,
@ -516,6 +557,7 @@ mdro <- function(x = NULL,
verbose = verbose, verbose = verbose,
info = info, info = info,
only_rsi_columns = only_rsi_columns, only_rsi_columns = only_rsi_columns,
fn = "mdro",
...) ...)
} else if (guideline$code == "mrgn") { } else if (guideline$code == "mrgn") {
cols_ab <- get_column_abx(x = x, cols_ab <- get_column_abx(x = x,
@ -528,12 +570,14 @@ mdro <- function(x = NULL,
verbose = verbose, verbose = verbose,
info = info, info = info,
only_rsi_columns = only_rsi_columns, only_rsi_columns = only_rsi_columns,
fn = "mdro",
...) ...)
} else { } else {
cols_ab <- get_column_abx(x = x, cols_ab <- get_column_abx(x = x,
verbose = verbose, verbose = verbose,
info = info, info = info,
only_rsi_columns = only_rsi_columns, only_rsi_columns = only_rsi_columns,
fn = "mdro",
...) ...)
} }
if (!"AMP" %in% names(cols_ab) & "AMX" %in% names(cols_ab)) { if (!"AMP" %in% names(cols_ab) & "AMX" %in% names(cols_ab)) {
@ -1171,10 +1215,80 @@ mdro <- function(x = NULL,
which(x$genus == "Streptococcus" & x$species == "pneumoniae"), which(x$genus == "Streptococcus" & x$species == "pneumoniae"),
c(carbapenems, VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC, RIF), c(carbapenems, VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC, RIF),
"any") "any")
streps <- MO_lookup[which(MO_lookup$genus == "Streptococcus"), "mo", drop = TRUE]
streps_ABCG <- streps[as.mo(streps, Lancefield = TRUE) %in% c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_GRPC", "B_STRPT_GRPG")]
trans_tbl(3, # Sr. groups A/B/C/G trans_tbl(3, # Sr. groups A/B/C/G
which(x$mo %in% streps_ABCG), which(x$mo %in% MO_STREP_ABCG),
c(PEN, cephalosporins, VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC),
"any")
trans_tbl(3,
which(x$genus == "Enterococcus"),
c(DAP, LNZ, TGC, ERV, OMC, TEC),
"any")
trans_tbl(3,
which(x$genus == "Enterococcus" & x$species == "faecalis"),
c(AMP, AMX),
"any")
# Table 8
trans_tbl(3,
which(x$genus == "Bacteroides"),
MTR,
"any")
trans_tbl(3,
which(x$genus == "Clostridium" & x$species == "difficile"),
c(MTR, VAN, FDX),
"any")
}
if (guideline$code == "eucast3.3") {
# EUCAST 3.3 --------------------------------------------------------------
# note: this guideline is equal to EUCAST 3.2 - no MDRO insights changed
# Table 6
trans_tbl(3,
which((x$order == "Enterobacterales" &
!x$family == "Morganellaceae" &
!(x$genus == "Serratia" & x$species == "marcescens"))
| (x$genus == "Pseudomonas" & x$species == "aeruginosa")
| x$genus == "Acinetobacter"),
COL,
"all")
trans_tbl(3,
which(x$genus == "Salmonella" & x$species == "Typhi"),
c(carbapenems),
"any")
trans_tbl(3,
which(x$genus == "Haemophilus" & x$species == "influenzae"),
c(cephalosporins_3rd, carbapenems, fluoroquinolones),
"any")
trans_tbl(3,
which(x$genus == "Moraxella" & x$species == "catarrhalis"),
c(cephalosporins_3rd, fluoroquinolones),
"any")
trans_tbl(3,
which(x$genus == "Neisseria" & x$species == "meningitidis"),
c(cephalosporins_3rd, fluoroquinolones),
"any")
trans_tbl(3,
which(x$genus == "Neisseria" & x$species == "gonorrhoeae"),
SPT,
"any")
# Table 7
trans_tbl(3,
which(x$genus == "Staphylococcus" & x$species == "aureus"),
c(VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC),
"any")
trans_tbl(3,
which(x$mo %in% MO_CONS), # coagulase-negative Staphylococcus
c(VAN, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC),
"any")
trans_tbl(3,
which(x$genus == "Corynebacterium"),
c(VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC),
"any")
trans_tbl(3,
which(x$genus == "Streptococcus" & x$species == "pneumoniae"),
c(carbapenems, VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC, RIF),
"any")
trans_tbl(3, # Sr. groups A/B/C/G
which(x$mo %in% MO_STREP_ABCG),
c(PEN, cephalosporins, VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC), c(PEN, cephalosporins, VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC),
"any") "any")
trans_tbl(3, trans_tbl(3,
@ -1435,7 +1549,7 @@ mdro <- function(x = NULL,
# Results ---- # Results ----
if (guideline$code == "cmi2012") { if (guideline$code == "cmi2012") {
if (any(x$MDRO == -1, na.rm = TRUE)) { if (any(x$MDRO == -1, na.rm = TRUE)) {
if (message_not_thrown_before("mdro.availability")) { if (message_not_thrown_before("mdro", "availability")) {
warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ", warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ",
percentage(pct_required_classes), " (set with `pct_required_classes`)", call = FALSE) percentage(pct_required_classes), " (set with `pct_required_classes`)", call = FALSE)
} }

20
R/mo.R
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@ -1481,15 +1481,23 @@ exec_as.mo <- function(x,
if (NROW(uncertainties) > 0 & initial_search == TRUE) { if (NROW(uncertainties) > 0 & initial_search == TRUE) {
uncertainties <- as.list(pm_distinct(uncertainties, input, .keep_all = TRUE)) uncertainties <- as.list(pm_distinct(uncertainties, input, .keep_all = TRUE))
pkg_env$mo_uncertainties <- uncertainties pkg_env$mo_uncertainties <- uncertainties
if (message_not_thrown_before("as.mo", "uncertainties", uncertainties$input)) {
plural <- c("", "it", "was") plural <- c("", "this", "uncertainty")
if (length(uncertainties$input) > 1) { if (length(uncertainties$input) > 1) {
plural <- c("s", "them", "were") plural <- c("s", "these", "uncertainties")
} }
msg <- paste0("Translation is uncertain of ", nr2char(length(uncertainties$input)), " microorganism", plural[1], if (length(uncertainties$input) <= 3) {
". Use `mo_uncertainties()` to review ", plural[2], ".") examples <- vector_and(paste0('"', uncertainties$input,
'" (assuming ', font_italic(uncertainties$fullname, collapse = NULL), ")"),
quotes = FALSE)
} else {
examples <- paste0(nr2char(length(uncertainties$input)), " microorganism", plural[1])
}
msg <- paste0("Function `as.mo()` is uncertain about ", examples,
". Run `mo_uncertainties()` to review ", plural[2], " ", plural[3], ".")
message_(msg) message_(msg)
} }
}
x[already_known] <- x_known x[already_known] <- x_known
} }
} }
@ -1505,7 +1513,7 @@ exec_as.mo <- function(x,
# nolint start # nolint start
# comment below code if all staphylococcal species are categorised as CoNS/CoPS # comment below code if all staphylococcal species are categorised as CoNS/CoPS
if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) { if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
if (message_not_thrown_before("as.mo_becker")) { if (message_not_thrown_before("as.mo", "becker")) {
warning_("Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ", warning_("Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
font_italic(paste("S.", font_italic(paste("S.",
sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))), sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),

