(v2.1.1.9111) add betalactams_with_inhibitor(), fixes #175

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9110
+Version: 2.1.1.9111
-Date: 2024-11-21
+Date: 2024-12-06
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NAMESPACE

@@ -182,6 +182,7 @@ export(av_tradenames)
 export(av_url)
 export(availability)
 export(betalactams)
+export(betalactams_with_inhibitor)
 export(brmo)
 export(bug_drug_combinations)
 export(carbapenems)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9110
+# AMR 2.1.1.9111
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
 

PythonPackage/AMR/AMR.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: AMR
-Version: 2.1.1.9110
+Version: 2.1.1.9111
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Dr. Matthijs Berends

PythonPackage/AMR/AMR/__init__.py

@@ -31,6 +31,7 @@ from .functions import aminopenicillins
 from .functions import antifungals
 from .functions import antimycobacterials
 from .functions import betalactams
+from .functions import betalactams_with_inhibitor
 from .functions import carbapenems
 from .functions import cephalosporins
 from .functions import cephalosporins_1st

PythonPackage/AMR/AMR/functions.py

@@ -123,6 +123,9 @@ def antimycobacterials(only_sir_columns = False, *args, **kwargs):
 def betalactams(only_sir_columns = False, *args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
     return convert_to_python(amr_r.betalactams(only_sir_columns = False, *args, **kwargs))
+def betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs):
+    """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+    return convert_to_python(amr_r.betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs))
 def carbapenems(only_sir_columns = False, *args, **kwargs):
     """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
     return convert_to_python(amr_r.carbapenems(only_sir_columns = False, *args, **kwargs))

PythonPackage/AMR/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AMR',
-    version='2.1.1.9110',
+    version='2.1.1.9111',
     packages=find_packages(),
     install_requires=[
         'rpy2',

R/ab_selectors.R

@@ -62,102 +62,88 @@
 #' \donttest{
 #' # dplyr -------------------------------------------------------------------
 #' 
-#' if (require("dplyr")) {
+#' library(dplyr, warn.conflicts = FALSE)
-#'   example_isolates %>% select(carbapenems())
+#' 
-#' }
+#' example_isolates %>% select(carbapenems())
 #' 
-#' if (require("dplyr")) {
 #' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
 #' example_isolates %>% select(mo, aminoglycosides())
-#' }
 #' 
-#' if (require("dplyr")) {
+#' # you can combine selectors like you are used with tidyverse
+#' # e.g., for betalactams, but not the ones with an enzyme inhibitor:
+#' example_isolates |> select(betalactams(), -betalactams_with_inhibitor())
+#' 
 #' # select only antibiotic columns with DDDs for oral treatment
 #' example_isolates %>% select(administrable_per_os())
-#' }
 #' 
-#' if (require("dplyr")) {
 #' # get AMR for all aminoglycosides e.g., per ward:
 #' example_isolates %>%
 #'   group_by(ward) %>%
 #'   summarise(across(aminoglycosides(),
 #'                    resistance))
-#' }
+#' 
-#' if (require("dplyr")) {
 #' # You can combine selectors with '&' to be more specific:
 #' example_isolates %>%
 #'   select(penicillins() & administrable_per_os())
-#' }
+#' 
-#' if (require("dplyr")) {
 #' # get AMR for only drugs that matter - no intrinsic resistance:
 #' example_isolates %>%
 #'   filter(mo_genus() %in% c("Escherichia", "Klebsiella")) %>%
 #'   group_by(ward) %>%
 #'   summarise_at(not_intrinsic_resistant(),
 #'                resistance)
-#' }
+#' 
-#' if (require("dplyr")) {
 #' # get susceptibility for antibiotics whose name contains "trim":
 #' example_isolates %>%
 #'   filter(first_isolate()) %>%
 #'   group_by(ward) %>%
 #'   summarise(across(ab_selector(name %like% "trim"), susceptibility))
-#' }
+#' 
-#' if (require("dplyr")) {
 #' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
 #' example_isolates %>%
 #'   select(carbapenems())
-#' }
+#' 
-#' if (require("dplyr")) {
 #' # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
 #' example_isolates %>%
 #'   select(mo, aminoglycosides())
-#' }
+#' 
-#' if (require("dplyr")) {
 #' # any() and all() work in dplyr's filter() too:
 #' example_isolates %>%
 #'   filter(
 #'     any(aminoglycosides() == "R"),
 #'     all(cephalosporins_2nd() == "R")
 #'   )
-#' }
+#' 
-#' if (require("dplyr")) {
 #' # also works with c():
 #' example_isolates %>%
 #'   filter(any(c(carbapenems(), aminoglycosides()) == "R"))
-#' }
+#' 
-#' if (require("dplyr")) {
 #' # not setting any/all will automatically apply all():
 #' example_isolates %>%
 #'   filter(aminoglycosides() == "R")
-#' }
+#' 
-#' if (require("dplyr")) {
 #' # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
 #' example_isolates %>%
 #'   select(mo, ab_class("mycobact"))
-#' }
+#' 
-#' if (require("dplyr")) {
 #' # get bug/drug combinations for only glycopeptides in Gram-positives:
 #' example_isolates %>%
 #'   filter(mo_is_gram_positive()) %>%
 #'   select(mo, glycopeptides()) %>%
 #'   bug_drug_combinations() %>%
 #'   format()
-#' }
+#' 
-#' if (require("dplyr")) {
 #' data.frame(
 #'   some_column = "some_value",
 #'   J01CA01 = "S"
 #' ) %>% # ATC code of ampicillin
 #'   select(penicillins()) # only the 'J01CA01' column will be selected
-#' }
+#' 
-#' if (require("dplyr")) {
 #' # with recent versions of dplyr, this is all equal:
 #' x <- example_isolates[carbapenems() == "R", ]
 #' y <- example_isolates %>% filter(carbapenems() == "R")
 #' z <- example_isolates %>% filter(if_all(carbapenems(), ~ .x == "R"))
 #' identical(x, y) && identical(y, z)
-#' }
 #'
 #'
 #' # base R ------------------------------------------------------------------
@@ -312,6 +298,13 @@ betalactams <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
   ab_select_exec("betalactams", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
 }
 
