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# Antimicrobial Selectors
These functions allow for filtering rows and selecting columns based on
antimicrobial test results that are of a specific antimicrobial class or
group, without the need to define the columns or antimicrobial
abbreviations. They can be used in base R, tidyverse, tidymodels, and
`data.table`.
Simply puy, if you have a column name that resembles an antimicrobial
drug, it will be picked up by any of these functions that matches its
pharmaceutical class, code or name: column names "cefazolin", "kefzol",
"CZO" and "J01DB04" would all be included in the following selection:
library(dplyr)
my_data_with_all_these_columns %>%
select(cephalosporins())
## Usage
``` r
aminoglycosides(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
aminopenicillins(only_sir_columns = FALSE, return_all = TRUE, ...)
antifungals(only_sir_columns = FALSE, return_all = TRUE, ...)
antimycobacterials(only_sir_columns = FALSE, return_all = TRUE, ...)
betalactams(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
betalactams_with_inhibitor(only_sir_columns = FALSE, return_all = TRUE,
...)
carbapenems(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
cephalosporins(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
cephalosporins_1st(only_sir_columns = FALSE, return_all = TRUE, ...)
cephalosporins_2nd(only_sir_columns = FALSE, return_all = TRUE, ...)
cephalosporins_3rd(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
cephalosporins_4th(only_sir_columns = FALSE, return_all = TRUE, ...)
cephalosporins_5th(only_sir_columns = FALSE, return_all = TRUE, ...)
fluoroquinolones(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
glycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)
isoxazolylpenicillins(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
lincosamides(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
lipoglycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)
macrolides(only_sir_columns = FALSE, return_all = TRUE, ...)
monobactams(only_sir_columns = FALSE, return_all = TRUE, ...)
nitrofurans(only_sir_columns = FALSE, return_all = TRUE, ...)
oxazolidinones(only_sir_columns = FALSE, return_all = TRUE, ...)
penicillins(only_sir_columns = FALSE, return_all = TRUE, ...)
phenicols(only_sir_columns = FALSE, return_all = TRUE, ...)
polymyxins(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
quinolones(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
rifamycins(only_sir_columns = FALSE, return_all = TRUE, ...)
streptogramins(only_sir_columns = FALSE, return_all = TRUE, ...)
sulfonamides(only_sir_columns = FALSE, return_all = TRUE, ...)
tetracyclines(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
trimethoprims(only_sir_columns = FALSE, return_all = TRUE, ...)
ureidopenicillins(only_sir_columns = FALSE, return_all = TRUE, ...)
amr_class(amr_class, only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
amr_selector(filter, only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
administrable_per_os(only_sir_columns = FALSE, return_all = TRUE, ...)
administrable_iv(only_sir_columns = FALSE, return_all = TRUE, ...)
not_intrinsic_resistant(only_sir_columns = FALSE, col_mo = NULL,
version_expected_phenotypes = 1.2, ...)
```
## Arguments
- only_sir_columns:
A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
only antimicrobial columns must be included that were transformed to
class [sir](https://amr-for-r.org/reference/as.sir.md) on beforehand.
Defaults to `FALSE`.
- only_treatable:
A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
antimicrobial drugs should be excluded that are only for laboratory
tests (default is `TRUE`), such as gentamicin-high (`GEH`) and
imipenem/EDTA (`IPE`).
- return_all:
A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
all matched columns must be returned (default is `TRUE`). With
`FALSE`, only the first of each unique antimicrobial will be returned,
e.g. if both columns `"genta"` and `"gentamicin"` exist in the data,
only the first hit for gentamicin will be returned.
- ...:
Ignored, only in place to allow future extensions.
- amr_class:
An antimicrobial class or a part of it, such as `"carba"` and
`"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of
the
[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md)
data set will be searched (case-insensitive) for this value.
- filter:
An [expression](https://rdrr.io/r/base/expression.html) to be
evaluated in the
[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md)
data set, such as `name %like% "trim"`.
- col_mo:
Column name of the names or codes of the microorganisms (see
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md)) - the default
is the first column of class
[`mo`](https://amr-for-r.org/reference/as.mo.md). Values will be
coerced using [`as.mo()`](https://amr-for-r.org/reference/as.mo.md).
- version_expected_phenotypes:
The version number to use for the EUCAST Expected Phenotypes. Can be
"1.2".
## Value
When used inside selecting or filtering, this returns a
[character](https://rdrr.io/r/base/character.html) vector of column
names, with additional class `"amr_selector"`. When used individually,
this returns an ['ab' vector](https://amr-for-r.org/reference/as.ab.md)
with all possible antimicrobials that the function would be able to
select or filter.
