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(v2.1.1.9111) add betalactams_with_inhibitor(), fixes #175
This commit is contained in:
@@ -440,6 +440,9 @@ pre_commit_lst$AB_TRIMETHOPRIMS <- antibiotics %>%
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pull(ab)
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pre_commit_lst$AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
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pre_commit_lst$AB_BETALACTAMS <- c(pre_commit_lst$AB_PENICILLINS, pre_commit_lst$AB_CEPHALOSPORINS, pre_commit_lst$AB_CARBAPENEMS)
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pre_commit_lst$AB_BETALACTAMS_WITH_INHIBITOR <- antibiotics %>%
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filter(name %like% "/" & name %unlike% "EDTA" & ab %in% pre_commit_lst$AB_BETALACTAMS) %>%
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pull(ab)
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# this will be used for documentation:
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pre_commit_lst$DEFINED_AB_GROUPS <- sort(names(pre_commit_lst)[names(pre_commit_lst) %like% "^AB_" & names(pre_commit_lst) != "AB_LOOKUP"])
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create_AB_AV_lookup <- function(df) {
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@@ -638,7 +641,7 @@ suppressMessages(set_AMR_locale("English"))
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# Update URLs -------------------------------------------------------------
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usethis::ui_info("Checking URLs for redirects")
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invisible(capture.output(urlchecker::url_update()))
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invisible(urlchecker::url_update("."))
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# Document pkg ------------------------------------------------------------
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@@ -1,6 +1,6 @@
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# -------------------------------------------------------------------------------------------------------------------------------
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# For editing this EUCAST reference file, these values can all be used for targeting antibiotics:
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# 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
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# 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
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# and all separate EARS-Net letter codes such as AMC. They can be separated by comma: 'AMC, fluoroquinolones'.
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# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or 'genus_species' or 'gramstain'.
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# The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression)
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@@ -11,7 +11,7 @@ if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values
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order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 10
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order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 10
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order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 10
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genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints 10
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genus is Staphylococcus PEN, FOX S betalactams_with_inhibitor S Staphylococcus Breakpoints 10
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genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 10
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genus is Staphylococcus FOX R betalactams R Staphylococcus Breakpoints 10
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genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 10
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@@ -117,7 +117,7 @@ genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei
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order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 11
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order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 11
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order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 11
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genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints 11
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genus is Staphylococcus PEN, FOX S betalactams_with_inhibitor S Staphylococcus Breakpoints 11
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genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 11
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genus is Staphylococcus FOX R betalactams R Staphylococcus Breakpoints 11
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genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 11
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@@ -226,7 +226,7 @@ genus is Bacillus NOR R fluoroquinolones R Bacillus Breakpoints 11 added in 11
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order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 12
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order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 12
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order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 12
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genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints 12
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genus is Staphylococcus PEN, FOX S betalactams_with_inhibitor S Staphylococcus Breakpoints 12
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genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 12
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genus is Staphylococcus FOX R betalactams R Staphylococcus Breakpoints 12
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genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 12
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@@ -500,8 +500,8 @@ genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules
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genus is Salmonella PEF R CIP R Expert Rules on Salmonella Expert Rules 3.2
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genus_species is Staphylococcus aureus FOX1 R betalactams R Expert Rules on Staphylococcus Expert Rules 3.2
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genus_species is Staphylococcus aureus FOX R betalactams R Expert Rules on Staphylococcus Expert Rules 3.2
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genus_species is Staphylococcus aureus FOX1 S betalactams S Expert Rules on Staphylococcus Expert Rules 3.2
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genus_species is Staphylococcus aureus FOX S betalactams S Expert Rules on Staphylococcus Expert Rules 3.2
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genus_species is Staphylococcus aureus FOX1 S betalactams_with_inhibitor S Expert Rules on Staphylococcus Expert Rules 3.2
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genus_species is Staphylococcus aureus FOX S betalactams_with_inhibitor S Expert Rules on Staphylococcus Expert Rules 3.2
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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
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genus is Staphylococcus ERY, CLI S macrolides, lincosamides S Expert Rules on Staphylococcus Expert Rules 3.2
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genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Expert Rules on Staphylococcus Expert Rules 3.2
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@@ -620,8 +620,8 @@ genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules
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genus is Salmonella PEF R CIP R Expert Rules on Salmonella Expert Rules 3.3
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genus_species is Staphylococcus aureus FOX1 R betalactams R Expert Rules on Staphylococcus Expert Rules 3.3
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genus_species is Staphylococcus aureus FOX R betalactams R Expert Rules on Staphylococcus Expert Rules 3.3
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genus_species is Staphylococcus aureus FOX1 S betalactams S Expert Rules on Staphylococcus Expert Rules 3.3
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genus_species is Staphylococcus aureus FOX S betalactams S Expert Rules on Staphylococcus Expert Rules 3.3
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genus_species is Staphylococcus aureus FOX1 S betalactams_with_inhibitor S Expert Rules on Staphylococcus Expert Rules 3.3
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genus_species is Staphylococcus aureus FOX S betalactams_with_inhibitor S Expert Rules on Staphylococcus Expert Rules 3.3
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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
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genus is Staphylococcus ERY, CLI S macrolides, lincosamides S Expert Rules on Staphylococcus Expert Rules 3.3
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genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Expert Rules on Staphylococcus Expert Rules 3.3
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Can't render this file because it has a wrong number of fields in line 9.
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@@ -1,5 +1,5 @@
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This files contains all context you must know about the AMR package for R.
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First and foremost, you are trained on version 2.1.1.9110. Remember this whenever someone asks which AMR package version you’re at.