+#' @rdname antibiotic_class_selectors
+#' @export
+betalactams_with_inhibitor <- function(only_sir_columns = FALSE, ...) {
+  meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("betalactams_with_inhibitor", only_sir_columns = only_sir_columns)
+}
+
 #' @rdname antibiotic_class_selectors
 #' @export
 carbapenems <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
@@ -595,7 +588,7 @@ ab_select_exec <- function(function_name,
                            only_treatable = FALSE,
                            ab_class_args = NULL) {
   # get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
-  # but it only takes a couple of milliseconds
+  # it only takes a couple of milliseconds, so no problem
   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
   ab_in_data <- get_column_abx(vars_df,
@@ -605,7 +598,7 @@ ab_select_exec <- function(function_name,
 
   # untreatable drugs
   if (only_treatable == TRUE) {
-    untreatable <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$name %like% "-high|EDTA|polysorbate|macromethod|screening|nacubactam"), "ab", drop = TRUE]
+    untreatable <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$name %like% "(-high|EDTA|polysorbate|macromethod|screening|nacubactam)"), "ab", drop = TRUE]
     if (any(untreatable %in% names(ab_in_data))) {
       if (message_not_thrown_before(function_name, "ab_class", "untreatable")) {
         warning_(
@@ -644,7 +637,7 @@ ab_select_exec <- function(function_name,
         custom_ab <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$ab %in% AMR_env$custom_ab_codes), ]
         check_string <- paste0(custom_ab$group, custom_ab$atc_group1, custom_ab$atc_group2)
         if (function_name == "betalactams") {
-          find_group <- "beta-lactams"
+          find_group <- "beta[-]?lactams"
         } else if (function_name %like% "cephalosporins_") {
           find_group <- gsub("_(.*)$", paste0(" (\\1 gen.)"), function_name)
         } else {