## Details
These functions can be used in data set calls for selecting columns and
filtering rows. They work with base R, the Tidyverse, and `data.table`.
They are heavily inspired by the [Tidyverse selection
helpers](https://tidyselect.r-lib.org/reference/language.html) such as
[`everything()`](https://tidyselect.r-lib.org/reference/everything.html),
but are not limited to `dplyr` verbs. Nonetheless, they are very
convenient to use with `dplyr` functions such as
[`select()`](https://dplyr.tidyverse.org/reference/select.html),
[`filter()`](https://dplyr.tidyverse.org/reference/filter.html) and
[`summarise()`](https://dplyr.tidyverse.org/reference/summarise.html),
see *Examples*.
All selectors can also be used in `tidymodels` packages such as `recipe`
and `parsnip`. See for more info [our
tutorial](https://amr-for-r.org/articles/AMR_with_tidymodels.html) on
using antimicrobial selectors for predictive modelling.
All columns in the data in which these functions are called will be
searched for known antimicrobial names, abbreviations, brand names, and
codes (ATC, EARS-Net, WHO, etc.) according to the
[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md) data
set. This means that a selector such as `aminoglycosides()` will pick up
column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
The `amr_class()` function can be used to filter/select on a manually
defined antimicrobial class. It searches for results in the
[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md) data
set within the columns `group`, `atc_group1` and `atc_group2`.
The `administrable_per_os()` and `administrable_iv()` functions also
rely on the
[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md) data
set - antimicrobials will be matched where a DDD (defined daily dose)
for resp. oral and IV treatment is available in the
[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md) data
set.
The `amr_selector()` function can be used to internally filter the
[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md) data
set on any results, see *Examples*. It allows for filtering on a (part
of) a certain name, and/or a group name or even a minimum of DDDs for
oral treatment. This function yields the highest flexibility, but is
also the least user-friendly, since it requires a hard-coded filter to
set.
The `not_intrinsic_resistant()` function can be used to only select
antimicrobials that pose no intrinsic resistance for the microorganisms
in the data set. For example, if a data set contains only microorganism
codes or names of *E. coli* and *K. pneumoniae* and contains a column
"vancomycin", this column will be removed (or rather, unselected) using
this function. It currently applies ['EUCAST Expected Resistant
Phenotypes'
v1.2](https://www.eucast.org/expert_rules_and_expected_phenotypes)
(2023) to determine intrinsic resistance, using the
[`eucast_rules()`](https://amr-for-r.org/reference/eucast_rules.md)
function internally. Because of this determination, this function is
quite slow in terms of performance.
## Full list of supported (antimicrobial) classes
- `aminoglycosides()` can select:
amikacin (AMK), amikacin/fosfomycin (AKF), apramycin (APR), arbekacin
(ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB),
framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin
(HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN),
kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR),
neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin
(PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS),
streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH),
tobramycin (TOB), and tobramycin-high (TOH)
- `aminopenicillins()` can select:
amoxicillin (AMX) and ampicillin (AMP)
- `antifungals()` can select:
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)
- `antimycobacterials()` can select:
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), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI),
terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1),
tiocarlide (TCR), and viomycin (VIO)
- `betalactams()` can select:
amoxicillin (AMX), amoxicillin/clavulanic acid (AMC),
amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam
(SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD),
azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA),
aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine
benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP),
benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S),
biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), carumonam
(CAR), 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/amikacin
(CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE),
cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA),
cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), 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 screening test (CTX-S),
cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS),
cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin
(FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), 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), nafcillin (NAF), oxacillin (OXA),
oxacillin screening test (OXA-S), 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), sulbenicillin
(SBC), sultamicillin (SLT6), talampicillin (TAL), taniborbactam (TAN),
tebipenem (TBP), temocillin (TEM), ticarcillin (TIC),
ticarcillin/clavulanic acid (TCC), and tigemonam (TMN)
- `betalactams_with_inhibitor()` can select:
amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS),
ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA),
aztreonam/nacubactam (ANC), cefepime/amikacin (CFA),
cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE),
cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA),
cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ),
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)
- `carbapenems()` can select:
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),
taniborbactam (TAN), and tebipenem (TBP)
- `cephalosporins()` can select:
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/amikacin (CFA),
cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE),
cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA),
cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), 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 screening test (CTX-S),
cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS),
cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin
(FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), 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)
- `cephalosporins_1st()` can select:
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)
- `cephalosporins_2nd()` can select:
cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID),
ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX),
cefoxitin screening test (FOX-S), cefprozil (CPR), cefuroxime (CXM),
cefuroxime axetil (CXA), and loracarbef (LOR)
- `cephalosporins_3rd()` can select:
cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren
(DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil
(CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ),
cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX),
cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC),
cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV),
cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime
proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS),
ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic
acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB),
ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP),
ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), and
latamoxef (LTM)
- `cephalosporins_4th()` can select:
cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid
(CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC),
cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT),
cefepime/zidebactam (FPZ), cefetecol (CCL), cefoselis (CSE),
cefozopran (ZOP), cefpirome (CPO), and cefquinome (CEQ)
- `cephalosporins_5th()` can select:
ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR),
ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT)
- `fluoroquinolones()` can select:
besifloxacin (BES), ciprofloxacin (CIP), ciprofloxacin/metronidazole
(CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT),
clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX),
difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin
(FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT),
gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC),
levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin
(LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT),
miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nemonoxacin
(NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR),
norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME),
norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole
(OOR), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF),
pefloxacin screening test (PEF-S), pradofloxacin (PRA), premafloxacin
(PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR),
sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX),
tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and
trovafloxacin (TVA)
- `glycopeptides()` can select:
avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin
(NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC),
teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), and
vancomycin-macromethod (VAM)
- `isoxazolylpenicillins()` can select:
cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC),
meticillin (MET), oxacillin (OXA), and oxacillin screening test
(OXA-S)
- `lincosamides()` can select:
clindamycin (CLI), lincomycin (LIN), and pirlimycin (PRL)
- `lipoglycopeptides()` can select:
dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV)
- `macrolides()` can select:
acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM),
clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY),
flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS),
kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin
(MCM), nafithromycin (ZWK), oleandomycin (OLE), rokitamycin (ROK),
roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI),
telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL),
troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL), and
tylvalosin (TYL1)
- `monobactams()` can select:
aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam
(ANC), carumonam (CAR), and tigemonam (TMN)
- `nitrofurans()` can select:
furazidin (FUR), furazolidone (FRZ), nifurtoinol (NFR), nitrofurantoin
(NIT), and nitrofurazone (NIZ)
- `oxazolidinones()` can select:
cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD),
and thiacetazone (THA)
- `penicillins()` can select:
amoxicillin (AMX), amoxicillin/clavulanic acid (AMC),
amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam
(SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD),
azlocillin (AZL), bacampicillin (BAM), benzathine benzylpenicillin
(BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin
(PEN), benzylpenicillin screening test (PEN-S), carbenicillin (CRB),
carindacillin (CRN), ciclacillin (CIC), clometocillin (CLM),
cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC),
flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN),
mecillinam (MEC), metampicillin (MTM), meticillin (MET), mezlocillin
(MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA),
oxacillin screening test (OXA-S), 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), sarmoxicillin (SRX),
sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL),
temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid
(TCC)
- `phenicols()` can select:
chloramphenicol (CHL), florfenicol (FLR), and thiamphenicol (THI)
- `polymyxins()` can select:
colistin (COL), polymyxin B (PLB), and polymyxin B/polysorbate 80
(POP)
- `quinolones()` can select:
besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP),
ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO),
ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin
(DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX),
enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine
(FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM),
grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX),
levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin
(LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL),
moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL),
nalidixic acid screening test (NAL-S), nemonoxacin (NEM), nifuroquine
(NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening
test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole
(NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin
(ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF),
pefloxacin screening test (PEF-S), pipemidic acid (PPA), piromidic
acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin
(PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR),
sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX),
tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and
trovafloxacin (TVA)
- `rifamycins()` can select:
rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid
(REI), rifampicin/isoniazid (RFI),
rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI),
rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), and
rifapentine (RFP)
- `streptogramins()` can select:
pristinamycin (PRI) and quinupristin/dalfopristin (QDA)
- `sulfonamides()` can select:
brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT),
sulfadimethoxine (SUD), sulfadimidine (SDM), sulfafurazole (SLF),
sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO),
sulfamerazine (SLF3), sulfamethizole (SLF4), sulfamethoxazole (SMX),
sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6),
sulfametoxydiazine (SLF7), sulfamoxole (SLF8), sulfanilamide (SLF9),
sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12),
sulfathiazole (SUT), and sulfathiourea (SLF13)
- `tetracyclines()` can select:
cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1),
demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV),
lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline
(OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline
(RLT), sarecycline (SRC), tetracycline (TCY), tetracycline screening
test (TCY-S), and tigecycline (TGC)
- `trimethoprims()` can select:
brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT),
sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD),
sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole
(SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO),
sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3),
sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine
(SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7),
sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8),
sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin
(SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole
(SUT), sulfathiourea (SLF13), trimethoprim (TMP), and
trimethoprim/sulfamethoxazole (SXT)
- `ureidopenicillins()` can select:
azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), and
piperacillin/tazobactam (TZP)
## Download Our Reference Data
All reference data sets in the AMR package - including information on
microorganisms, antimicrobials, and clinical breakpoints - are freely
available for download in multiple formats: R, MS Excel, Apache Feather,
Apache Parquet, SPSS, and Stata.