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First and foremost, you are trained on version 2.1.1.9111. Remember this whenever someone asks which AMR package version you’re at.
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--------------------------------
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THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'NAMESPACE':
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@@ -189,6 +189,7 @@ export(av_tradenames)
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export(av_url)
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export(availability)
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export(betalactams)
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export(betalactams_with_inhibitor)
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export(brmo)
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export(bug_drug_combinations)
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export(carbapenems)
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@@ -1935,6 +1936,7 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/antibiotic_class_selectors.R
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\alias{antifungals}
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\alias{antimycobacterials}
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\alias{betalactams}
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\alias{betalactams_with_inhibitor}
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\alias{carbapenems}
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\alias{cephalosporins}
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\alias{cephalosporins_1st}
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@@ -1976,6 +1978,8 @@ antimycobacterials(only_sir_columns = FALSE, ...)
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betalactams(only_sir_columns = FALSE, only_treatable = TRUE, ...)
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betalactams_with_inhibitor(only_sir_columns = FALSE, ...)
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carbapenems(only_sir_columns = FALSE, only_treatable = TRUE, ...)
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cephalosporins(only_sir_columns = FALSE, ...)
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@@ -2075,6 +2079,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
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\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)
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\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)
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\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)
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\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)
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\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)
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\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)
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\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)
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@@ -2116,102 +2121,88 @@ example_isolates
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\donttest{
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# dplyr -------------------------------------------------------------------
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if (require("dplyr")) {
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example_isolates \%>\% select(carbapenems())
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}
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library(dplyr, warn.conflicts = FALSE)
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if (require("dplyr")) {
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# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
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example_isolates \%>\% select(mo, aminoglycosides())
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}
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example_isolates \%>\% select(carbapenems())
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if (require("dplyr")) {
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# select only antibiotic columns with DDDs for oral treatment
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example_isolates \%>\% select(administrable_per_os())
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}
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# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
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example_isolates \%>\% select(mo, aminoglycosides())
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if (require("dplyr")) {
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# get AMR for all aminoglycosides e.g., per ward:
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example_isolates \%>\%
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group_by(ward) \%>\%
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summarise(across(aminoglycosides(),
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resistance))
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}
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if (require("dplyr")) {
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# You can combine selectors with '&' to be more specific:
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example_isolates \%>\%
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select(penicillins() & administrable_per_os())
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}
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if (require("dplyr")) {
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# get AMR for only drugs that matter - no intrinsic resistance:
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example_isolates \%>\%
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filter(mo_genus() \%in\% c("Escherichia", "Klebsiella")) \%>\%
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group_by(ward) \%>\%
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summarise_at(not_intrinsic_resistant(),
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resistance)
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}
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if (require("dplyr")) {
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# get susceptibility for antibiotics whose name contains "trim":
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example_isolates \%>\%
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filter(first_isolate()) \%>\%
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group_by(ward) \%>\%
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summarise(across(ab_selector(name \%like\% "trim"), susceptibility))
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}
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if (require("dplyr")) {
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# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
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example_isolates \%>\%
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select(carbapenems())
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}
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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)
|
||||
}
|
||||
# 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())
|
||||
|
||||
# get AMR for all aminoglycosides e.g., per ward:
|
||||
example_isolates \%>\%
|
||||
group_by(ward) \%>\%
|
||||
summarise(across(aminoglycosides(),
|
||||
resistance))
|
||||
|
||||
# You can combine selectors with '&' to be more specific:
|
||||
example_isolates \%>\%
|
||||
select(penicillins() & administrable_per_os())
|
||||
|
||||
# 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)
|
||||
|
||||
# get susceptibility for antibiotics whose name contains "trim":
|
||||
example_isolates \%>\%
|
||||
filter(first_isolate()) \%>\%
|
||||
group_by(ward) \%>\%
|
||||
summarise(across(ab_selector(name \%like\% "trim"), susceptibility))
|
||||
|
||||
# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
|
||||
example_isolates \%>\%
|
||||
select(carbapenems())
|
||||
|
||||
# this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
|
||||
example_isolates \%>\%
|
||||
select(mo, aminoglycosides())
|
||||
|
||||
# any() and all() work in dplyr's filter() too:
|
||||
example_isolates \%>\%
|
||||
filter(
|
||||
any(aminoglycosides() == "R"),
|
||||
all(cephalosporins_2nd() == "R")
|
||||
)
|
||||
|
||||
# also works with c():
|
||||
example_isolates \%>\%
|
||||
filter(any(c(carbapenems(), aminoglycosides()) == "R"))
|
||||
|
||||
# not setting any/all will automatically apply all():
|
||||
example_isolates \%>\%
|
||||
filter(aminoglycosides() == "R")
|
||||
|
||||
# this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
|
||||
example_isolates \%>\%
|
||||
select(mo, ab_class("mycobact"))
|
||||
|
||||
# get bug/drug combinations for only glycopeptides in Gram-positives:
|
||||
example_isolates \%>\%
|
||||
filter(mo_is_gram_positive()) \%>\%
|
||||
select(mo, glycopeptides()) \%>\%
|
||||
bug_drug_combinations() \%>\%
|
||||
format()
|
||||
|
||||
data.frame(
|
||||
some_column = "some_value",
|
||||
J01CA01 = "S"
|
||||
) \%>\% # ATC code of ampicillin
|
||||
select(penicillins()) # only the 'J01CA01' column will be selected
|
||||
|
||||
# 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 ------------------------------------------------------------------
|
||||
@@ -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)
|
||||
Reference in New Issue
Block a user