data-raw/_pre_commit_checks.R

@@ -440,6 +440,9 @@ pre_commit_lst$AB_TRIMETHOPRIMS <- antibiotics %>%
   pull(ab)
 pre_commit_lst$AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
 pre_commit_lst$AB_BETALACTAMS <- c(pre_commit_lst$AB_PENICILLINS, pre_commit_lst$AB_CEPHALOSPORINS, pre_commit_lst$AB_CARBAPENEMS)
+pre_commit_lst$AB_BETALACTAMS_WITH_INHIBITOR <- antibiotics %>%
+  filter(name %like% "/" & name %unlike% "EDTA" & ab %in% pre_commit_lst$AB_BETALACTAMS) %>%
+  pull(ab)
 # this will be used for documentation:
 pre_commit_lst$DEFINED_AB_GROUPS <- sort(names(pre_commit_lst)[names(pre_commit_lst) %like% "^AB_" & names(pre_commit_lst) != "AB_LOOKUP"])
 create_AB_AV_lookup <- function(df) {
@@ -638,7 +641,7 @@ suppressMessages(set_AMR_locale("English"))
 
 # Update URLs -------------------------------------------------------------
 usethis::ui_info("Checking URLs for redirects")
-invisible(capture.output(urlchecker::url_update()))
+invisible(urlchecker::url_update("."))
 