For maximum compatibility, we also provide machine-readable,
tab-separated plain text files suitable for use in any software,
including laboratory information systems.
Visit [our website for direct download
links](https://amr-for-r.org/articles/datasets.html), or explore the
actual files in [our GitHub
repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
## Examples
``` r
# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.
example_isolates
#> # A tibble: 2,000 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
#> 1 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
#> 2 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
#> 3 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
#> 4 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
#> 5 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
#> 6 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
#> 7 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
#> 8 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
#> 9 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA
#> 10 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA
#> # ℹ 1,990 more rows
#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
#> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
#> # TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
#> # FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,
#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
# you can use the selectors separately to retrieve all possible antimicrobials:
carbapenems()
#> ℹ in `carbapenems()`: Imipenem/EDTA (`IPE`) and meropenem/nacubactam
#> (`MNC`) are not included since `only_treatable = TRUE`.
#> ℹ This 'ab' vector was retrieved using `carbapenems()`, which should
#> normally be used inside a `dplyr` verb or `data.frame` call, e.g.:
#> • your_data %>% select(carbapenems())
#> • your_data %>% select(column_a, column_b, carbapenems())
#> • your_data %>% filter(any(carbapenems() == "R"))
#> • your_data[, carbapenems()]
#> • your_data[, c("column_a", "column_b", carbapenems())]
#> Class 'ab'
#> [1] BIA DOR ETP IMR IPM MEM MEV PAN RIA RIT RZM TAN TBP
# Though they are primarily intended to use for selections and filters.
# Examples sections below are split into 'dplyr', 'base R', and 'data.table':
# \donttest{
if (FALSE) { # \dontrun{
# dplyr -------------------------------------------------------------------
library(dplyr, warn.conflicts = FALSE)
example_isolates %>% select(carbapenems())
# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
example_isolates %>% select(mo, aminoglycosides())
# 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 antimicrobials 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 antimicrobials whose name contains "trim":
example_isolates %>%
filter(first_isolate()) %>%
group_by(ward) %>%
summarise(across(amr_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, amr_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 ------------------------------------------------------------------
# select columns 'IPM' (imipenem) and 'MEM' (meropenem)
example_isolates[, carbapenems()]
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> # A tibble: 2,000 × 2
#> IPM MEM
#> <sir> <sir>
#> 1 NA NA
#> 2 NA NA
#> 3 NA NA
#> 4 NA NA
#> 5 NA NA
#> 6 NA NA
#> 7 NA NA
#> 8 NA NA
#> 9 NA NA
#> 10 NA NA
#> # ℹ 1,990 more rows
# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
example_isolates[, c("mo", aminoglycosides())]
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> # A tibble: 2,000 × 5
#> mo GEN TOB AMK KAN
#> <mo> <sir> <sir> <sir> <sir>
#> 1 B_ESCHR_COLI NA NA NA NA
#> 2 B_ESCHR_COLI NA NA NA NA
#> 3 B_STPHY_EPDR NA NA NA NA
#> 4 B_STPHY_EPDR NA NA NA NA
#> 5 B_STPHY_EPDR NA NA NA NA
#> 6 B_STPHY_EPDR NA NA NA NA
#> 7 B_STPHY_AURS NA S NA NA
#> 8 B_STPHY_AURS NA S NA NA
#> 9 B_STPHY_EPDR NA NA NA NA
#> 10 B_STPHY_EPDR NA NA NA NA
#> # ℹ 1,990 more rows
# select only antimicrobials with DDDs for oral treatment
example_isolates[, administrable_per_os()]
#> ℹ For `administrable_per_os()` using columns 'OXA' (oxacillin), 'FLC'
#> (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid),
#> 'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP'
#> (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ'
#> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN'
#> (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY'
#> (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR'
#> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF'
#> (rifampicin)
#> # A tibble: 2,000 × 23
#> OXA FLC AMX AMC AMP CXM KAN TMP NIT FOS LNZ CIP MFX
#> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir>
#> 1 NA NA NA I NA I NA R NA NA R NA NA
#> 2 NA NA NA I NA I NA R NA NA R NA NA
#> 3 NA R NA NA NA R NA S NA NA NA NA NA
#> 4 NA R NA NA NA R NA S NA NA NA NA NA
#> 5 NA R NA NA NA R NA R NA NA NA NA NA
#> 6 NA R NA NA NA R NA R NA NA NA NA NA
#> 7 NA S R S R S NA R NA NA NA NA NA
#> 8 NA S R S R S NA R NA NA NA NA NA
#> 9 NA R NA NA NA R NA S NA NA NA S NA
#> 10 NA S NA NA NA S NA S NA NA NA S NA
#> # ℹ 1,990 more rows
#> # ℹ 10 more variables: VAN <sir>, TCY <sir>, DOX <sir>, ERY <sir>, CLI <sir>,
#> # AZM <sir>, MTR <sir>, CHL <sir>, COL <sir>, RIF <sir>
# filter using any() or all()
example_isolates[any(carbapenems() == "R"), ]
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> # A tibble: 55 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
#> 1 2004-06-09 529296 69 M ICU B_ENTRC_FACM NA NA NA NA
#> 2 2004-06-09 529296 69 M ICU B_ENTRC_FACM NA NA NA NA
#> 3 2004-11-03 D65308 80 F ICU B_STNTR_MLTP R NA NA R
#> 4 2005-04-21 452212 82 F ICU B_ENTRC NA NA NA NA
#> 5 2005-04-22 452212 82 F ICU B_ENTRC NA NA NA NA
#> 6 2005-04-22 452212 82 F ICU B_ENTRC_FACM NA NA NA NA
#> 7 2007-02-21 8BBC46 61 F Clinical B_ENTRC_FACM NA NA NA NA
#> 8 2007-12-15 401043 72 M Clinical B_ENTRC_FACM NA NA NA NA
#> 9 2008-01-22 1710B8 82 M Clinical B_PROTS_MRBL R NA NA NA
#> 10 2008-01-22 1710B8 82 M Clinical B_PROTS_MRBL R NA NA NA
#> # ℹ 45 more rows
#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
#> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
#> # TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
#> # FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,
#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
subset(example_isolates, any(carbapenems() == "R"))
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> # A tibble: 55 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
#> 1 2004-06-09 529296 69 M ICU B_ENTRC_FACM NA NA NA NA
#> 2 2004-06-09 529296 69 M ICU B_ENTRC_FACM NA NA NA NA
#> 3 2004-11-03 D65308 80 F ICU B_STNTR_MLTP R NA NA R
#> 4 2005-04-21 452212 82 F ICU B_ENTRC NA NA NA NA
#> 5 2005-04-22 452212 82 F ICU B_ENTRC NA NA NA NA
#> 6 2005-04-22 452212 82 F ICU B_ENTRC_FACM NA NA NA NA
#> 7 2007-02-21 8BBC46 61 F Clinical B_ENTRC_FACM NA NA NA NA
#> 8 2007-12-15 401043 72 M Clinical B_ENTRC_FACM NA NA NA NA
#> 9 2008-01-22 1710B8 82 M Clinical B_PROTS_MRBL R NA NA NA
#> 10 2008-01-22 1710B8 82 M Clinical B_PROTS_MRBL R NA NA NA
#> # ℹ 45 more rows
#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
#> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
#> # TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
#> # FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,
#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
# filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
example_isolates[any(carbapenems()), ]
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ Filtering any of columns 'IPM' and 'MEM' to contain value "S", "I" or "R"
#> # A tibble: 962 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
#> 1 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA
#> 2 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA
#> 3 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R NA NA NA
#> 4 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R NA NA NA
#> 5 2002-02-05 067927 45 F ICU B_SERRT_MRCS R NA NA R
#> 6 2002-02-05 067927 45 F ICU B_SERRT_MRCS R NA NA R
#> 7 2002-02-05 067927 45 F ICU B_SERRT_MRCS R NA NA R
#> 8 2002-02-27 066895 85 F Clinical B_KLBSL_PNMN R NA NA R
#> 9 2002-02-27 066895 85 F Clinical B_KLBSL_PNMN R NA NA R
#> 10 2002-03-08 4FC193 69 M Clinical B_ESCHR_COLI R NA NA R
#> # ℹ 952 more rows
#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
#> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
#> # TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
#> # FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,
#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
example_isolates[all(carbapenems()), ]
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ Filtering all of columns 'IPM' and 'MEM' to contain value "S", "I" or "R"
#> # A tibble: 756 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
#> 1 2002-04-14 F30196 73 M Outpat… B_STRPT_GRPB S NA S S
#> 2 2003-04-08 114570 74 M ICU B_STRPT_PYGN S NA S S