6
R/mo_property.R
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@ -46,7 +46,7 @@
#' #'
#' Determination of yeasts - [mo_is_yeast()] - will be based on the taxonomic kingdom and class. *Budding yeasts* are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). *True yeasts* are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (except when the input is `NA` or the MO code is `UNKNOWN`). #' Determination of yeasts - [mo_is_yeast()] - will be based on the taxonomic kingdom and class. *Budding yeasts* are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). *True yeasts* are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (except when the input is `NA` or the MO code is `UNKNOWN`).
#' #'
#' Intrinsic resistance - [mo_is_intrinsic_resistant()] - will be determined based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.2)`. The [mo_is_intrinsic_resistant()] functions can be vectorised over arguments `x` (input for microorganisms) and over `ab` (input for antibiotics). #' Intrinsic resistance - [mo_is_intrinsic_resistant()] - will be determined based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.3)`. The [mo_is_intrinsic_resistant()] functions can be vectorised over arguments `x` (input for microorganisms) and over `ab` (input for antibiotics).
#' #'
#' All output [will be translated][translate] where possible. #' All output [will be translated][translate] where possible.
#' #'
@ -471,9 +471,9 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
} }
# show used version number once per session (pkg_env will reload every session) # show used version number once per session (pkg_env will reload every session)
if (message_not_thrown_before("intrinsic_resistant_version.mo", entire_session = TRUE)) { if (message_not_thrown_before("mo_is_intrinsic_resistant", "version.mo", entire_session = TRUE)) {
message_("Determining intrinsic resistance based on ", message_("Determining intrinsic resistance based on ",
format_eucast_version_nr(3.2, markdown = FALSE), ". ", format_eucast_version_nr(3.3, markdown = FALSE), ". ",
font_red("This note will be shown once per session.")) font_red("This note will be shown once per session."))
} }

14
R/rsi.R
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@ -35,10 +35,10 @@
#' @inheritParams first_isolate #' @inheritParams first_isolate
#' @param guideline defaults to the latest included EUCAST guideline, see *Details* for all options #' @param guideline defaults to the latest included EUCAST guideline, see *Details* for all options
#' @param conserve_capped_values a [logical] to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S" #' @param conserve_capped_values a [logical] to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
#' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.2)`. #' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.3)`.
#' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [rsi_translation] data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the [rsi_translation] data set (same column names and column types). Please note that the `guideline` argument will be ignored when `reference_data` is manually set. #' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [rsi_translation] data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the [rsi_translation] data set (same column names and column types). Please note that the `guideline` argument will be ignored when `reference_data` is manually set.
#' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, see *Examples* #' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, see *Examples*
#' @param ... for using on a [data.frame]: names of columns to apply [as.rsi()] on (supports tidy selection like `AMX:VAN`). Otherwise: arguments passed on to methods. #' @param ... for using on a [data.frame]: names of columns to apply [as.rsi()] on (supports tidy selection such as `column1:column4`). Otherwise: arguments passed on to methods.
#' @details #' @details
#' ## How it Works #' ## How it Works
#' #'
@ -61,7 +61,7 @@
#' your_data %>% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0 #' your_data %>% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
#' ``` #' ```
#' #'
#' 4. For **interpreting a complete data set**, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running `as.rsi(data)`. #' 4. For **interpreting a complete data set**, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running `as.rsi(your_data)`.
#' #'
#' ## Supported Guidelines #' ## Supported Guidelines
#' #'
@ -550,7 +550,7 @@ as.rsi.data.frame <- function(x,
x.bak <- x x.bak <- x
for (i in seq_len(ncol(x))) { for (i in seq_len(ncol(x))) {
# don't keep factors # don't keep factors, overwriting them is hard
if (is.factor(x[, i, drop = TRUE])) { if (is.factor(x[, i, drop = TRUE])) {
x[, i] <- as.character(x[, i, drop = TRUE]) x[, i] <- as.character(x[, i, drop = TRUE])
} }
@ -775,7 +775,7 @@ exec_as.rsi <- function(method,
guideline_coerced <- get_guideline(guideline, reference_data) guideline_coerced <- get_guideline(guideline, reference_data)
if (guideline_coerced != guideline) { if (guideline_coerced != guideline) {
if (message_not_thrown_before("as.rsi")) { if (message_not_thrown_before("as.rsi", "msg1")) {
message_("Using guideline ", font_bold(guideline_coerced), " as input for `guideline`.") message_("Using guideline ", font_bold(guideline_coerced), " as input for `guideline`.")
} }
} }
@ -813,7 +813,7 @@ exec_as.rsi <- function(method,
if (isTRUE(add_intrinsic_resistance) & is_intrinsic_r) { if (isTRUE(add_intrinsic_resistance) & is_intrinsic_r) {
if (guideline_coerced %unlike% "EUCAST") { if (guideline_coerced %unlike% "EUCAST") {
if (message_not_thrown_before("as.rsi2")) { if (message_not_thrown_before("as.rsi", "msg2")) {
warning_("Using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.", call = FALSE) warning_("Using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.", call = FALSE)
} }
} else { } else {
@ -877,7 +877,7 @@ exec_as.rsi <- function(method,
if (any_is_intrinsic_resistant & guideline_coerced %like% "EUCAST" & !isTRUE(add_intrinsic_resistance)) { if (any_is_intrinsic_resistant & guideline_coerced %like% "EUCAST" & !isTRUE(add_intrinsic_resistance)) {
# found some intrinsic resistance, but was not applied # found some intrinsic resistance, but was not applied
message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE) message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
if (message_not_thrown_before("as.rsi3")) { if (message_not_thrown_before("as.rsi", "msg3")) {
warning_("Found intrinsic resistance in some bug/drug combinations, although it was not applied.\nUse `as.rsi(..., add_intrinsic_resistance = TRUE)` to apply it.", call = FALSE) warning_("Found intrinsic resistance in some bug/drug combinations, although it was not applied.\nUse `as.rsi(..., add_intrinsic_resistance = TRUE)` to apply it.", call = FALSE)
} }
warned <- TRUE warned <- TRUE