 
 # Document pkg ------------------------------------------------------------

data-raw/eucast_rules.tsv

@@ -1,6 +1,6 @@
 # -------------------------------------------------------------------------------------------------------------------------------
 # For editing this EUCAST reference file, these values can all be used for targeting antibiotics:
-# aminoglycosides, aminopenicillins, antifungals, antimycobacterials, betalactams, carbapenems, cephalosporins, cephalosporins_1st, cephalosporins_2nd, cephalosporins_3rd, cephalosporins_4th, cephalosporins_5th, cephalosporins_except_CAZ, fluoroquinolones, glycopeptides, glycopeptides_except_lipo, lincosamides, lipoglycopeptides, macrolides, oxazolidinones, penicillins, polymyxins, quinolones, streptogramins, tetracyclines, tetracyclines_except_TGC, trimethoprims, ureidopenicillins
+# aminoglycosides, aminopenicillins, antifungals, antimycobacterials, betalactams, betalactams_with_inhibitor, carbapenems, cephalosporins, cephalosporins_1st, cephalosporins_2nd, cephalosporins_3rd, cephalosporins_4th, cephalosporins_5th, cephalosporins_except_CAZ, fluoroquinolones, glycopeptides, glycopeptides_except_lipo, lincosamides, lipoglycopeptides, macrolides, oxazolidinones, penicillins, polymyxins, quinolones, streptogramins, tetracyclines, tetracyclines_except_TGC, trimethoprims, ureidopenicillins
 # and all separate EARS-Net letter codes such as AMC. They can be separated by comma: 'AMC, fluoroquinolones'.
 # The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or 'genus_species' or 'gramstain'.
 # The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression)
@@ -11,7 +11,7 @@ if_mo_property	like.is.one_of	this_value	and_these_antibiotics	have_these_values
 order	is	Enterobacterales	AMP	S	AMX	S	Enterobacterales (Order)	Breakpoints	10	
 order	is	Enterobacterales	AMP	I	AMX	I	Enterobacterales (Order)	Breakpoints	10	
 order	is	Enterobacterales	AMP	R	AMX	R	Enterobacterales (Order)	Breakpoints	10	
-genus	is	Staphylococcus	PEN, FOX	S	AMP, AMX, PIP, TIC	S	Staphylococcus	Breakpoints	10	
+genus	is	Staphylococcus	PEN, FOX	S	betalactams_with_inhibitor	S	Staphylococcus	Breakpoints	10	
 genus	is	Staphylococcus	PEN, FOX	R, S	OXA, FLC	S	Staphylococcus	Breakpoints	10	
 genus	is	Staphylococcus	FOX	R	betalactams	R	Staphylococcus	Breakpoints	10	
 genus_species	is	Staphylococcus saprophyticus	AMP	S	AMX, AMC, PIP, TZP	S	Staphylococcus	Breakpoints	10	
@@ -117,7 +117,7 @@ genus_species	is	Burkholderia pseudomallei	TCY	R	DOX	R	Burkholderia pseudomallei
 order	is	Enterobacterales	AMP	S	AMX	S	Enterobacterales (Order)	Breakpoints	11	
 order	is	Enterobacterales	AMP	I	AMX	I	Enterobacterales (Order)	Breakpoints	11	
 order	is	Enterobacterales	AMP	R	AMX	R	Enterobacterales (Order)	Breakpoints	11	
-genus	is	Staphylococcus	PEN, FOX	S	AMP, AMX, PIP, TIC	S	Staphylococcus	Breakpoints	11	
+genus	is	Staphylococcus	PEN, FOX	S	betalactams_with_inhibitor	S	Staphylococcus	Breakpoints	11	
 genus	is	Staphylococcus	PEN, FOX	R, S	OXA, FLC	S	Staphylococcus	Breakpoints	11	
 genus	is	Staphylococcus	FOX	R	betalactams	R	Staphylococcus	Breakpoints	11	
 genus_species	is	Staphylococcus saprophyticus	AMP	S	AMX, AMC, PIP, TZP	S	Staphylococcus	Breakpoints	11	
@@ -226,7 +226,7 @@ genus	is	Bacillus	NOR	R	fluoroquinolones	R	Bacillus	Breakpoints	11	added in 11
 order	is	Enterobacterales	AMP	S	AMX	S	Enterobacterales (Order)	Breakpoints	12	
 order	is	Enterobacterales	AMP	I	AMX	I	Enterobacterales (Order)	Breakpoints	12	
 order	is	Enterobacterales	AMP	R	AMX	R	Enterobacterales (Order)	Breakpoints	12	
-genus	is	Staphylococcus	PEN, FOX	S	AMP, AMX, PIP, TIC	S	Staphylococcus	Breakpoints	12	
+genus	is	Staphylococcus	PEN, FOX	S	betalactams_with_inhibitor	S	Staphylococcus	Breakpoints	12	
 genus	is	Staphylococcus	PEN, FOX	R, S	OXA, FLC	S	Staphylococcus	Breakpoints	12	
 genus	is	Staphylococcus	FOX	R	betalactams	R	Staphylococcus	Breakpoints	12	
 genus_species	is	Staphylococcus saprophyticus	AMP	S	AMX, AMC, PIP, TZP	S	Staphylococcus	Breakpoints	12	
@@ -500,8 +500,8 @@ genus	is	Salmonella			aminoglycosides	R	Expert Rules on Salmonella	Expert Rules
 genus	is	Salmonella	PEF	R	CIP	R	Expert Rules on Salmonella	Expert Rules	3.2	
 genus_species	is	Staphylococcus aureus	FOX1	R	betalactams	R	Expert Rules on Staphylococcus	Expert Rules	3.2	
 genus_species	is	Staphylococcus aureus	FOX	R	betalactams	R	Expert Rules on Staphylococcus	Expert Rules	3.2	
-genus_species	is	Staphylococcus aureus	FOX1	S	betalactams	S	Expert Rules on Staphylococcus	Expert Rules	3.2	
+genus_species	is	Staphylococcus aureus	FOX1	S	betalactams_with_inhibitor	S	Expert Rules on Staphylococcus	Expert Rules	3.2	
-genus_species	is	Staphylococcus aureus	FOX	S	betalactams	S	Expert Rules on Staphylococcus	Expert Rules	3.2	
+genus_species	is	Staphylococcus aureus	FOX	S	betalactams_with_inhibitor	S	Expert Rules on Staphylococcus	Expert Rules	3.2	
 genus_species	one_of	Staphylococcus aureus, Staphylococcus lugdunensis	PEN	R	AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC	R	Expert Rules on Staphylococcus	Expert Rules	3.2	all penicillins without beta-lactamse inhibitor
 genus	is	Staphylococcus	ERY, CLI	S	macrolides, lincosamides	S	Expert Rules on Staphylococcus	Expert Rules	3.2	
 genus	is	Staphylococcus	NOR	S	CIP, LVX, MFX, OFX	S	Expert Rules on Staphylococcus	Expert Rules	3.2	
@@ -620,8 +620,8 @@ genus	is	Salmonella			aminoglycosides	R	Expert Rules on Salmonella	Expert Rules
 genus	is	Salmonella	PEF	R	CIP	R	Expert Rules on Salmonella	Expert Rules	3.3	
 genus_species	is	Staphylococcus aureus	FOX1	R	betalactams	R	Expert Rules on Staphylococcus	Expert Rules	3.3	
 genus_species	is	Staphylococcus aureus	FOX	R	betalactams	R	Expert Rules on Staphylococcus	Expert Rules	3.3	
-genus_species	is	Staphylococcus aureus	FOX1	S	betalactams	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus_species	is	Staphylococcus aureus	FOX1	S	betalactams_with_inhibitor	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
-genus_species	is	Staphylococcus aureus	FOX	S	betalactams	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus_species	is	Staphylococcus aureus	FOX	S	betalactams_with_inhibitor	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
 genus_species	one_of	Staphylococcus aureus, Staphylococcus lugdunensis	PEN	R	AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC	R	Expert Rules on Staphylococcus	Expert Rules	3.3	all penicillins without beta-lactamse inhibitor
 genus	is	Staphylococcus	ERY, CLI	S	macrolides, lincosamides	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
 genus	is	Staphylococcus	NOR	S	CIP, LVX, MFX, OFX	S	Expert Rules on Staphylococcus	Expert Rules	3.3	