#> 3 2003-04-08 114570 74 M ICU B_STRPT_GRPA S NA S S
#> 4 2003-04-08 114570 74 M ICU B_STRPT_GRPA S NA S S
#> 5 2003-08-14 F71508 0 F Clinic… B_STRPT_GRPB S NA S S
#> 6 2003-10-16 650870 63 F ICU B_ESCHR_COLI R NA NA R
#> 7 2003-10-20 F35553 52 M ICU B_ENTRBC_CLOC R NA NA R
#> 8 2003-10-20 F35553 52 M ICU B_ENTRBC_CLOC R NA NA R
#> 9 2003-11-04 2FC253 87 F ICU B_ESCHR_COLI R NA NA NA
#> 10 2003-11-04 2FC253 87 F ICU B_ESCHR_COLI R NA NA NA
#> # ℹ 746 more rows
#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
#> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
#> # TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
#> # FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,
#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
# filter with multiple antimicrobial selectors using c()
example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> # A tibble: 26 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
#> 1 2004-11-03 D65308 80 F ICU B_STNTR_MLTP R NA NA R
#> 2 2005-04-22 452212 82 F ICU B_ENTRC_FACM NA NA NA NA
#> 3 2007-02-21 8BBC46 61 F Clinical B_ENTRC_FACM NA NA NA NA
#> 4 2007-12-15 401043 72 M Clinical B_ENTRC_FACM NA NA NA NA
#> 5 2008-12-06 501361 43 F Clinical B_STNTR_MLTP R NA NA R
#> 6 2011-05-09 207325 82 F ICU B_ENTRC_FACM NA NA NA NA
#> 7 2012-03-12 582258 80 M ICU B_STPHY_CONS R R R R
#> 8 2012-05-19 C25552 89 F Outpati… B_STPHY_CONS R R R R
#> 9 2012-07-17 F05015 83 M ICU B_STPHY_CONS R R R R
#> 10 2012-07-20 404299 66 F Clinical B_STPHY_CONS R R R R
#> # ℹ 16 more rows
#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
#> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
#> # TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
#> # FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,
#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
# filter + select in one go: get penicillins in carbapenem-resistant strains
example_isolates[any(carbapenems() == "R"), penicillins()]
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `penicillins()` using columns 'PEN' (benzylpenicillin), 'OXA'
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP'
#> (piperacillin/tazobactam)
#> # A tibble: 55 × 7
#> PEN OXA FLC AMX AMC AMP TZP
#> <sir> <sir> <sir> <sir> <sir> <sir> <sir>
#> 1 NA NA NA NA NA NA NA
#> 2 NA NA NA NA NA NA NA
#> 3 R NA NA R R R R
#> 4 NA NA NA NA NA NA R
#> 5 NA NA NA NA NA NA R
#> 6 NA NA NA NA NA NA R
#> 7 NA NA NA NA NA NA R
#> 8 NA NA NA NA NA NA R
#> 9 R NA NA NA S NA S
#> 10 R NA NA NA S NA S
#> # ℹ 45 more rows
# You can combine selectors with '&' to be more specific. For example,
# penicillins() would select benzylpenicillin ('peni G') and
# administrable_per_os() would select erythromycin. Yet, when combined these
# drugs are both omitted since benzylpenicillin is not administrable per os
# and erythromycin is not a penicillin:
example_isolates[, penicillins() & administrable_per_os()]
#> ℹ For `penicillins()` using columns 'PEN' (benzylpenicillin), 'OXA'
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP'
#> (piperacillin/tazobactam)
#> ℹ For `administrable_per_os()` using columns 'OXA' (oxacillin), 'FLC'
#> (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid),
#> 'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP'
#> (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ'
#> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN'
#> (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY'
#> (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR'
#> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF'
#> (rifampicin)
#> # A tibble: 2,000 × 5
#> OXA FLC AMX AMC AMP
#> <sir> <sir> <sir> <sir> <sir>
#> 1 NA NA NA I NA
#> 2 NA NA NA I NA
#> 3 NA R NA NA NA
#> 4 NA R NA NA NA
#> 5 NA R NA NA NA
#> 6 NA R NA NA NA
#> 7 NA S R S R
#> 8 NA S R S R
#> 9 NA R NA NA NA
#> 10 NA S NA NA NA
#> # ℹ 1,990 more rows
# amr_selector() applies a filter in the `antimicrobials` data set and is thus
# very flexible. For instance, to select antimicrobials with an oral DDD
# of at least 1 gram:
example_isolates[, amr_selector(oral_ddd > 1 & oral_units == "g")]
#> ℹ For `amr_selector(oral_ddd > 1 & oral_units == "g")` using columns 'OXA'
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'KAN' (kanamycin), 'FOS'
#> (fosfomycin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'ERY' (erythromycin),
#> 'CLI' (clindamycin), 'MTR' (metronidazole), and 'CHL' (chloramphenicol)