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R/vctrs.R
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@ -28,6 +28,18 @@
# They are to convert AMR-specific classes to bare characters and integers. # They are to convert AMR-specific classes to bare characters and integers.
# All of them will be exported using s3_register() in R/zzz.R when loading the package. # All of them will be exported using s3_register() in R/zzz.R when loading the package.
# S3: ab_selector
# see https://github.com/tidyverse/dplyr/issues/5955 why this is required
vec_ptype2.character.ab_selector <- function(x, y, ...) {
x
}
vec_ptype2.ab_selector.character <- function(x, y, ...) {
y
}
vec_cast.character.ab_selector <- function(x, to, ...) {
unclass(x)
}
# S3: ab # S3: ab
vec_ptype2.character.ab <- function(x, y, ...) { vec_ptype2.character.ab <- function(x, y, ...) {
x x
@ -60,15 +72,3 @@ vec_ptype2.disk.integer <- function(x, y, ...) {
vec_cast.integer.disk <- function(x, to, ...) { vec_cast.integer.disk <- function(x, to, ...) {
unclass(x) unclass(x)
} }
# S3: ab_selector
# see https://github.com/tidyverse/dplyr/issues/5955 why this is required
vec_ptype2.character.ab_selector <- function(x, y, ...) {
x
}
vec_ptype2.ab_selector.character <- function(x, y, ...) {
y
}
vec_cast.character.ab_selector <- function(x, to, ...) {
unclass(x)
}

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2
data-raw/_internals.R
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@ -115,6 +115,7 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
} }
MO_CONS <- create_species_cons_cops("CoNS") MO_CONS <- create_species_cons_cops("CoNS")
MO_COPS <- create_species_cons_cops("CoPS") MO_COPS <- create_species_cons_cops("CoPS")
MO_STREP_ABCG <- as.mo(MO_lookup[which(MO_lookup$genus == "Streptococcus"), "mo", drop = TRUE], Lancefield = TRUE) %in% c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_GRPC", "B_STRPT_GRPG")
# antibiotic groups # antibiotic groups
# (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv) # (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
@ -158,6 +159,7 @@ usethis::use_data(EUCAST_RULES_DF,
# EXAMPLE_ISOLATES, # EXAMPLE_ISOLATES,
MO_CONS, MO_CONS,
MO_COPS, MO_COPS,
MO_STREP_ABCG,
AB_AMINOGLYCOSIDES, AB_AMINOGLYCOSIDES,
AB_AMINOPENICILLINS, AB_AMINOPENICILLINS,
AB_ANTIFUNGALS, AB_ANTIFUNGALS,

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data-raw/intrinsic_resistant.md5
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@ -1 +1 @@
43d5b2e1df4e0d12d6ad0c7a4591199c d4e080899f438bc1eacb8ec9cfa117b8

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data-raw/reproduction_of_intrinsic_resistant.R
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@ -33,7 +33,7 @@ for (i in seq_len(nrow(antibiotics))) {
int_resis <- eucast_rules(int_resis, int_resis <- eucast_rules(int_resis,
eucast_rules_df = subset(AMR:::EUCAST_RULES_DF, eucast_rules_df = subset(AMR:::EUCAST_RULES_DF,
is.na(have_these_values) & reference.version == 3.2), is.na(have_these_values) & reference.version == 3.3),
info = FALSE) info = FALSE)
int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R"))] %>% int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R"))] %>%
@ -41,6 +41,12 @@ int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R
filter(value == "R") %>% filter(value == "R") %>%
select(microorganism, antibiotic = name) select(microorganism, antibiotic = name)
# remove lab drugs
untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening"), "name", drop = TRUE]
int_resis2 <- int_resis2 %>%
filter(!antibiotic %in% untreatable) %>%
arrange(microorganism, antibiotic)
int_resis2$microorganism <- mo_name(int_resis2$microorganism, language = NULL) int_resis2$microorganism <- mo_name(int_resis2$microorganism, language = NULL)
intrinsic_resistant <- as.data.frame(int_resis2, stringsAsFactors = FALSE) intrinsic_resistant <- as.data.frame(int_resis2, stringsAsFactors = FALSE)

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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>

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docs/LICENSE-text.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>
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<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1> <h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4> <h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">06 December 2021</h4> <h4 data-toc-skip class="date">11 December 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="hidden name"><code>SPSS.Rmd</code></div> <div class="hidden name"><code>SPSS.Rmd</code></div>

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>
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<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1> <h1 data-toc-skip>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">09 December 2021</h4> <h4 data-toc-skip class="date">11 December 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div> <div class="hidden name"><code>datasets.Rmd</code></div>
@ -788,22 +788,22 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<div class="section level2"> <div class="section level2">
<h2 id="intrinsic-bacterial-resistance">Intrinsic bacterial resistance<a class="anchor" aria-label="anchor" href="#intrinsic-bacterial-resistance"></a> <h2 id="intrinsic-bacterial-resistance">Intrinsic bacterial resistance<a class="anchor" aria-label="anchor" href="#intrinsic-bacterial-resistance"></a>
</h2> </h2>
<p>A data set with 93,892 rows and 2 columns, containing the following column names:<br><em>microorganism</em> and <em>antibiotic</em>.</p> <p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>microorganism</em> and <em>antibiotic</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p> <p>It was last updated on 11 December 2021 11:49:52 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R file</a> (69 kB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R file</a> (78 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel file</a> (0.9 MB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel file</a> (0.9 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain text file</a> (3.5 MB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain text file</a> (5.1 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS file</a> (7.1 MB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS file</a> (10.4 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS file</a> (5.1 MB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS file</a> (7.4 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata file</a> (7 MB)</li> <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata file</a> (10.2 MB)</li>
</ul> </ul>
<div class="section level3"> <div class="section level3">
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a> <h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
@ -822,6 +822,14 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Acetylmidecamycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Acetylspiramycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Amoxicillin</td> <td align="center">Amoxicillin</td>
</tr> </tr>
<tr class="even"> <tr class="even">
@ -846,6 +854,14 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Benzylpenicillin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cadazolid</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefadroxil</td> <td align="center">Cefadroxil</td>
</tr> </tr>
<tr class="even"> <tr class="even">
@ -898,8 +914,16 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Gamithromycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Josamycin</td> <td align="center">Josamycin</td>
</tr> </tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Kitasamycin (Leucomycin)</td>
</tr>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Lincomycin</td> <td align="center">Lincomycin</td>
@ -910,12 +934,20 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Midecamycin</td> <td align="center">Meleumycin</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Midecamycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Miocamycin</td> <td align="center">Miocamycin</td>
</tr> </tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Nafithromycin</td>
</tr>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Norvancomycin</td> <td align="center">Norvancomycin</td>
@ -930,11 +962,11 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Benzylpenicillin</td> <td align="center">Pirlimycin</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Pirlimycin</td> <td align="center">Primycin</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
@ -962,19 +994,19 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Spiramycin</td> <td align="center">Solithromycin</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Tedizolid</td> <td align="center">Spiramycin</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Teicoplanin</td> <td align="center">Tedizolid</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Teicoplanin-macromethod</td> <td align="center">Teicoplanin</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
@ -990,10 +1022,30 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Tildipirosin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Tilmicosin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Troleandomycin</td> <td align="center">Troleandomycin</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Enterobacter cloacae</td> <td align="center">Enterobacter cloacae</td>
<td align="center">Tulathromycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Tylosin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Tylvalosin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Vancomycin</td> <td align="center">Vancomycin</td>
</tr> </tr>
</tbody> </tbody>