data-raw/gpt_training_text_v2.1.1.9111.txt

@@ -1,5 +1,5 @@
 This files contains all context you must know about the AMR package for R.
-First and foremost, you are trained on version 2.1.1.9110. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9111. Remember this whenever someone asks which AMR package version you’re at.
 --------------------------------
 
 THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'NAMESPACE':
@@ -189,6 +189,7 @@ export(av_tradenames)
 export(av_url)
 export(availability)
 export(betalactams)
+export(betalactams_with_inhibitor)
 export(brmo)
 export(bug_drug_combinations)
 export(carbapenems)
@@ -1935,6 +1936,7 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/antibiotic_class_selectors.R
 \alias{antifungals}
 \alias{antimycobacterials}
 \alias{betalactams}
+\alias{betalactams_with_inhibitor}
 \alias{carbapenems}
 \alias{cephalosporins}
 \alias{cephalosporins_1st}
@@ -1976,6 +1978,8 @@ antimycobacterials(only_sir_columns = FALSE, ...)
 
 betalactams(only_sir_columns = FALSE, only_treatable = TRUE, ...)
 
+betalactams_with_inhibitor(only_sir_columns = FALSE, ...)
+
 carbapenems(only_sir_columns = FALSE, only_treatable = TRUE, ...)
 
 cephalosporins(only_sir_columns = FALSE, ...)
@@ -2075,6 +2079,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
 \item \code{\link[=antifungals]{antifungals()}} can select: \cr amorolfine (AMO), amphotericin B (AMB), amphotericin B-high (AMH), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), and voriconazole (VOR)
 \item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)
 \item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC)
+\item \code{\link[=betalactams_with_inhibitor]{betalactams_with_inhibitor()}} can select: \cr amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC), ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)
 \item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), and tebipenem (TBP)
 \item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)
 \item \code{\link[=cephalosporins_1st]{cephalosporins_1st()}} can select: \cr cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), and cephradine (CED)
@@ -2116,102 +2121,88 @@ example_isolates
 \donttest{
 # dplyr -------------------------------------------------------------------
 
-if (require("dplyr")) {
+library(dplyr, warn.conflicts = FALSE)
-  example_isolates \%>\% select(carbapenems())
-}
 
-if (require("dplyr")) {
+example_isolates \%>\% select(carbapenems())
-  # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
-  example_isolates \%>\% select(mo, aminoglycosides())
-}
 
-if (require("dplyr")) {
+# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
-  # select only antibiotic columns with DDDs for oral treatment
+example_isolates \%>\% select(mo, aminoglycosides())
-  example_isolates \%>\% select(administrable_per_os())
-}
 