#> # A tibble: 2,000 × 13
#> OXA FLC AMX AMC AMP KAN FOS LNZ VAN ERY CLI MTR CHL
#> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir>
#> 1 NA NA NA I NA NA NA R R R R NA NA
#> 2 NA NA NA I NA NA NA R R R R NA NA
#> 3 NA R NA NA NA NA NA NA S R NA NA NA
#> 4 NA R NA NA NA NA NA NA S R NA NA NA
#> 5 NA R NA NA NA NA NA NA S R NA NA NA
#> 6 NA R NA NA NA NA NA NA S R R NA NA
#> 7 NA S R S R NA NA NA S S NA NA NA
#> 8 NA S R S R NA NA NA S S NA NA NA
#> 9 NA R NA NA NA NA NA NA S R NA NA NA
#> 10 NA S NA NA NA NA NA NA S S NA NA NA
#> # ℹ 1,990 more rows
# data.table --------------------------------------------------------------
# data.table is supported as well, just use it in the same way as with
# base R, but add `with = FALSE` if using a single AB selector.
if (require("data.table")) {
dt <- as.data.table(example_isolates)
# this does not work, it returns column *names*
dt[, carbapenems()]
}
#> Loading required package: data.table
#>
#> Attaching package: ‘data.table’
#> The following objects are masked from ‘package:dplyr’:
#>
#> between, first, last
#> The following objects are masked from ‘package:AMR’:
#>
#> %like%, like
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> Warning: It should never be needed to print an antimicrobial selector class. Are you
#> using data.table? Then add the argument `with = FALSE`, see our examples at
#> `?amr_selector`.
#> Class 'amr_selector'
#> [1] IPM MEM
if (require("data.table")) {
# so `with = FALSE` is required
dt[, carbapenems(), with = FALSE]
}
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> IPM MEM
#> <sir> <sir>
#> 1: <NA> <NA>
#> 2: <NA> <NA>
#> 3: <NA> <NA>
#> 4: <NA> <NA>
#> 5: <NA> <NA>
#> ---
#> 1996: <NA> <NA>
#> 1997: S S
#> 1998: S S
#> 1999: S S
#> 2000: S S
# for multiple selections or AB selectors, `with = FALSE` is not needed:
if (require("data.table")) {
dt[, c("mo", aminoglycosides())]
}
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> mo GEN TOB AMK KAN
#> <mo> <sir> <sir> <sir> <sir>
#> 1: B_ESCHR_COLI <NA> <NA> <NA> <NA>
#> 2: B_ESCHR_COLI <NA> <NA> <NA> <NA>
#> 3: B_STPHY_EPDR <NA> <NA> <NA> <NA>
#> 4: B_STPHY_EPDR <NA> <NA> <NA> <NA>
#> 5: B_STPHY_EPDR <NA> <NA> <NA> <NA>
#> ---
#> 1996: B_STRPT_PNMN R R R R
#> 1997: B_ESCHR_COLI S S S <NA>
#> 1998: B_STPHY_CONS S <NA> <NA> <NA>
#> 1999: B_ESCHR_COLI S S <NA> <NA>
#> 2000: B_KLBSL_PNMN S S <NA> <NA>
if (require("data.table")) {
dt[, c(carbapenems(), aminoglycosides())]
}
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> IPM MEM GEN TOB AMK KAN
#> <sir> <sir> <sir> <sir> <sir> <sir>
#> 1: <NA> <NA> <NA> <NA> <NA> <NA>
#> 2: <NA> <NA> <NA> <NA> <NA> <NA>
#> 3: <NA> <NA> <NA> <NA> <NA> <NA>
#> 4: <NA> <NA> <NA> <NA> <NA> <NA>
#> 5: <NA> <NA> <NA> <NA> <NA> <NA>
#> ---
#> 1996: <NA> <NA> R R R R
#> 1997: S S S S S <NA>
#> 1998: S S S <NA> <NA> <NA>
#> 1999: S S S S <NA> <NA>
#> 2000: S S S S <NA> <NA>
# row filters are also supported:
if (require("data.table")) {
dt[any(carbapenems() == "S"), ]
}
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> date patient age gender ward mo PEN OXA FLC
#> <Date> <char> <num> <char> <char> <mo> <sir> <sir> <sir>
#> 1: 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R <NA> <NA>