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>
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<li>Principal component analysis for AMR</li> <li>Principal component analysis for AMR</li>
</ul> </ul>
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p> <p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
<p>This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.177417131</a>) but is actively and durably maintained (see <a href="https://msberends.github.io/AMR/news/index.html">changelog)</a>) by two public healthcare organisations in the Netherlands.</p> <p>This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>) but is actively and durably maintained (see <a href="https://msberends.github.io/AMR/news/index.html">changelog)</a>) by two public healthcare organisations in the Netherlands.</p>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>
@ -195,14 +195,14 @@
<code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px"><a class="anchor" aria-label="anchor" href="#amr-for-r-"></a> <code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px"><a class="anchor" aria-label="anchor" href="#amr-for-r-"></a>
</h1></div> </h1></div>
<blockquote> <blockquote>
<p>Update: The latest <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST guideline for intrinsic resistance</a> (v3.3, October 2021) is now supported, and our taxonomy tables has been updated as well (LPSN, 5 October 2021). <strong>A new version will be released after the <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">EUCAST guideline for clinical breakpoints</a> (v12.0, likely January 2022) are implemented, to be expected shortly after the official guideline release.</strong></p> <p>Update: The latest <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST guideline for intrinsic resistance</a> (v3.3, October 2021) is now supported, and our taxonomy tables have been updated as well (LPSN, 5 October 2021). <strong>A new version will be released after the <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">EUCAST guideline for clinical breakpoints</a> (v12.0, likely January 2022) are implemented, to be expected shortly after the official guideline release.</strong></p>
</blockquote> </blockquote>
<div class="section level3"> <div class="section level3">
<h3 id="what-is-amr-for-r">What is <code>AMR</code> (for R)?<a class="anchor" aria-label="anchor" href="#what-is-amr-for-r"></a> <h3 id="what-is-amr-for-r">What is <code>AMR</code> (for R)?<a class="anchor" aria-label="anchor" href="#what-is-amr-for-r"></a>
</h3> </h3>
<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> (see <a href="#copyright">Copyright</a>) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p> <p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> (see <a href="#copyright">Copyright</a>) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~71,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~560 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.</p> <p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~71,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~560 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.</p>
<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.177417131</a>) but is <a href="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p> <p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>) but is <a href="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p>
<div class="main-content" style="display: inline-block;"> <div class="main-content" style="display: inline-block;">
<p> <p>
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 175 countries</strong><br> Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names. <a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 175 countries</strong><br> Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>
@ -157,20 +157,20 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="page-header" data-toc-text="1.7.1.9063" id="amr-1719063"> <h2 class="page-header" data-toc-text="1.7.1.9064" id="amr-1719064">
<code>AMR</code> 1.7.1.9063<a class="anchor" aria-label="anchor" href="#amr-1719063"></a></h2> <code>AMR</code> 1.7.1.9064<a class="anchor" aria-label="anchor" href="#amr-1719064"></a></h2>
<div class="section level3"> <div class="section level3">
<h3 id="last-updated-december-1-7-1-9063"><small>Last updated: 9 December 2021</small><a class="anchor" aria-label="anchor" href="#last-updated-december-1-7-1-9063"></a></h3> <h3 id="last-updated-december-1-7-1-9064"><small>Last updated: 11 December 2021</small><a class="anchor" aria-label="anchor" href="#last-updated-december-1-7-1-9064"></a></h3>
<div class="section level4"> <div class="section level4">
<h4 id="breaking-changes-1-7-1-9063">Breaking changes<a class="anchor" aria-label="anchor" href="#breaking-changes-1-7-1-9063"></a></h4> <h4 id="breaking-changes-1-7-1-9064">Breaking changes<a class="anchor" aria-label="anchor" href="#breaking-changes-1-7-1-9064"></a></h4>
<ul><li>Removed <code>p_symbol()</code> and all <code>filter_*()</code> functions (except for <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>), which were all deprecated in a previous package version</li> <ul><li>Removed <code>p_symbol()</code> and all <code>filter_*()</code> functions (except for <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>), which were all deprecated in a previous package version</li>
<li>Removed the <code>key_antibiotics()</code> and <code>key_antibiotics_equal()</code> functions, which were deprecated and superseded by <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> and <code><a href="../reference/key_antimicrobials.html">antimicrobials_equal()</a></code> <li>Removed the <code>key_antibiotics()</code> and <code>key_antibiotics_equal()</code> functions, which were deprecated and superseded by <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> and <code><a href="../reference/key_antimicrobials.html">antimicrobials_equal()</a></code>
</li> </li>
<li>Removed all previously implemented <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot2::ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code>, <code>&lt;rsi&gt;</code> and <code>&lt;resistance_predict&gt;</code> as they did not follow the <code>ggplot2</code> logic. They were replaced with <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">ggplot2::autoplot()</a></code> generics.</li> <li>Removed all previously implemented <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot2::ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code>, <code>&lt;rsi&gt;</code> and <code>&lt;resistance_predict&gt;</code> as they did not follow the <code>ggplot2</code> logic. They were replaced with <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">ggplot2::autoplot()</a></code> generics.</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="new-1-7-1-9063">New<a class="anchor" aria-label="anchor" href="#new-1-7-1-9063"></a></h4> <h4 id="new-1-7-1-9064">New<a class="anchor" aria-label="anchor" href="#new-1-7-1-9064"></a></h4>
<ul><li><p>Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021), effective in the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function. This is now the default guideline (all other guidelines are still available).</p></li> <ul><li><p>Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021). This is now the default EUCAST guideline in the package (all older guidelines are still available) for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code>mo_intrinsic_resistant()</code> and <code><a href="../reference/mdro.html">mdro()</a></code>. The <code>intrinsic_resistant</code> data set was also updated accordingly.</p></li>
<li><p>Support for Danish, and also added missing translations of all antimicrobial drugs in Italian, French and Portuguese</p></li> <li><p>Support for Danish, and also added missing translations of all antimicrobial drugs in Italian, French and Portuguese</p></li>
<li> <li>
<p>Function <code><a href="../reference/ab_property.html">set_ab_names()</a></code> to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc. Its second argument can be a tidyverse way of selecting:</p> <p>Function <code><a href="../reference/ab_property.html">set_ab_names()</a></code> to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc. Its second argument can be a tidyverse way of selecting:</p>
@ -180,9 +180,10 @@
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="va">AMC</span><span class="op">:</span><span class="va">GEN</span>, property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></code></pre></div> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="va">AMC</span><span class="op">:</span><span class="va">GEN</span>, property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></code></pre></div>
</li> </li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_lpsn()</a></code> to retrieve the <a href="https://lpsn.dsmz.de" class="external-link">LPSN</a> record ID</p></li> <li><p>Function <code><a href="../reference/mo_property.html">mo_lpsn()</a></code> to retrieve the <a href="https://lpsn.dsmz.de" class="external-link">LPSN</a> record ID</p></li>
<li><p>Function <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> to get units of DDDs (daily defined doses), deprecating the use of <code>ab_ddd(..., units = TRUE)</code> to be more consistent in data types of function output</p></li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="changed-1-7-1-9063">Changed<a class="anchor" aria-label="anchor" href="#changed-1-7-1-9063"></a></h4> <h4 id="changed-1-7-1-9064">Changed<a class="anchor" aria-label="anchor" href="#changed-1-7-1-9064"></a></h4>
<ul><li>Updated the bacterial taxonomy to 5 October 2021 (according to <a href="https://lpsn.dsmz.de" class="external-link">LPSN</a>), including all 11 new staphylococcal species named since 1 January last year</li> <ul><li>Updated the bacterial taxonomy to 5 October 2021 (according to <a href="https://lpsn.dsmz.de" class="external-link">LPSN</a>), including all 11 new staphylococcal species named since 1 January last year</li>
<li>The <code>antibiotics</code> data set now contains <strong>all ATC codes</strong> that are available through the <a href="https://www.whocc.no" class="external-link">WHOCC website</a>, regardless of drugs being present in more than one ATC group. This means that: <li>The <code>antibiotics</code> data set now contains <strong>all ATC codes</strong> that are available through the <a href="https://www.whocc.no" class="external-link">WHOCC website</a>, regardless of drugs being present in more than one ATC group. This means that:
<ul><li>Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)</li> <ul><li>Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)</li>
@ -212,9 +213,10 @@
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">ab_selector</a></span><span class="op">(</span><span class="va">oral_ddd</span> <span class="op">&gt;</span> <span class="fl">1</span> <span class="op">&amp;</span> <span class="va">oral_units</span> <span class="op">==</span> <span class="st">"g"</span><span class="op">)</span><span class="op">)</span> <span class="co"># dplyr</span></code></pre></div> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">ab_selector</a></span><span class="op">(</span><span class="va">oral_ddd</span> <span class="op">&gt;</span> <span class="fl">1</span> <span class="op">&amp;</span> <span class="va">oral_units</span> <span class="op">==</span> <span class="st">"g"</span><span class="op">)</span><span class="op">)</span> <span class="co"># dplyr</span></code></pre></div>
</li> </li>
<li><p>Added the selector <code><a href="../reference/antibiotic_class_selectors.html">not_intrinsic_resistant()</a></code>, which only keeps antibiotic columns that are not intrinsic resistant for all microorganisms in a data set, based on the latest EUCAST guideline on intrinsic resistance. For example, if a data set contains only microorganism codes or names of <em>E. coli</em> and <em>K. pneumoniae</em> and contains a column “vancomycin”, this column will be removed (or rather, unselected) using this function.</p></li> <li><p>Added the selector <code><a href="../reference/antibiotic_class_selectors.html">not_intrinsic_resistant()</a></code>, which only keeps antibiotic columns that are not intrinsic resistant for all microorganisms in a data set, based on the latest EUCAST guideline on intrinsic resistance. For example, if a data set contains only microorganism codes or names of <em>E. coli</em> and <em>K. pneumoniae</em> and contains a column “vancomycin”, this column will be removed (or rather, unselected) using this function.</p></li>
<li><p>Added argument <code>only_treatable</code>, which defaults to <code>TRUE</code> and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)</p></li>
<li><p>Fix for using selectors multiple times in one call (e.g., using them in <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">dplyr::filter()</a></code> and immediately after in <code><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">dplyr::select()</a></code>)</p></li> <li><p>Fix for using selectors multiple times in one call (e.g., using them in <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">dplyr::filter()</a></code> and immediately after in <code><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">dplyr::select()</a></code>)</p></li>
<li><p>Fix for using having multiple columns that are coerced to the same antibiotic agent</p></li> <li><p>Fix for using having multiple columns that are coerced to the same antibiotic agent</p></li>
<li><p>Added argument <code>only_treatable</code>, which defaults to <code>TRUE</code> and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)</p></li> <li><p>Fixed for using <code><a href="https://rdrr.io/r/base/all.html" class="external-link">all()</a></code> or <code><a href="https://rdrr.io/r/base/any.html" class="external-link">any()</a></code> on antibiotic selectors in an R Markdown file</p></li>
</ul></li> </ul></li>
<li>Fixed the Gram stain (<code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) determination of the taxonomic class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as <em>Negativicoccus</em> and <em>Veillonella</em>.</li> <li>Fixed the Gram stain (<code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) determination of the taxonomic class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as <em>Negativicoccus</em> and <em>Veillonella</em>.</li>
<li>Dramatic speed improvement for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> <li>Dramatic speed improvement for <code><a href="../reference/first_isolate.html">first_isolate()</a></code>
@ -250,7 +252,7 @@
<code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> can now cope with <code>NA</code>s</li> <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> can now cope with <code>NA</code>s</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="other-1-7-1-9063">Other<a class="anchor" aria-label="anchor" href="#other-1-7-1-9063"></a></h4> <h4 id="other-1-7-1-9064">Other<a class="anchor" aria-label="anchor" href="#other-1-7-1-9064"></a></h4>
<ul><li>This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations. All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.</li> <ul><li>This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations. All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.</li>
</ul></div> </ul></div>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>
@ -206,7 +206,7 @@
<dt>tolower</dt> <dt>tolower</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the first <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> of every output should be transformed to a lower case <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>. This will lead to e.g. "polymyxin B" and not "polymyxin b".</p></dd> <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the first <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> of every output should be transformed to a lower case <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>. This will lead to e.g. "polymyxin B" and not "polymyxin b".</p></dd>
<dt>...</dt> <dt>...</dt>
<dd><p>in case of <code>set_ab_names()</code> and <code>data</code> is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: variables to select (supports tidy selection like <code>AMX:VAN</code>), otherwise other arguments passed on to <code><a href="as.ab.html">as.ab()</a></code></p></dd> <dd><p>in case of <code>set_ab_names()</code> and <code>data</code> is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: variables to select (supports tidy selection such as <code>column1:column4</code>), otherwise other arguments passed on to <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dt>only_first</dt> <dt>only_first</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)</p></dd> <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)</p></dd>
<dt>administration</dt> <dt>administration</dt>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>
@ -215,7 +215,7 @@
<dl><dt>x</dt> <dl><dt>x</dt>
<dd><p>vector of values (for class <code><a href="as.mic.html">mic</a></code>: MIC values in mg/L, for class <code><a href="as.disk.html">disk</a></code>: a disk diffusion radius in millimetres)</p></dd> <dd><p>vector of values (for class <code><a href="as.mic.html">mic</a></code>: MIC values in mg/L, for class <code><a href="as.disk.html">disk</a></code>: a disk diffusion radius in millimetres)</p></dd>
<dt>...</dt> <dt>...</dt>
<dd><p>for using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: names of columns to apply <code>as.rsi()</code> on (supports tidy selection like <code>AMX:VAN</code>). Otherwise: arguments passed on to methods.</p></dd> <dd><p>for using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: names of columns to apply <code>as.rsi()</code> on (supports tidy selection such as <code>column1:column4</code>). Otherwise: arguments passed on to methods.</p></dd>
<dt>threshold</dt> <dt>threshold</dt>
<dd><p>maximum fraction of invalid antimicrobial interpretations of <code>x</code>, see <em>Examples</em></p></dd> <dd><p>maximum fraction of invalid antimicrobial interpretations of <code>x</code>, see <em>Examples</em></p></dd>
<dt>mo</dt> <dt>mo</dt>
@ -229,7 +229,7 @@
<dt>conserve_capped_values</dt> <dt>conserve_capped_values</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that MIC values starting with <code>"&gt;"</code> (but not <code>"&gt;="</code>) must always return "R" , and that MIC values starting with <code>"&lt;"</code> (but not <code>"&lt;="</code>) must always return "S"</p></dd> <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that MIC values starting with <code>"&gt;"</code> (but not <code>"&gt;="</code>) must always return "R" , and that MIC values starting with <code>"&lt;"</code> (but not <code>"&lt;="</code>) must always return "S"</p></dd>
<dt>add_intrinsic_resistance</dt> <dt>add_intrinsic_resistance</dt>
<dd><p><em>(only useful when using a EUCAST guideline)</em> a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in <em>Klebsiella</em> species. Determination is based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, that itself is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> (2020).</p></dd> <dd><p><em>(only useful when using a EUCAST guideline)</em> a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in <em>Klebsiella</em> species. Determination is based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, that itself is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021).</p></dd>
<dt>reference_data</dt> <dt>reference_data</dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> to be used for interpretation, which defaults to the <a href="rsi_translation.html">rsi_translation</a> data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the <a href="rsi_translation.html">rsi_translation</a> data set (same column names and column types). Please note that the <code>guideline</code> argument will be ignored when <code>reference_data</code> is manually set.</p></dd> <dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> to be used for interpretation, which defaults to the <a href="rsi_translation.html">rsi_translation</a> data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the <a href="rsi_translation.html">rsi_translation</a> data set (same column names and column types). Please note that the <code>guideline</code> argument will be ignored when <code>reference_data</code> is manually set.</p></dd>
<dt>col_mo</dt> <dt>col_mo</dt>

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>
@ -165,13 +165,13 @@
<div id="format"> <div id="format">
<h2>Format</h2> <h2>Format</h2>
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 93,892 observations and 2 variables:</p><ul><li><p><code>microorganism</code><br> Name of the microorganism</p></li> <p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 134,956 observations and 2 variables:</p><ul><li><p><code>microorganism</code><br> Official taxonomic name of the microorganism, according to the LPSN</p></li>
<li><p><code>antibiotic</code><br> Name of the antibiotic drug</p></li> <li><p><code>antibiotic</code><br> Official name of the antibiotic drug, according to the WHOCC</p></li>
</ul></div> </ul></div>
<div id="details"> <div id="details">
<h2>Details</h2> <h2>Details</h2>
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href="https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt</a>. This file <strong>allows for machine reading EUCAST guidelines about intrinsic resistance</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.</p> <p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href="https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt</a>. This file <strong>allows for machine reading EUCAST guidelines about intrinsic resistance</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.</p>
<p>This data set is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> (2020).</p> <p>This data set is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021).</p>
</div> </div>
<div id="reference-data-publicly-available"> <div id="reference-data-publicly-available">
<h2>Reference Data Publicly Available</h2> <h2>Reference Data Publicly Available</h2>
@ -188,12 +188,16 @@
<div id="ref-examples"> <div id="ref-examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># \donttest{</span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">intrinsic_resistant</span>,
<span class="va">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span> <span class="op">&amp;</span> <span class="va">microorganism</span> <span class="op"><a href="like.html">%like%</a></span> <span class="st">"Enterococcus"</span><span class="op">)</span><span class="op">$</span><span class="va">microorganism</span>
<span class="co">#&gt; [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"</span>
<span class="co"># \donttest{</span>
<span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span> <span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
<span class="va">intrinsic_resistant</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="va">intrinsic_resistant</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span>, <span class="va">microorganism</span> <span class="op"><a href="like.html">%like%</a></span> <span class="st">"Enterococcus"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span> <span class="op">&amp;</span> <span class="va">microorganism</span> <span class="op"><a href="like.html">%like%</a></span> <span class="st">"Enterococcus"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html" class="external-link">pull</a></span><span class="op">(</span><span class="va">microorganism</span><span class="op">)</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html" class="external-link">pull</a></span><span class="op">(</span><span class="va">microorganism</span><span class="op">)</span>
<span class="co"># [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"</span> <span class="co">#&gt; [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"</span>
<span class="op">}</span> <span class="op">}</span>
<span class="co"># }</span> <span class="co"># }</span>
</code></pre></div> </code></pre></div>

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>
@ -240,7 +240,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<span class="co"># get isolates whose name start with 'Ent' or 'ent'</span> <span class="co"># get isolates whose name start with 'Ent' or 'ent'</span>
<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^ent"</span><span class="op">)</span>, <span class="op">]</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^ent"</span><span class="op">)</span>, <span class="op">]</span>
<span class="co"># \donttest{</span> <span class="co"># \donttest{</span>
<span class="co"># faster way, only works in R 3.2 and later:</span> <span class="co"># faster way, since mo_name() is context-aware:</span>
<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^ent"</span><span class="op">)</span>, <span class="op">]</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^ent"</span><span class="op">)</span>, <span class="op">]</span>
<span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span> <span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>
@ -236,7 +236,9 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
<p>Currently supported guidelines are (case-insensitive):</p><ul><li><p><code>guideline = "CMI2012"</code> (default)</p> <p>Currently supported guidelines are (case-insensitive):</p><ul><li><p><code>guideline = "CMI2012"</code> (default)</p>
<p>Magiorakos AP, Srinivasan A <em>et al.</em> "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (<a href="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext" class="external-link">link</a>)</p></li> <p>Magiorakos AP, Srinivasan A <em>et al.</em> "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (<a href="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext" class="external-link">link</a>)</p></li>
<li><p><code>guideline = "EUCAST3.2"</code> (or simply <code>guideline = "EUCAST"</code>)</p> <li><p><code>guideline = "EUCAST3.3"</code> (or simply <code>guideline = "EUCAST"</code>)</p>
<p>The European international guideline - EUCAST Expert Rules Version 3.3 "Intrinsic Resistance and Unusual Phenotypes" (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf" class="external-link">link</a>)</p></li>
<li><p><code>guideline = "EUCAST3.2"</code></p>
<p>The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf" class="external-link">link</a>)</p></li> <p>The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf" class="external-link">link</a>)</p></li>
<li><p><code>guideline = "EUCAST3.1"</code></p> <li><p><code>guideline = "EUCAST3.1"</code></p>
<p>The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf" class="external-link">link</a>)</p></li> <p>The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf" class="external-link">link</a>)</p></li>

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>
@ -251,7 +251,7 @@
<p>Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions <code>mo_kingdom()</code> and <code>mo_domain()</code> return the exact same results.</p> <p>Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions <code>mo_kingdom()</code> and <code>mo_domain()</code> return the exact same results.</p>
<p>The Gram stain - <code>mo_gramstain()</code> - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318" class="external-link">PMID 11837318</a>), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p> <p>The Gram stain - <code>mo_gramstain()</code> - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318" class="external-link">PMID 11837318</a>), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
<p>Determination of yeasts - <code>mo_is_yeast()</code> - will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). <em>True yeasts</em> are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p> <p>Determination of yeasts - <code>mo_is_yeast()</code> - will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). <em>True yeasts</em> are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
<p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> (2020). The <code>mo_is_intrinsic_resistant()</code> functions can be vectorised over arguments <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p> <p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021). The <code>mo_is_intrinsic_resistant()</code> functions can be vectorised over arguments <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p>
<p>All output <a href="translate.html">will be translated</a> where possible.</p> <p>All output <a href="translate.html">will be translated</a> where possible.</p>
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p> <p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
<p>SNOMED codes - <code>mo_snomed()</code> - are from the US Edition of SNOMED CT from 1 September 2020. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p> <p>SNOMED codes - <code>mo_snomed()</code> - are from the US Edition of SNOMED CT from 1 September 2020. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
</span> </span>
</div> </div>

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# `AMR` (for R) <img src="./logo.png" align="right" height="120px" /> # `AMR` (for R) <img src="./logo.png" align="right" height="120px" />
> Update: The latest [EUCAST guideline for intrinsic resistance](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) (v3.3, October 2021) is now supported, and our taxonomy tables has been updated as well (LPSN, 5 October 2021). > Update: The latest [EUCAST guideline for intrinsic resistance](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) (v3.3, October 2021) is now supported, and our taxonomy tables have been updated as well (LPSN, 5 October 2021).
> **A new version will be released after the [EUCAST guideline for clinical breakpoints](https://www.eucast.org/clinical_breakpoints/) (v12.0, likely January 2022) are implemented, to be expected shortly after the official guideline release.** > **A new version will be released after the [EUCAST guideline for clinical breakpoints](https://www.eucast.org/clinical_breakpoints/) (v12.0, likely January 2022) are implemented, to be expected shortly after the official guideline release.**
### What is `AMR` (for R)? ### What is `AMR` (for R)?
@ -9,7 +9,7 @@
After installing this package, R knows [**~71,000 distinct microbial species**](./reference/microorganisms.html) and all [**~560 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish. After installing this package, R knows [**~71,000 distinct microbial species**](./reference/microorganisms.html) and all [**~560 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.
This package is [fully independent of any other R package](https://en.wikipedia.org/wiki/Dependency_hell) and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.192486375)) but is [actively and durably maintained](./news) by two public healthcare organisations in the Netherlands. This package is [fully independent of any other R package](https://en.wikipedia.org/wiki/Dependency_hell) and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)) but is [actively and durably maintained](./news) by two public healthcare organisations in the Netherlands.
<div class="main-content" style="display: inline-block;"> <div class="main-content" style="display: inline-block;">
<p> <p>

2
man/ab_property.Rd
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@ -62,7 +62,7 @@ set_ab_names(
\item{tolower}{a \link{logical} to indicate whether the first \link{character} of every output should be transformed to a lower case \link{character}. This will lead to e.g. "polymyxin B" and not "polymyxin b".} \item{tolower}{a \link{logical} to indicate whether the first \link{character} of every output should be transformed to a lower case \link{character}. This will lead to e.g. "polymyxin B" and not "polymyxin b".}
\item{...}{in case of \code{\link[=set_ab_names]{set_ab_names()}} and \code{data} is a \link{data.frame}: variables to select (supports tidy selection like \code{AMX:VAN}), otherwise other arguments passed on to \code{\link[=as.ab]{as.ab()}}} \item{...}{in case of \code{\link[=set_ab_names]{set_ab_names()}} and \code{data} is a \link{data.frame}: variables to select (supports tidy selection such as \code{column1:column4}), otherwise other arguments passed on to \code{\link[=as.ab]{as.ab()}}}
\item{only_first}{a \link{logical} to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)} \item{only_first}{a \link{logical} to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)}

6
man/as.rsi.Rd
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@ -60,7 +60,7 @@ is.rsi.eligible(x, threshold = 0.05)
\arguments{ \arguments{
\item{x}{vector of values (for class \code{\link{mic}}: MIC values in mg/L, for class \code{\link{disk}}: a disk diffusion radius in millimetres)} \item{x}{vector of values (for class \code{\link{mic}}: MIC values in mg/L, for class \code{\link{disk}}: a disk diffusion radius in millimetres)}
\item{...}{for using on a \link{data.frame}: names of columns to apply \code{\link[=as.rsi]{as.rsi()}} on (supports tidy selection like \code{AMX:VAN}). Otherwise: arguments passed on to methods.} \item{...}{for using on a \link{data.frame}: names of columns to apply \code{\link[=as.rsi]{as.rsi()}} on (supports tidy selection such as \code{column1:column4}). Otherwise: arguments passed on to methods.}
\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, see \emph{Examples}} \item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, see \emph{Examples}}
@ -74,7 +74,7 @@ is.rsi.eligible(x, threshold = 0.05)
\item{conserve_capped_values}{a \link{logical} to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"} \item{conserve_capped_values}{a \link{logical} to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"}
\item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a \link{logical} to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2} (2020).} \item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a \link{logical} to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).}
\item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{rsi_translation} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{rsi_translation} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.} \item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{rsi_translation} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{rsi_translation} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.}
@ -105,7 +105,7 @@ your_data \%>\% mutate(across(where(is.mic), as.rsi)) # since dplyr 1.0.0
your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0 your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
} }
} }
\item For \strong{interpreting a complete data set}, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running \code{as.rsi(data)}. \item For \strong{interpreting a complete data set}, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running \code{as.rsi(your_data)}.
} }
} }

16
man/intrinsic_resistant.Rd
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@ -5,10 +5,10 @@
\alias{intrinsic_resistant} \alias{intrinsic_resistant}
\title{Data Set with Bacterial Intrinsic Resistance} \title{Data Set with Bacterial Intrinsic Resistance}
\format{ \format{
A \link{data.frame} with 93,892 observations and 2 variables: A \link{data.frame} with 134,956 observations and 2 variables:
\itemize{ \itemize{
\item \code{microorganism}\cr Name of the microorganism \item \code{microorganism}\cr Official taxonomic name of the microorganism, according to the LPSN
\item \code{antibiotic}\cr Name of the antibiotic drug \item \code{antibiotic}\cr Official name of the antibiotic drug, according to the WHOCC
} }
} }
\usage{ \usage{
@ -20,7 +20,7 @@ Data set containing defined intrinsic resistance by EUCAST of all bug-drug combi
\details{ \details{
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt}. This file \strong{allows for machine reading EUCAST guidelines about intrinsic resistance}, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically. The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt}. This file \strong{allows for machine reading EUCAST guidelines about intrinsic resistance}, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
This data set is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2} (2020). This data set is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).
} }
\section{Reference Data Publicly Available}{ \section{Reference Data Publicly Available}{
@ -33,12 +33,16 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
} }
\examples{ \examples{
subset(intrinsic_resistant,
antibiotic == "Vancomycin" & microorganism \%like\% "Enterococcus")$microorganism
#> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
\donttest{ \donttest{
if (require("dplyr")) { if (require("dplyr")) {
intrinsic_resistant \%>\% intrinsic_resistant \%>\%
filter(antibiotic == "Vancomycin", microorganism \%like\% "Enterococcus") \%>\% filter(antibiotic == "Vancomycin" & microorganism \%like\% "Enterococcus") \%>\%
pull(microorganism) pull(microorganism)
# [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" #> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
} }
} }
} }

2
man/like.Rd
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@ -82,7 +82,7 @@ a \%like\% b[1]
# get isolates whose name start with 'Ent' or 'ent' # get isolates whose name start with 'Ent' or 'ent'
example_isolates[which(mo_name(example_isolates$mo) \%like\% "^ent"), ] example_isolates[which(mo_name(example_isolates$mo) \%like\% "^ent"), ]
\donttest{ \donttest{
# faster way, only works in R 3.2 and later: # faster way, since mo_name() is context-aware:
example_isolates[which(mo_name() \%like\% "^ent"), ] example_isolates[which(mo_name() \%like\% "^ent"), ]
if (require("dplyr")) { if (require("dplyr")) {

5
man/mdro.Rd
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@ -94,7 +94,10 @@ Currently supported guidelines are (case-insensitive):
\item \code{guideline = "CMI2012"} (default) \item \code{guideline = "CMI2012"} (default)
Magiorakos AP, Srinivasan A \emph{et al.} "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (\href{https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext}{link}) Magiorakos AP, Srinivasan A \emph{et al.} "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (\href{https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext}{link})
\item \code{guideline = "EUCAST3.2"} (or simply \code{guideline = "EUCAST"}) \item \code{guideline = "EUCAST3.3"} (or simply \code{guideline = "EUCAST"})
The European international guideline - EUCAST Expert Rules Version 3.3 "Intrinsic Resistance and Unusual Phenotypes" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf}{link})
\item \code{guideline = "EUCAST3.2"}
The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf}{link}) The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf}{link})
\item \code{guideline = "EUCAST3.1"} \item \code{guideline = "EUCAST3.1"}

2
man/mo_property.Rd
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@ -131,7 +131,7 @@ The Gram stain - \code{\link[=mo_gramstain]{mo_gramstain()}} - will be determine
Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). \emph{True yeasts} are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (except when the input is \code{NA} or the MO code is \code{UNKNOWN}). Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). \emph{True yeasts} are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (except when the input is \code{NA} or the MO code is \code{UNKNOWN}).
Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2} (2020). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} functions can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics). Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} functions can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics).
All output \link[=translate]{will be translated} where possible. All output \link[=translate]{will be translated} where possible.

2
vignettes/welcome_to_AMR.Rmd
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@ -53,4 +53,4 @@ This package can be used for:
All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this `AMR` package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find [all download links on our website](https://msberends.github.io/AMR/articles/datasets.html), which is automatically updated with every code change. All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this `AMR` package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find [all download links on our website](https://msberends.github.io/AMR/articles/datasets.html), which is automatically updated with every code change.
This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.192486375)) but is actively and durably maintained (see [changelog)](https://msberends.github.io/AMR/news/index.html)) by two public healthcare organisations in the Netherlands. This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)) but is actively and durably maintained (see [changelog)](https://msberends.github.io/AMR/news/index.html)) by two public healthcare organisations in the Netherlands.