-if (require("dplyr")) {
+# you can combine selectors like you are used with tidyverse
-  # get AMR for all aminoglycosides e.g., per ward:
+# e.g., for betalactams, but not the ones with an enzyme inhibitor:
-  example_isolates \%>\%
+example_isolates |> select(betalactams(), -betalactams_with_inhibitor())
+
+# select only antibiotic columns with DDDs for oral treatment
+example_isolates \%>\% select(administrable_per_os())
+
+# get AMR for all aminoglycosides e.g., per ward:
+example_isolates \%>\%
   group_by(ward) \%>\%
   summarise(across(aminoglycosides(),
                    resistance))
-}
+
-if (require("dplyr")) {
+# You can combine selectors with '&' to be more specific:
-  # You can combine selectors with '&' to be more specific:
+example_isolates \%>\%
-  example_isolates \%>\%
   select(penicillins() & administrable_per_os())
-}
+
-if (require("dplyr")) {
+# get AMR for only drugs that matter - no intrinsic resistance:
-  # get AMR for only drugs that matter - no intrinsic resistance:
+example_isolates \%>\%
-  example_isolates \%>\%
   filter(mo_genus() \%in\% c("Escherichia", "Klebsiella")) \%>\%
   group_by(ward) \%>\%
   summarise_at(not_intrinsic_resistant(),
                resistance)
-}
+
-if (require("dplyr")) {
+# get susceptibility for antibiotics whose name contains "trim":
-  # get susceptibility for antibiotics whose name contains "trim":
+example_isolates \%>\%
-  example_isolates \%>\%
   filter(first_isolate()) \%>\%
   group_by(ward) \%>\%
   summarise(across(ab_selector(name \%like\% "trim"), susceptibility))
-}
+
-if (require("dplyr")) {
+# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
-  # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
+example_isolates \%>\%
-  example_isolates \%>\%
   select(carbapenems())
-}
+
-if (require("dplyr")) {
+# this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
-  # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
+example_isolates \%>\%
-  example_isolates \%>\%
   select(mo, aminoglycosides())
-}
+
-if (require("dplyr")) {
+# any() and all() work in dplyr's filter() too:
-  # any() and all() work in dplyr's filter() too:
+example_isolates \%>\%
-  example_isolates \%>\%
   filter(
     any(aminoglycosides() == "R"),
     all(cephalosporins_2nd() == "R")
   )
-}
+
-if (require("dplyr")) {
+# also works with c():
-  # also works with c():
+example_isolates \%>\%
-  example_isolates \%>\%
   filter(any(c(carbapenems(), aminoglycosides()) == "R"))
-}
+
-if (require("dplyr")) {
+# not setting any/all will automatically apply all():
-  # not setting any/all will automatically apply all():
+example_isolates \%>\%
-  example_isolates \%>\%
   filter(aminoglycosides() == "R")
-}
+
-if (require("dplyr")) {
+# this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
-  # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
+example_isolates \%>\%
-  example_isolates \%>\%
   select(mo, ab_class("mycobact"))
-}
+
-if (require("dplyr")) {
+# get bug/drug combinations for only glycopeptides in Gram-positives:
-  # get bug/drug combinations for only glycopeptides in Gram-positives:
+example_isolates \%>\%
-  example_isolates \%>\%
   filter(mo_is_gram_positive()) \%>\%
   select(mo, glycopeptides()) \%>\%
   bug_drug_combinations() \%>\%
   format()
-}
+
-if (require("dplyr")) {
+data.frame(
-  data.frame(
   some_column = "some_value",
   J01CA01 = "S"
-  ) \%>\% # ATC code of ampicillin
+) \%>\% # ATC code of ampicillin
   select(penicillins()) # only the 'J01CA01' column will be selected
-}
+
-if (require("dplyr")) {
+# with recent versions of dplyr, this is all equal:
-  # with recent versions of dplyr, this is all equal:
+x <- example_isolates[carbapenems() == "R", ]
-  x <- example_isolates[carbapenems() == "R", ]
+y <- example_isolates \%>\% filter(carbapenems() == "R")
-  y <- example_isolates \%>\% filter(carbapenems() == "R")
+z <- example_isolates \%>\% filter(if_all(carbapenems(), ~ .x == "R"))
-  z <- example_isolates \%>\% filter(if_all(carbapenems(), ~ .x == "R"))
+identical(x, y) && identical(y, z)
-  identical(x, y) && identical(y, z)
-}
 