#> 2: 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R <NA> <NA>
#> 3: 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R <NA> <NA>
#> 4: 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R <NA> <NA>
#> 5: 2002-02-05 067927 45 F ICU B_SERRT_MRCS R <NA> <NA>
#> ---
#> 905: 2005-04-12 D71461 70 M ICU B_ESCHR_COLI R <NA> <NA>
#> 906: 2009-11-12 650870 69 F Outpatient B_ESCHR_COLI R <NA> <NA>
#> 907: 2012-06-14 8CBCF2 41 F Clinical B_STPHY_CONS R S S
#> 908: 2012-10-11 175532 78 M Clinical B_ESCHR_COLI R <NA> <NA>
#> 909: 2013-11-23 A97263 77 M Clinical B_KLBSL_PNMN R <NA> <NA>
#> AMX AMC AMP TZP CZO FEP CXM FOX CTX CAZ CRO GEN
#> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir>
#> 1: <NA> I <NA> <NA> <NA> <NA> S <NA> S <NA> S <NA>
#> 2: <NA> I <NA> <NA> <NA> <NA> S <NA> S <NA> S <NA>
#> 3: <NA> I <NA> <NA> <NA> <NA> S <NA> S S S <NA>
#> 4: <NA> I <NA> <NA> <NA> <NA> S <NA> S S S <NA>
#> 5: R R R <NA> R <NA> R R <NA> <NA> <NA> <NA>
#> ---
#> 905: S S S S <NA> S S S S S S S
#> 906: S S S S S S S S S S S S
#> 907: <NA> S <NA> <NA> S S S S S R S S
#> 908: R S R S <NA> S R R S S S S
#> 909: R S R S <NA> S S S S S S S
#> TOB AMK KAN TMP SXT NIT FOS LNZ CIP MFX VAN TEC
#> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir>
#> 1: S <NA> <NA> S S <NA> <NA> R <NA> <NA> R R
#> 2: S <NA> <NA> S S <NA> <NA> R <NA> <NA> R R
#> 3: <NA> <NA> <NA> S S R <NA> R S <NA> R R
#> 4: <NA> <NA> <NA> S S R <NA> R S <NA> R R
#> 5: <NA> <NA> <NA> S S R <NA> R S <NA> R R
#> ---
#> 905: S S <NA> <NA> S S <NA> R S <NA> R R
#> 906: S S <NA> S S S <NA> R S <NA> R R
#> 907: <NA> <NA> <NA> S S <NA> <NA> <NA> S <NA> S <NA>
#> 908: S <NA> <NA> R R R <NA> R R R R R
#> 909: S <NA> <NA> S S S <NA> R S <NA> R R
#> TCY TGC DOX ERY CLI AZM IPM MEM MTR CHL COL MUP
#> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir>
#> 1: <NA> <NA> <NA> R R R S <NA> <NA> <NA> <NA> <NA>
#> 2: <NA> <NA> <NA> R R R S <NA> <NA> <NA> <NA> <NA>
#> 3: R R R R R R S <NA> <NA> <NA> R <NA>
#> 4: R R R R R R S <NA> <NA> <NA> R <NA>
#> 5: R R R R R R S <NA> <NA> <NA> R <NA>
#> ---
#> 905: <NA> <NA> <NA> R R R S S <NA> <NA> <NA> <NA>
#> 906: <NA> <NA> <NA> R R R S S <NA> <NA> <NA> <NA>
#> 907: <NA> <NA> <NA> S S S S S <NA> <NA> R <NA>
#> 908: <NA> <NA> <NA> R R R S S <NA> <NA> S <NA>
#> 909: <NA> <NA> <NA> R R R S S <NA> <NA> S <NA>
#> RIF
#> <sir>
#> 1: R
#> 2: R
#> 3: R
#> 4: R
#> 5: R
#> ---
#> 905: R
#> 906: R
#> 907: <NA>
#> 908: R
#> 909: R
if (require("data.table")) {
dt[any(carbapenems() == "S"), penicillins(), with = FALSE]
}
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `penicillins()` using columns 'PEN' (benzylpenicillin), 'OXA'
#> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP'
#> (piperacillin/tazobactam)
#> PEN OXA FLC AMX AMC AMP TZP
#> <sir> <sir> <sir> <sir> <sir> <sir> <sir>
#> 1: R <NA> <NA> <NA> I <NA> <NA>
#> 2: R <NA> <NA> <NA> I <NA> <NA>
#> 3: R <NA> <NA> <NA> I <NA> <NA>
#> 4: R <NA> <NA> <NA> I <NA> <NA>
#> 5: R <NA> <NA> R R R <NA>
#> ---
#> 905: R <NA> <NA> S S S S
#> 906: R <NA> <NA> S S S S
#> 907: R S S <NA> S <NA> <NA>
#> 908: R <NA> <NA> R S R S
#> 909: R <NA> <NA> R S R S
# }
```
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