 
 # base R ------------------------------------------------------------------
@@ -4291,13 +4282,14 @@ x
 #>      amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
 }\if{html}{\out{</div>}}
 
-These 30 antibiotic groups are allowed in the rules (case-insensitive) and can be used in any combination:
+These 31 antibiotic groups are allowed in the rules (case-insensitive) and can be used in any combination:
 \itemize{
 \item aminoglycosides\cr(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)
 \item aminopenicillins\cr(amoxicillin and ampicillin)
 \item antifungals\cr(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)
 \item antimycobacterials\cr(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)
 \item betalactams\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin, and ticarcillin/clavulanic acid)
+\item betalactams_with_inhibitor\cr(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)
 \item carbapenems\cr(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem)
 \item cephalosporins\cr(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)
 \item cephalosporins_1st\cr(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine)

man/antibiotic_class_selectors.Rd

@@ -9,6 +9,7 @@
 \alias{antifungals}
 \alias{antimycobacterials}
 \alias{betalactams}
+\alias{betalactams_with_inhibitor}
 \alias{carbapenems}
 \alias{cephalosporins}
 \alias{cephalosporins_1st}
@@ -50,6 +51,8 @@ antimycobacterials(only_sir_columns = FALSE, ...)
 
 betalactams(only_sir_columns = FALSE, only_treatable = TRUE, ...)
 
+betalactams_with_inhibitor(only_sir_columns = FALSE, ...)
+
 carbapenems(only_sir_columns = FALSE, only_treatable = TRUE, ...)
 
 cephalosporins(only_sir_columns = FALSE, ...)
@@ -149,6 +152,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
 \item \code{\link[=antifungals]{antifungals()}} can select: \cr amorolfine (AMO), amphotericin B (AMB), amphotericin B-high (AMH), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), and voriconazole (VOR)
 \item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)
 \item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC)
+\item \code{\link[=betalactams_with_inhibitor]{betalactams_with_inhibitor()}} can select: \cr amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC), ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)
 \item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), and tebipenem (TBP)
 \item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)
 \item \code{\link[=cephalosporins_1st]{cephalosporins_1st()}} can select: \cr cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), and cephradine (CED)
@@ -190,102 +194,88 @@ example_isolates
 \donttest{
 # dplyr -------------------------------------------------------------------
 
-if (require("dplyr")) {
+library(dplyr, warn.conflicts = FALSE)
-  example_isolates \%>\% select(carbapenems())
-}
 
-if (require("dplyr")) {
+example_isolates \%>\% select(carbapenems())
-  # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
-  example_isolates \%>\% select(mo, aminoglycosides())
-}
 
-if (require("dplyr")) {
+# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
-  # select only antibiotic columns with DDDs for oral treatment
+example_isolates \%>\% select(mo, aminoglycosides())
-  example_isolates \%>\% select(administrable_per_os())
-}
 
-if (require("dplyr")) {
+# you can combine selectors like you are used with tidyverse
-  # get AMR for all aminoglycosides e.g., per ward:
+# e.g., for betalactams, but not the ones with an enzyme inhibitor:
-  example_isolates \%>\%
+example_isolates |> select(betalactams(), -betalactams_with_inhibitor())
+
+# select only antibiotic columns with DDDs for oral treatment
+example_isolates \%>\% select(administrable_per_os())
+
+# get AMR for all aminoglycosides e.g., per ward:
+example_isolates \%>\%
   group_by(ward) \%>\%
   summarise(across(aminoglycosides(),
                    resistance))
-}
+
-if (require("dplyr")) {
+# You can combine selectors with '&' to be more specific:
-  # You can combine selectors with '&' to be more specific:
+example_isolates \%>\%
-  example_isolates \%>\%
   select(penicillins() & administrable_per_os())
-}
+
-if (require("dplyr")) {
+# get AMR for only drugs that matter - no intrinsic resistance:
-  # get AMR for only drugs that matter - no intrinsic resistance:
+example_isolates \%>\%
-  example_isolates \%>\%
   filter(mo_genus() \%in\% c("Escherichia", "Klebsiella")) \%>\%
   group_by(ward) \%>\%
   summarise_at(not_intrinsic_resistant(),
                resistance)
-}
+
-if (require("dplyr")) {
+# get susceptibility for antibiotics whose name contains "trim":
-  # get susceptibility for antibiotics whose name contains "trim":
+example_isolates \%>\%
-  example_isolates \%>\%
   filter(first_isolate()) \%>\%
   group_by(ward) \%>\%
   summarise(across(ab_selector(name \%like\% "trim"), susceptibility))
-}
+
-if (require("dplyr")) {
+# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
-  # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
+example_isolates \%>\%
-  example_isolates \%>\%
   select(carbapenems())
-}
+
-if (require("dplyr")) {
+# this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
-  # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
+example_isolates \%>\%
-  example_isolates \%>\%
   select(mo, aminoglycosides())
-}
+
-if (require("dplyr")) {
+# any() and all() work in dplyr's filter() too:
-  # any() and all() work in dplyr's filter() too:
+example_isolates \%>\%
-  example_isolates \%>\%
   filter(
     any(aminoglycosides() == "R"),
     all(cephalosporins_2nd() == "R")
   )
-}
+
-if (require("dplyr")) {
+# also works with c():
-  # also works with c():
+example_isolates \%>\%
-  example_isolates \%>\%
   filter(any(c(carbapenems(), aminoglycosides()) == "R"))
-}
+
-if (require("dplyr")) {
+# not setting any/all will automatically apply all():
-  # not setting any/all will automatically apply all():
+example_isolates \%>\%
-  example_isolates \%>\%
   filter(aminoglycosides() == "R")
-}
+
-if (require("dplyr")) {
+# this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
-  # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
+example_isolates \%>\%
-  example_isolates \%>\%
   select(mo, ab_class("mycobact"))
-}
+
-if (require("dplyr")) {
+# get bug/drug combinations for only glycopeptides in Gram-positives:
-  # get bug/drug combinations for only glycopeptides in Gram-positives:
+example_isolates \%>\%
-  example_isolates \%>\%
   filter(mo_is_gram_positive()) \%>\%
   select(mo, glycopeptides()) \%>\%
   bug_drug_combinations() \%>\%
   format()
-}
+
-if (require("dplyr")) {
+data.frame(
-  data.frame(
   some_column = "some_value",
   J01CA01 = "S"
-  ) \%>\% # ATC code of ampicillin
+) \%>\% # ATC code of ampicillin
   select(penicillins()) # only the 'J01CA01' column will be selected
-}
+
-if (require("dplyr")) {
+# with recent versions of dplyr, this is all equal:
-  # with recent versions of dplyr, this is all equal:
+x <- example_isolates[carbapenems() == "R", ]
-  x <- example_isolates[carbapenems() == "R", ]
+y <- example_isolates \%>\% filter(carbapenems() == "R")
-  y <- example_isolates \%>\% filter(carbapenems() == "R")
+z <- example_isolates \%>\% filter(if_all(carbapenems(), ~ .x == "R"))
-  z <- example_isolates \%>\% filter(if_all(carbapenems(), ~ .x == "R"))
+identical(x, y) && identical(y, z)
-  identical(x, y) && identical(y, z)
-}
 
 
 # base R ------------------------------------------------------------------

man/custom_eucast_rules.Rd

@@ -86,13 +86,14 @@ x
 #>      amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
 }\if{html}{\out{</div>}}
 
-These 30 antibiotic groups are allowed in the rules (case-insensitive) and can be used in any combination:
+These 31 antibiotic groups are allowed in the rules (case-insensitive) and can be used in any combination:
 \itemize{
 \item aminoglycosides\cr(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)
 \item aminopenicillins\cr(amoxicillin and ampicillin)
 \item antifungals\cr(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)
 \item antimycobacterials\cr(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)
 \item betalactams\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin, and ticarcillin/clavulanic acid)
+\item betalactams_with_inhibitor\cr(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)
 \item carbapenems\cr(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem)
 \item cephalosporins\cr(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)
 \item cephalosporins_1st\cr(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine)